MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.88, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000347300.6

Genbank transcript ID

NM_018262 (by similarity)

UniProt / AlphaMissense peptide

IF122_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1241	CHAIN		lost
3	10	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE
NLALEMYTDL CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK
AIEICGDHGW VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ
LHVETQRWDE AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE
QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH
RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY
DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ
PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE
TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL
PDASITMCPS CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE
NLALEMYTDL CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK
AIEICGDHGW VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ
LHVETQRWDE AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE
QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH
RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY
DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ
PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE
TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL
PDASITMCPS CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Position of stopcodon in wt / mu CDS

3549 / 3549

Position (AA) of stopcodon in wt / mu AA sequence

1183 / 1183

Position of stopcodon in wt / mu cDNA

3755 / 3755

Position of start ATG in wt / mu cDNA

207 / 207

Last intron/exon boundary

3665

Theoretical NMD boundary in CDS

3408

Length of CDS

3549

Coding sequence (CDS) position

21

cDNA position

227

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_12_ENST00000685921

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000685921.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQDGVRLGT VGEQNSWVWT CQAKPDSNYV
VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH LITEQKVRIK CKELVKKIAI
YRNRLAIQLP EKILIYELYS EDLSDMHYRV KEKIIKKFEC NLLVVCANHI ILCQEKRLQC
LSFSGVKERE WQMESLIRYI KVIGGPPGRE GLLVGLKNGQ ILKIFVDNLF AIVLLKQATA
VRCLDMSASR KKLAVVDEND TCLVYDIDTK ELLFQEPNAN SVAWNTQCED MLCFSGGGYL
NIKASTFPVH RQKLQGFVVG YNGSKIFCLH VFSISAVEVP QSAPMYQYLD RKLFKEAYQI
ACLGVTDTDW RELAMEALEG LDFETAKKAF IRVQDLRYLE LISSIEERKK RGETNNDLFL
ADVFSYQGKF HEAAKLYKRS GHENLALEMY TDLCMFEYAK DFLGSGDPKE TKMLITKQAD
WARNIKEPKA AVEMYISAGE HVKAIEICGD HGWVDMLIDI ARKLDKAERE PLLLCATYLK
KLDSPGYAAE TYLKMGDLKS LVQLHVETQR WDEAFALGEK HPEFKDDIYM PYAQWLAEND
RFEEAQKAFH KAGRQREAVQ VLEQLTNNAV AESRFNDAAY YYWMLSMQCL DIAQDPAQKD
TMLGKFYHFQ RLAELYHGYH AIHRHTEDPF SVHRPETLFN ISRFLLHSLP KDTPSGISKV
KILFTLAKQS KALGAYRLAR HAYDKLRGLY IPARFQKSIE LGTLTIRAKP FHDSEELVPL
CYRCSTNNPL LNNLGNVCIN CRQPFIFSAS SYDVLHLVEF YLEEGITDEE AISLIDLEVL
RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF EQGGSEFVPV VVSRLVLRSM
SRRDVLIKRW PPPLRWQYFR SLLPDASITM CPSCFQMFHS EDYELLVLQH GCCPYCRRCK
DDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQDGVRLGT VGEQNSWVWT CQAKPDSNYV
VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH LITEQKVRIK CKELVKKIAI
YRNRLAIQLP EKILIYELYS EDLSDMHYRV KEKIIKKFEC NLLVVCANHI ILCQEKRLQC
LSFSGVKERE WQMESLIRYI KVIGGPPGRE GLLVGLKNGQ ILKIFVDNLF AIVLLKQATA
VRCLDMSASR KKLAVVDEND TCLVYDIDTK ELLFQEPNAN SVAWNTQCED MLCFSGGGYL
NIKASTFPVH RQKLQGFVVG YNGSKIFCLH VFSISAVEVP QSAPMYQYLD RKLFKEAYQI
ACLGVTDTDW RELAMEALEG LDFETAKKAF IRVQDLRYLE LISSIEERKK RGETNNDLFL
ADVFSYQGKF HEAAKLYKRS GHENLALEMY TDLCMFEYAK DFLGSGDPKE TKMLITKQAD
WARNIKEPKA AVEMYISAGE HVKAIEICGD HGWVDMLIDI ARKLDKAERE PLLLCATYLK
KLDSPGYAAE TYLKMGDLKS LVQLHVETQR WDEAFALGEK HPEFKDDIYM PYAQWLAEND
RFEEAQKAFH KAGRQREAVQ VLEQLTNNAV AESRFNDAAY YYWMLSMQCL DIAQDPAQKD
TMLGKFYHFQ RLAELYHGYH AIHRHTEDPF SVHRPETLFN ISRFLLHSLP KDTPSGISKV
KILFTLAKQS KALGAYRLAR HAYDKLRGLY IPARFQKSIE LGTLTIRAKP FHDSEELVPL
CYRCSTNNPL LNNLGNVCIN CRQPFIFSAS SYDVLHLVEF YLEEGITDEE AISLIDLEVL
RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF EQGGSEFVPV VVSRLVLRSM
SRRDVLIKRW PPPLRWQYFR SLLPDASITM CPSCFQMFHS EDYELLVLQH GCCPYCRRCK
DDPGP*

Position of stopcodon in wt / mu CDS

3438 / 3438

Position (AA) of stopcodon in wt / mu AA sequence

1146 / 1146

Position of stopcodon in wt / mu cDNA

3635 / 3635

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3545

Theoretical NMD boundary in CDS

3297

Length of CDS

3438

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_13_ENST00000689332

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.88, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000689332.1

Genbank transcript ID

NM_001410810 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE
NLALEMYTDL CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK
AIEICGDHGW VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ
LHVETQRWDE AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE
QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QADPAQKDTM LGKFYHFQRL AELYHGYHAI
HRHTEDPFSV HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA
YDKLRGLYIP ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR
QPFIFSASSY DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV
ETKDSIGDED PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL
LPDASITMCP SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE
NLALEMYTDL CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK
AIEICGDHGW VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ
LHVETQRWDE AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE
QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QADPAQKDTM LGKFYHFQRL AELYHGYHAI
HRHTEDPFSV HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA
YDKLRGLYIP ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR
QPFIFSASSY DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV
ETKDSIGDED PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL
LPDASITMCP SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Position of stopcodon in wt / mu CDS

3552 / 3552

Position (AA) of stopcodon in wt / mu AA sequence

1184 / 1184

Position of stopcodon in wt / mu cDNA

3749 / 3749

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3659

Theoretical NMD boundary in CDS

3411

Length of CDS

3552

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_15_ENST00000296266

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000296266.7

Genbank transcript ID

NM_052985 (by similarity)

UniProt / AlphaMissense peptide

IF122_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1241	CHAIN		lost
3	10	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY TSWSVMSSLH LHLPFLGLHK TVRVTATDKA
PKGQGGRIDC LRPSVQNQPG QKHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH
KSSSKIICCS WTNDGQYLAL GMFNGIISIR NKNGEEKVKI ERPGGSLSPI WSICWNPSSR
WESFWMNREN EDAEDVIVNR YIQEIPSTLK SAVYSSQGSE AEEEEPEEED DSPRDDNLEE
RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG SDKQVSLFTK
DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY KDRYAYRDSM
TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL SDMHYRVKEK
IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI GGPPGREGLL
VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL VYDIDTKELL
FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG SKIFCLHVFS
ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF ETAKKAFIRV
QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL
CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW
VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE
AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES
RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH
RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY DKLRGLYIPA
RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ PFIFSASSYD
VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE TKDSIGDEDP
FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL PDASITMCPS
CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY TSWSVMSSLH LHLPFLGLHK TVRVTATDKA
PKGQGGRIDC LRPSVQNQPG QKHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH
KSSSKIICCS WTNDGQYLAL GMFNGIISIR NKNGEEKVKI ERPGGSLSPI WSICWNPSSR
WESFWMNREN EDAEDVIVNR YIQEIPSTLK SAVYSSQGSE AEEEEPEEED DSPRDDNLEE
RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG SDKQVSLFTK
DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY KDRYAYRDSM
TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL SDMHYRVKEK
IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI GGPPGREGLL
VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL VYDIDTKELL
FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG SKIFCLHVFS
ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF ETAKKAFIRV
QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL
CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW
VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE
AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES
RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH
RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY DKLRGLYIPA
RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ PFIFSASSYD
VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE TKDSIGDEDP
FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL PDASITMCPS
CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Position of stopcodon in wt / mu CDS

3879 / 3879

Position (AA) of stopcodon in wt / mu AA sequence

1293 / 1293

Position of stopcodon in wt / mu cDNA

4071 / 4071

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

3981

Theoretical NMD boundary in CDS

3738

Length of CDS

3879

Coding sequence (CDS) position

21

cDNA position

213

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_24_ENST00000692321

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: 5utr
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000692321.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.105G>C
g.10745G>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MFNGIISIRN KNGEEKVKIE RPGGSLSPIW SICWNPSREE RNDILAVADW GQKVSFYQLS
GKQIGKDRAL NFDPCCISYF TKGEYILLGG SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA
KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE
LVKKIAIYRN RLAIQLPEKI LIYELYSEDL SDMHYRVKEK IIKKFECNLL VVCANHIILC
QEKRLQCLSF SGVKEREWQM ESLIRYIKVI GGPPGREGLL VGLKNGQILK IFVDNLFAIV
LLKQATAVRC LDMSASRKKL AVVDENDTCL VYDIDTKELL FQEPNANSVA WNTQCEDMLC
FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL
FKEAYQIACL GVTDTDWREL AMEALEGLDF ETAKKERKKR GETNNDLFLA DVFSYQGKFH
EAAKLYKRSG HENLALEMYT DLCMFEYAKD FLGSGDPKET KMLITKQADW ARNIKEPKAA
VEMYISAGEH VKAIEICGDH GWVDMLIDIA RKLDKAEREP LLLCATYLKK LDSPGYAAET
YLKMGDLKSL VQLHVETQRW DEAFALGEKH PEFKDDIYMP YAQWLAENDR FEEAQKAFHK
AGRQREAVQV LEQLTNNAVA ESRFNDAAYY YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR
LAELYHGYHA IHRHTEDPFS VHRPETLFNI SRFLLHSLPK DTPSGISKVK ILFTLAKQSK
ALGAYRLARH AYDKLRGLYI PARFQKSIEL GTLTIRAKPF HDSEELVPLC YRCSTNNPLL
NNLGNVCINC RQPFIFSASS YDVLHLVEFY LEEGITDEEA ISLIDLEVLR PKRDDRQLEI
ANNSSQILRL VETKDSIGDE DPFTAKLSFE QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP
PPLRWQYFRS LLPDASITMC PSCFQMFHSE DYELLVLQHG CCPYCRRCKD DPGP*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

227 / 227

Last intron/exon boundary

3181

Theoretical NMD boundary in CDS

2904

Length of CDS

3045

Coding sequence (CDS) position

N/A

cDNA position

105

gDNA position

10745

Chromosomal position

129440351

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_26_ENST00000692728

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: 5utr
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000692728.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.91G>C
g.10745G>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MFNGIISIRN KNGEEKVKIE RPGGSLSPIW SICWNPSREE RNDILAVADW GQKVSFYQLS
GKQIGKDRAL NFDPCCISYF TKGEYILLGG SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA
KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE
LVKKIAIYRN RLAIQLPEKI LIYELYSEDL SDMHYRVKEK IIKKFECNLL VVCANHIILC
QEKRLQCLSF SGVKEREWQM ESLIRYIKVI GGPPGREGLL VGLKNGQILK IFVDNLFAIV
LLKQATAVRC LDMSASRKKL AVVDENDTCL VYDIDTKELL FQEPNANSVA WNTQCEDMLC
FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL
FKEAYQIACL GVTDTDWREL AMEALEGLDF ETAKKERKKR GETNNDLFLA DVFSYQGKFH
EAAKLYKRSG HENLALEMYT DLCMFEYAKD FLGSGDPKET KMLITKQADW ARNIKEPKAA
VEMYISAGEH VKAIEICGDH GWVDMLIDIA RKLDKAEREP LLLCATYLKK LDSPGYAAET
YLKMGDLKSL VQLHVETQRW DEAFALGEKH PEFKDDIYMP YAQWLAENDR FEEAQKAFHK
AGRQREAVQV LEQLTNNAVA ESRFNDAAYY YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR
LAELYHGYHA IHRHTEDPFS VHRPETLFNI SRFLLHSLPK DTPSGISKVK ILFTLAKQSK
ALGAYRLARH AYDKLRGLYI PARFQKSIEL GTLTIRAKPF HDSEELVPLC YRCSTNNPLL
NNLGNVCINC RQPFIFSASS YDVLHLVEFY LEEGITDEEA ISLIDLEVLR PKRDDRQLEI
ANNSSQILRL VETKDSIGDE DPFTAKLSFE QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP
PPLRWQYFRS LLPDASITMC PSCFQMFHSE DYELLVLQHG CCPYCRRCKD DPGP*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

369 / 369

Last intron/exon boundary

3323

Theoretical NMD boundary in CDS

2904

Length of CDS

3045

Coding sequence (CDS) position

N/A

cDNA position

91

gDNA position

10745

Chromosomal position

129440351

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_30_ENST00000687377

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000687377.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD LCMFEYAKDF
LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG WVDMLIDIAR
KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD EAFALGEKHP
EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE SRFNDAAYYY
WMLSMQCLDI AQADPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY
LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE DPFTAKLSFE
QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC PSCFQMFHSE
DYELLVLQHG CCPYCRRCKD DPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD LCMFEYAKDF
LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG WVDMLIDIAR
KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD EAFALGEKHP
EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE SRFNDAAYYY
WMLSMQCLDI AQADPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY
LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE DPFTAKLSFE
QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC PSCFQMFHSE
DYELLVLQHG CCPYCRRCKD DPGP*

Position of stopcodon in wt / mu CDS

3675 / 3675

Position (AA) of stopcodon in wt / mu AA sequence

1225 / 1225

Position of stopcodon in wt / mu cDNA

3879 / 3879

Position of start ATG in wt / mu cDNA

205 / 205

Last intron/exon boundary

3789

Theoretical NMD boundary in CDS

3534

Length of CDS

3675

Coding sequence (CDS) position

21

cDNA position

225

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_31_ENST00000689643

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000689643.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF SYQGKFHEAA KLYKRSGHEN
LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN IKEPKAAVEM YISAGEHVKA
IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL
HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAGR QREAVQVLEQ
LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ DPAQKDTMLG KFYHFQRLAE LYHGYHAIHR
HTEDPFSVHR PETLFNISRF LLHSLPKDTP SGISKVKILF TLAKQSKALG AYRLARHAYD
KLRGLYIPAR FQKSIELGTL TIRAKPFHDS EELVPLCYRC STNNPLLNNL GNVCINCRQP
FIFSASSYDV LHLVEFYLEE GITDEEAISL IDLEVLRPKR DDRQLEIANN SSQILRLVET
KDSIGDEDPF TAKLSFEQGG SEFVPVVVSR LVLRSMSRRD VLIKRWPPPL RWQYFRSLLP
DASITMCPSC FQLSSLRCSI LRTMSCWCFS MAAAPTAAGA RMTLAHDQHP GDGLHPLPAL
GSAGL*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF SYQGKFHEAA KLYKRSGHEN
LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN IKEPKAAVEM YISAGEHVKA
IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL
HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAGR QREAVQVLEQ
LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ DPAQKDTMLG KFYHFQRLAE LYHGYHAIHR
HTEDPFSVHR PETLFNISRF LLHSLPKDTP SGISKVKILF TLAKQSKALG AYRLARHAYD
KLRGLYIPAR FQKSIELGTL TIRAKPFHDS EELVPLCYRC STNNPLLNNL GNVCINCRQP
FIFSASSYDV LHLVEFYLEE GITDEEAISL IDLEVLRPKR DDRQLEIANN SSQILRLVET
KDSIGDEDPF TAKLSFEQGG SEFVPVVVSR LVLRSMSRRD VLIKRWPPPL RWQYFRSLLP
DASITMCPSC FQLSSLRCSI LRTMSCWCFS MAAAPTAAGA RMTLAHDQHP GDGLHPLPAL
GSAGL*

Position of stopcodon in wt / mu CDS

3798 / 3798

Position (AA) of stopcodon in wt / mu AA sequence

1266 / 1266

Position of stopcodon in wt / mu cDNA

4002 / 4002

Position of start ATG in wt / mu cDNA

205 / 205

Last intron/exon boundary

3840

Theoretical NMD boundary in CDS

3585

Length of CDS

3798

Coding sequence (CDS) position

21

cDNA position

225

gDNA position

10745

Chromosomal position

129440351

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_33_ENST00000693129

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000693129.1

Genbank transcript ID

NM_001410809 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD LCMFEYAKDF
LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG WVDMLIDIAR
KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD EAFALGEKHP
EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE SRFNDAAYYY
WMLSMQCLDI AQDPAQKDTM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV HRPETLFNIS
RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP ARFQKSIELG
TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY DVLHLVEFYL
EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED PFTAKLSFEQ
GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP SCFQMFHSED
YELLVLQHGC CPYCRRCKDD PGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD LCMFEYAKDF
LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG WVDMLIDIAR
KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD EAFALGEKHP
EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE SRFNDAAYYY
WMLSMQCLDI AQDPAQKDTM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV HRPETLFNIS
RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP ARFQKSIELG
TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY DVLHLVEFYL
EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED PFTAKLSFEQ
GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP SCFQMFHSED
YELLVLQHGC CPYCRRCKDD PGP*

Position of stopcodon in wt / mu CDS

3672 / 3672

Position (AA) of stopcodon in wt / mu AA sequence

1224 / 1224

Position of stopcodon in wt / mu cDNA

3869 / 3869

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3779

Theoretical NMD boundary in CDS

3531

Length of CDS

3672

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_1_ENST00000689801

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000689801.1

Genbank transcript ID

NM_001410811 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQADPAQKD TMLGKFYHFQ RLAELYHGYH AIHRHTEDPF SVHRPETLFN
ISRFLLHSLP KDTPSGISKV KILFTLAKQS KALGAYRLAR HAYDKLRGLY IPARFQKSIE
LGTLTIRAKP FHDSEELVPL CYRCSTNNPL LNNLGNVCIN CRQPFIFSAS SYDVLHLVEF
YLEEGITDEE AISLIDLEVL RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF
EQGGSEFVPV VVSRLVLRSM SRRDVLIKRW PPPLRWQYFR SLLPDASITM CPSCFQMFHS
EDYELLVLQH GCCPYCRRCK DDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQADPAQKD TMLGKFYHFQ RLAELYHGYH AIHRHTEDPF SVHRPETLFN
ISRFLLHSLP KDTPSGISKV KILFTLAKQS KALGAYRLAR HAYDKLRGLY IPARFQKSIE
LGTLTIRAKP FHDSEELVPL CYRCSTNNPL LNNLGNVCIN CRQPFIFSAS SYDVLHLVEF
YLEEGITDEE AISLIDLEVL RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF
EQGGSEFVPV VVSRLVLRSM SRRDVLIKRW PPPLRWQYFR SLLPDASITM CPSCFQMFHS
EDYELLVLQH GCCPYCRRCK DDPGP*

Position of stopcodon in wt / mu CDS

3498 / 3498

Position (AA) of stopcodon in wt / mu AA sequence

1166 / 1166

Position of stopcodon in wt / mu cDNA

3713 / 3713

Position of start ATG in wt / mu cDNA

216 / 216

Last intron/exon boundary

3623

Theoretical NMD boundary in CDS

3357

Length of CDS

3498

Coding sequence (CDS) position

21

cDNA position

236

gDNA position

10745

Chromosomal position

129440351

Speed

0.13 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_3_ENST00000691583

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000691583.1

Genbank transcript ID

NM_001410813 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY
LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE DPFTAKLSFE
QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC PSCFQMFHSE
DYELLVLQHG CCPYCRRCKD DPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY
LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE DPFTAKLSFE
QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC PSCFQMFHSE
DYELLVLQHG CCPYCRRCKD DPGP*

Position of stopcodon in wt / mu CDS

3495 / 3495

Position (AA) of stopcodon in wt / mu AA sequence

1165 / 1165

Position of stopcodon in wt / mu cDNA

3701 / 3701

Position of start ATG in wt / mu cDNA

207 / 207

Last intron/exon boundary

3611

Theoretical NMD boundary in CDS

3354

Length of CDS

3495

Coding sequence (CDS) position

21

cDNA position

227

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_4_ENST00000692242

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.69, misssense (oe): 0.88, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000692242.1

Genbank transcript ID

NM_001410808 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF SYQGKFHEAA KLYKRSGHEN
LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN IKEPKAAVEM YISAGEHVKA
IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL
HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAGR QREAVQVLEQ
LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ ADPAQKDTML GKFYHFQRLA ELYHGYHAIH
RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY
DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ
PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE
TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL
PDASITMCPS CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF SYQGKFHEAA KLYKRSGHEN
LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN IKEPKAAVEM YISAGEHVKA
IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL
HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAGR QREAVQVLEQ
LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ ADPAQKDTML GKFYHFQRLA ELYHGYHAIH
RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY
DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ
PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE
TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL
PDASITMCPS CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Position of stopcodon in wt / mu CDS

3729 / 3729

Position (AA) of stopcodon in wt / mu AA sequence

1243 / 1243

Position of stopcodon in wt / mu cDNA

3933 / 3933

Position of start ATG in wt / mu cDNA

205 / 205

Last intron/exon boundary

3843

Theoretical NMD boundary in CDS

3588

Length of CDS

3729

Coding sequence (CDS) position

21

cDNA position

225

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_5_ENST00000693489

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000693489.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEGKFHEAAK LYKRSGHENL ALEMYTDLCM FEYAKDFLGS
GDPKETKMLI TKQADWARNI KEPKAAVEMY ISAGEHVKAI EICGDHGWVD MLIDIARKLD
KAEREPLLLC ATYLKKLDSP GYAAETYLKM GDLKSLVQLH VETQRWDEAF ALGEKHPEFK
DDIYMPYAQW LAENDRFEEA QKAFHKAGRQ REAVQVLEQL TNNAVAESRF NDAAYYYWML
SMQCLDIAQD PAQKDTMLGK FYHFQRLAEL YHGYHAIHRH TEDPFSVHRP ETLFNISRFL
LHSLPKDTPS GISKVKILFT LAKQSKALGA YRLARHAYDK LRGLYIPARF QKSIELGTLT
IRAKPFHDSE ELVPLCYRCS TNNPLLNNLG NVCINCRQPF IFSASSYDVL HLVEFYLEEG
ITDEEAISLI DLEVLRPKRD DRQLEIANNS SQILRLVETK DSIGDEDPFT AKLSFEQGGS
EFVPVVVSRL VLRSMSRRDV LIKRWPPPLR WQYFRSLLPD ASITMCPSCF QMFHSEDYEL
LVLQHGCCPY CRRCKDDPGP *

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEGKFHEAAK LYKRSGHENL ALEMYTDLCM FEYAKDFLGS
GDPKETKMLI TKQADWARNI KEPKAAVEMY ISAGEHVKAI EICGDHGWVD MLIDIARKLD
KAEREPLLLC ATYLKKLDSP GYAAETYLKM GDLKSLVQLH VETQRWDEAF ALGEKHPEFK
DDIYMPYAQW LAENDRFEEA QKAFHKAGRQ REAVQVLEQL TNNAVAESRF NDAAYYYWML
SMQCLDIAQD PAQKDTMLGK FYHFQRLAEL YHGYHAIHRH TEDPFSVHRP ETLFNISRFL
LHSLPKDTPS GISKVKILFT LAKQSKALGA YRLARHAYDK LRGLYIPARF QKSIELGTLT
IRAKPFHDSE ELVPLCYRCS TNNPLLNNLG NVCINCRQPF IFSASSYDVL HLVEFYLEEG
ITDEEAISLI DLEVLRPKRD DRQLEIANNS SQILRLVETK DSIGDEDPFT AKLSFEQGGS
EFVPVVVSRL VLRSMSRRDV LIKRWPPPLR WQYFRSLLPD ASITMCPSCF QMFHSEDYEL
LVLQHGCCPY CRRCKDDPGP *

Position of stopcodon in wt / mu CDS

3663 / 3663

Position (AA) of stopcodon in wt / mu AA sequence

1221 / 1221

Position of stopcodon in wt / mu cDNA

3867 / 3867

Position of start ATG in wt / mu cDNA

205 / 205

Last intron/exon boundary

3777

Theoretical NMD boundary in CDS

3522

Length of CDS

3663

Coding sequence (CDS) position

21

cDNA position

225

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_6_ENST00000691733

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.79, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000691733.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE
NLALEMYTDL CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK
AIEICGDHGW VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ
LHVETQRWDE AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE
QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH
RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY
DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ
PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE
TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL
PDASITMCPS CFQLSSLRCS ILRTMSCWCF SMAAAPTAAG ARMTLAHDQH PGDGLHPLPA
LGSAGL*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE
NLALEMYTDL CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK
AIEICGDHGW VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ
LHVETQRWDE AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE
QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH
RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY
DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ
PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE
TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL
PDASITMCPS CFQLSSLRCS ILRTMSCWCF SMAAAPTAAG ARMTLAHDQH PGDGLHPLPA
LGSAGL*

Position of stopcodon in wt / mu CDS

3621 / 3621

Position (AA) of stopcodon in wt / mu AA sequence

1207 / 1207

Position of stopcodon in wt / mu cDNA

3818 / 3818

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3656

Theoretical NMD boundary in CDS

3408

Length of CDS

3621

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_7_ENST00000691964

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000691964.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY DVLHLVEFYL
EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED PFTAKLSFEQ
GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP SCFQMFHSED
YELLVLQHGC CPYCRRCKDD PGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY DVLHLVEFYL
EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED PFTAKLSFEQ
GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP SCFQMFHSED
YELLVLQHGC CPYCRRCKDD PGP*

Position of stopcodon in wt / mu CDS

3492 / 3492

Position (AA) of stopcodon in wt / mu AA sequence

1164 / 1164

Position of stopcodon in wt / mu cDNA

3689 / 3689

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3599

Theoretical NMD boundary in CDS

3351

Length of CDS

3492

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_8_ENST00000686473

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000686473.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQDGVRLGT VGEQNSWVWT CQAKPDSNYV
VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH LITEQKVRIK CKELVKKIAI
YRNRLAIQLP EKILIYELYS EDLSDMHYRV KEKIIKKFEC NLLVVCANHI ILCQEKRLQC
LSFSGVKERE WQMESLIRYI KVIGGPPGRE GLLVGLKNGQ ILKIFVDNLF AIVLLKQATA
VRCLDMSASR KKLAVVDEND TCLVYDIDTK ELLFQEPNAN SVAWNTQCED MLCFSGGGYL
NIKASTFPVH RQKLQGFVVG YNGSKIFCLH VFSISAVEVP QSAPMYQYLD RKLFKEAYQI
ACLGVTDTDW RELAMEALEG LDFETAKKER KKRGETNNDL FLADVFSYQG KFHEAAKLYK
RSGHENLALE MYTDLCMFEY AKDFLGSGDP KETKMLITKQ ADWARNIKEP KAAVEMYISA
GEHVKAIEIC GDHGWVDMLI DIARKLDKAE REPLLLCATY LKKLDSPGYA AETYLKMGDL
KSLVQLHVET QRWDEAFALG EKHPEFKDDI YMPYAQWLAE NDRFEEAQKA FHKAGRQREA
VQVLEQLTNN AVAESRFNDA AYYYWMLSMQ CLDIAQDPAQ KDTMLGKFYH FQRLAELYHG
YHAIHRHTED PFSVHRPETL FNISRFLLHS LPKDTPSGIS KVKILFTLAK QSKALGAYRL
ARHAYDKLRG LYIPARFQKS IELGTLTIRA KPFHDSEELV PLCYRCSTNN PLLNNLGNVC
INCRQPFIFS ASSYDVLHLV EFYLEEGITD EEAISLIDLE VLRPKRDDRQ LEIANNSSQI
LRLVETKDSI GDEDPFTAKL SFEQGGSEFV PVVVSRLVLR SMSRRDVLIK RWPPPLRWQY
FRSLLPDASI TMCPSCFQMF HSEDYELLVL QHGCCPYCRR CKDDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQDGVRLGT VGEQNSWVWT CQAKPDSNYV
VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH LITEQKVRIK CKELVKKIAI
YRNRLAIQLP EKILIYELYS EDLSDMHYRV KEKIIKKFEC NLLVVCANHI ILCQEKRLQC
LSFSGVKERE WQMESLIRYI KVIGGPPGRE GLLVGLKNGQ ILKIFVDNLF AIVLLKQATA
VRCLDMSASR KKLAVVDEND TCLVYDIDTK ELLFQEPNAN SVAWNTQCED MLCFSGGGYL
NIKASTFPVH RQKLQGFVVG YNGSKIFCLH VFSISAVEVP QSAPMYQYLD RKLFKEAYQI
ACLGVTDTDW RELAMEALEG LDFETAKKER KKRGETNNDL FLADVFSYQG KFHEAAKLYK
RSGHENLALE MYTDLCMFEY AKDFLGSGDP KETKMLITKQ ADWARNIKEP KAAVEMYISA
GEHVKAIEIC GDHGWVDMLI DIARKLDKAE REPLLLCATY LKKLDSPGYA AETYLKMGDL
KSLVQLHVET QRWDEAFALG EKHPEFKDDI YMPYAQWLAE NDRFEEAQKA FHKAGRQREA
VQVLEQLTNN AVAESRFNDA AYYYWMLSMQ CLDIAQDPAQ KDTMLGKFYH FQRLAELYHG
YHAIHRHTED PFSVHRPETL FNISRFLLHS LPKDTPSGIS KVKILFTLAK QSKALGAYRL
ARHAYDKLRG LYIPARFQKS IELGTLTIRA KPFHDSEELV PLCYRCSTNN PLLNNLGNVC
INCRQPFIFS ASSYDVLHLV EFYLEEGITD EEAISLIDLE VLRPKRDDRQ LEIANNSSQI
LRLVETKDSI GDEDPFTAKL SFEQGGSEFV PVVVSRLVLR SMSRRDVLIK RWPPPLRWQY
FRSLLPDASI TMCPSCFQMF HSEDYELLVL QHGCCPYCRR CKDDPGP*

Position of stopcodon in wt / mu CDS

3384 / 3384

Position (AA) of stopcodon in wt / mu AA sequence

1128 / 1128

Position of stopcodon in wt / mu cDNA

3581 / 3581

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3491

Theoretical NMD boundary in CDS

3243

Length of CDS

3384

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_9_ENST00000686531

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000686531.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EGKFHEAAKL YKRSGHENLA LEMYTDLCMF
EYAKDFLGSG DPKETKMLIT KQADWARNIK EPKAAVEMYI SAGEHVKAIE ICGDHGWVDM
LIDIARKLDK AEREPLLLCA TYLKKLDSPG YAAETYLKMG DLKSLVQLHV ETQRWDEAFA
LGEKHPEFKD DIYMPYAQWL AENDRFEEAQ KAFHKAGRQR EAVQVLEQLT NNAVAESRFN
DAAYYYWMLS MQCLDIAQDP AQKDTMLGKF YHFQRLAELY HGYHAIHRHT EDPFSVHRPE
TLFNISRFLL HSLPKDTPSG ISKVKILFTL AKQSKALGAY RLARHAYDKL RGLYIPARFQ
KSIELGTLTI RAKPFHDSEE LVPLCYRCST NNPLLNNLGN VCINCRQPFI FSASSYDVLH
LVEFYLEEGI TDEEAISLID LEVLRPKRDD RQLEIANNSS QILRLVETKD SIGDEDPFTA
KLSFEQGGSE FVPVVVSRLV LRSMSRRDVL IKRWPPPLRW QYFRSLLPDA SITMCPSCFQ
MFHSEDYELL VLQHGCCPYC RRCKDDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EGKFHEAAKL YKRSGHENLA LEMYTDLCMF
EYAKDFLGSG DPKETKMLIT KQADWARNIK EPKAAVEMYI SAGEHVKAIE ICGDHGWVDM
LIDIARKLDK AEREPLLLCA TYLKKLDSPG YAAETYLKMG DLKSLVQLHV ETQRWDEAFA
LGEKHPEFKD DIYMPYAQWL AENDRFEEAQ KAFHKAGRQR EAVQVLEQLT NNAVAESRFN
DAAYYYWMLS MQCLDIAQDP AQKDTMLGKF YHFQRLAELY HGYHAIHRHT EDPFSVHRPE
TLFNISRFLL HSLPKDTPSG ISKVKILFTL AKQSKALGAY RLARHAYDKL RGLYIPARFQ
KSIELGTLTI RAKPFHDSEE LVPLCYRCST NNPLLNNLGN VCINCRQPFI FSASSYDVLH
LVEFYLEEGI TDEEAISLID LEVLRPKRDD RQLEIANNSS QILRLVETKD SIGDEDPFTA
KLSFEQGGSE FVPVVVSRLV LRSMSRRDVL IKRWPPPLRW QYFRSLLPDA SITMCPSCFQ
MFHSEDYELL VLQHGCCPYC RRCKDDPGP*

Position of stopcodon in wt / mu CDS

3330 / 3330

Position (AA) of stopcodon in wt / mu AA sequence

1110 / 1110

Position of stopcodon in wt / mu cDNA

3527 / 3527

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3437

Theoretical NMD boundary in CDS

3189

Length of CDS

3330

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_10_ENST00000686830

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.88, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000686830.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEDFLGSGD PKETKMLITK QADWARNIKE PKAAVEMYIS
AGEHVKAIEI CGDHGWVDML IDIARKLDKA EREPLLLCAT YLKKLDSPGY AAETYLKMGD
LKSLVQLHVE TQRWDEAFAL GEKHPEFKDD IYMPYAQWLA ENDRFEEAQK AFHKAGRQRE
AVQVLEQLTN NAVAESRFND AAYYYWMLSM QCLDIAQDPA QKDTMLGKFY HFQRLAELYH
GYHAIHRHTE DPFSVHRPET LFNISRFLLH SLPKDTPSGI SKVKILFTLA KQSKALGAYR
LARHAYDKLR GLYIPARFQK SIELGTLTIR AKPFHDSEEL VPLCYRCSTN NPLLNNLGNV
CINCRQPFIF SASSYDVLHL VEFYLEEGIT DEEAISLIDL EVLRPKRDDR QLEIANNSSQ
ILRLVETKDS IGDEDPFTAK LSFEQGGSEF VPVVVSRLVL RSMSRRDVLI KRWPPPLRWQ
YFRSLLPDAS ITMCPSCFQM FHSEDYELLV LQHGCCPYCR RCKDDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEDFLGSGD PKETKMLITK QADWARNIKE PKAAVEMYIS
AGEHVKAIEI CGDHGWVDML IDIARKLDKA EREPLLLCAT YLKKLDSPGY AAETYLKMGD
LKSLVQLHVE TQRWDEAFAL GEKHPEFKDD IYMPYAQWLA ENDRFEEAQK AFHKAGRQRE
AVQVLEQLTN NAVAESRFND AAYYYWMLSM QCLDIAQDPA QKDTMLGKFY HFQRLAELYH
GYHAIHRHTE DPFSVHRPET LFNISRFLLH SLPKDTPSGI SKVKILFTLA KQSKALGAYR
LARHAYDKLR GLYIPARFQK SIELGTLTIR AKPFHDSEEL VPLCYRCSTN NPLLNNLGNV
CINCRQPFIF SASSYDVLHL VEFYLEEGIT DEEAISLIDL EVLRPKRDDR QLEIANNSSQ
ILRLVETKDS IGDEDPFTAK LSFEQGGSEF VPVVVSRLVL RSMSRRDVLI KRWPPPLRWQ
YFRSLLPDAS ITMCPSCFQM FHSEDYELLV LQHGCCPYCR RCKDDPGP*

Position of stopcodon in wt / mu CDS

3387 / 3387

Position (AA) of stopcodon in wt / mu AA sequence

1129 / 1129

Position of stopcodon in wt / mu cDNA

3584 / 3584

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3494

Theoretical NMD boundary in CDS

3246

Length of CDS

3387

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_11_ENST00000689796

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.88, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000689796.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEDFLGSGD PKETKMLITK QADWARNIKE PKAAVEMYIS
AGEHVKAIEI CGDHGWVDML IDIARKLDKA EREPLLLCAT YLKKLDSPGY AAETYLKMGD
LKSLVQLHVE TQRWDEAFAL GEKHPEFKDD IYMPYAQWLA ENDRFEEAQK AFHKAGRQRE
AVQVLEQLTN NAVAESRFND AAYYYWMLSM QCLDIAQADP AQKDTMLGKF YHFQRLAELY
HGYHAIHRHT EDPFSVHRPE TLFNISRFLL HSLPKDTPSG ISKVKILFTL AKQSKALGAY
RLARHAYDKL RGLYIPARFQ KSIELGTLTI RAKPFHDSEE LVPLCYRCST NNPLLNNLGN
VCINCRQPFI FSASSYDVLH LVEFYLEEGI TDEEAISLID LEVLRPKRDD RQLEIANNSS
QILRLVETKD SIGDEDPFTA KLSFEQGGSE FVPVVVSRLV LRSMSRRDVL IKRWPPPLRW
QYFRSLLPDA SITMCPSCFQ MFHSEDYELL VLQHGCCPYC RRCKDDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKAFIRV QDLRYLELIS SIEDFLGSGD PKETKMLITK QADWARNIKE PKAAVEMYIS
AGEHVKAIEI CGDHGWVDML IDIARKLDKA EREPLLLCAT YLKKLDSPGY AAETYLKMGD
LKSLVQLHVE TQRWDEAFAL GEKHPEFKDD IYMPYAQWLA ENDRFEEAQK AFHKAGRQRE
AVQVLEQLTN NAVAESRFND AAYYYWMLSM QCLDIAQADP AQKDTMLGKF YHFQRLAELY
HGYHAIHRHT EDPFSVHRPE TLFNISRFLL HSLPKDTPSG ISKVKILFTL AKQSKALGAY
RLARHAYDKL RGLYIPARFQ KSIELGTLTI RAKPFHDSEE LVPLCYRCST NNPLLNNLGN
VCINCRQPFI FSASSYDVLH LVEFYLEEGI TDEEAISLID LEVLRPKRDD RQLEIANNSS
QILRLVETKD SIGDEDPFTA KLSFEQGGSE FVPVVVSRLV LRSMSRRDVL IKRWPPPLRW
QYFRSLLPDA SITMCPSCFQ MFHSEDYELL VLQHGCCPYC RRCKDDPGP*

Position of stopcodon in wt / mu CDS

3390 / 3390

Position (AA) of stopcodon in wt / mu AA sequence

1130 / 1130

Position of stopcodon in wt / mu cDNA

3587 / 3587

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3497

Theoretical NMD boundary in CDS

3249

Length of CDS

3390

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_14_ENST00000690862

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.79, LOF (oe): 0.65, misssense (oe): 0.88, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000690862.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY
LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE DPFTAKLSFE
QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC PSCFQVGGHP
GSSHVLLLAT FPLPKCPSGR RGPWEEGHIH GSKLGQRLVC PLPCLHSMCI *

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSREE RNDILAVADW GQKVSFYQLS GKQIGKDRAL NFDPCCISYF TKGEYILLGG
SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY
KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE LVKKIAIYRN RLAIQLPEKI LIYELYSEDL
SDMHYRVKEK IIKKFECNLL VVCANHIILC QEKRLQCLSF SGVKEREWQM ESLIRYIKVI
GGPPGREGLL VGLKNGQILK IFVDNLFAIV LLKQATAVRC LDMSASRKKL AVVDENDTCL
VYDIDTKELL FQEPNANSVA WNTQCEDMLC FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG
SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL FKEAYQIACL GVTDTDWREL AMEALEGLDF
ETAKKERKKR GETNNDLFLA DVFSYQGKFH EAAKLYKRSG HENLALEMYT DLCMFEYAKD
FLGSGDPKET KMLITKQADW ARNIKEPKAA VEMYISAGEH VKAIEICGDH GWVDMLIDIA
RKLDKAEREP LLLCATYLKK LDSPGYAAET YLKMGDLKSL VQLHVETQRW DEAFALGEKH
PEFKDDIYMP YAQWLAENDR FEEAQKAFHK AGRQREAVQV LEQLTNNAVA ESRFNDAAYY
YWMLSMQCLD IAQDPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS VHRPETLFNI
SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI PARFQKSIEL
GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEFY
LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE DPFTAKLSFE
QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC PSCFQVGGHP
GSSHVLLLAT FPLPKCPSGR RGPWEEGHIH GSKLGQRLVC PLPCLHSMCI *

Position of stopcodon in wt / mu CDS

3573 / 3573

Position (AA) of stopcodon in wt / mu AA sequence

1191 / 1191

Position of stopcodon in wt / mu cDNA

3770 / 3770

Position of start ATG in wt / mu cDNA

198 / 198

Last intron/exon boundary

3437

Theoretical NMD boundary in CDS

3189

Length of CDS

3573

Coding sequence (CDS) position

21

cDNA position

218

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_16_ENST00000690663

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000690663.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL
CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW
VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE
AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES
RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH
RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY DKLRGLYIPA
RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ PFIFSASSYD
VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE TKDSIGDEDP
FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL PDASITMCPS
CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL
CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW
VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE
AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES
RFNDAAYYYW MLSMQCLDIA QDPAQKDTML GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH
RPETLFNISR FLLHSLPKDT PSGISKVKIL FTLAKQSKAL GAYRLARHAY DKLRGLYIPA
RFQKSIELGT LTIRAKPFHD SEELVPLCYR CSTNNPLLNN LGNVCINCRQ PFIFSASSYD
VLHLVEFYLE EGITDEEAIS LIDLEVLRPK RDDRQLEIAN NSSQILRLVE TKDSIGDEDP
FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL PDASITMCPS
CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP GP*

Position of stopcodon in wt / mu CDS

3339 / 3339

Position (AA) of stopcodon in wt / mu AA sequence

1113 / 1113

Position of stopcodon in wt / mu cDNA

3518 / 3518

Position of start ATG in wt / mu cDNA

180 / 180

Last intron/exon boundary

3428

Theoretical NMD boundary in CDS

3198

Length of CDS

3339

Coding sequence (CDS) position

21

cDNA position

200

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_17_ENST00000689492

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000689492.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCRE ERNDILAVAD WGQKVSFYQL SGKQIGKDRA LNFDPCCISY
FTKGEYILLG GSDKQVSLFT KDGVRLGTVG EQNSWVWTCQ AKPDSNYVVV GCQDGTISFY
QLIFSTVHGL YKDRYAYRDS MTDVIVQHLI TEQKVRIKCK ELVKKIAIYR NRLAIQLPEK
ILIYELYSED LSDMHYRVKE KIIKKFECNL LVVCANHIIL CQEKRLQCLS FSGVKEREWQ
MESLIRYIKV IGGPPGREGL LVGLKNGQIL KIFVDNLFAI VLLKQATAVR CLDMSASRKK
LAVVDENDTC LVYDIDTKEL LFQEPNANSV AWNTQCEDML CFSGGGYLNI KASTFPVHRQ
KLQGFVVGYN GSKIFCLHVF SISAVEVPQS APMYQYLDRK LFKEAYQIAC LGVTDTDWRE
LAMEALEGLD FETAKKAFIR VQDLRYLELI SSIEERKKRG ETNNDLFLAD VFSYQGKFHE
AAKLYKRSGH ENLALEMYTD LCMFEYAKDF LGSGDPKETK MLITKQADWA RNIKEPKAAV
EMYISAGEHV KAIEICGDHG WVDMLIDIAR KLDKAEREPL LLCATYLKKL DSPGYAAETY
LKMGDLKSLV QLHVETQRWD EAFALGEKHP EFKDDIYMPY AQWLAENDRF EEAQKAFHKA
GRQREAVQVL EQLTNNAVAE SRFNDAAYYY WMLSMQCLDI AQDPAQKDTM LGKFYHFQRL
AELYHGYHAI HRHTEDPFSV HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA
LGAYRLARHA YDKLRGLYIP ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN
NLGNVCINCR QPFIFSASSY DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA
NNSSQILRLV ETKDSIGDED PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP
PLRWQYFRSL LPDASITMCP SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCRE ERNDILAVAD WGQKVSFYQL SGKQIGKDRA LNFDPCCISY
FTKGEYILLG GSDKQVSLFT KDGVRLGTVG EQNSWVWTCQ AKPDSNYVVV GCQDGTISFY
QLIFSTVHGL YKDRYAYRDS MTDVIVQHLI TEQKVRIKCK ELVKKIAIYR NRLAIQLPEK
ILIYELYSED LSDMHYRVKE KIIKKFECNL LVVCANHIIL CQEKRLQCLS FSGVKEREWQ
MESLIRYIKV IGGPPGREGL LVGLKNGQIL KIFVDNLFAI VLLKQATAVR CLDMSASRKK
LAVVDENDTC LVYDIDTKEL LFQEPNANSV AWNTQCEDML CFSGGGYLNI KASTFPVHRQ
KLQGFVVGYN GSKIFCLHVF SISAVEVPQS APMYQYLDRK LFKEAYQIAC LGVTDTDWRE
LAMEALEGLD FETAKKAFIR VQDLRYLELI SSIEERKKRG ETNNDLFLAD VFSYQGKFHE
AAKLYKRSGH ENLALEMYTD LCMFEYAKDF LGSGDPKETK MLITKQADWA RNIKEPKAAV
EMYISAGEHV KAIEICGDHG WVDMLIDIAR KLDKAEREPL LLCATYLKKL DSPGYAAETY
LKMGDLKSLV QLHVETQRWD EAFALGEKHP EFKDDIYMPY AQWLAENDRF EEAQKAFHKA
GRQREAVQVL EQLTNNAVAE SRFNDAAYYY WMLSMQCLDI AQDPAQKDTM LGKFYHFQRL
AELYHGYHAI HRHTEDPFSV HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA
LGAYRLARHA YDKLRGLYIP ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN
NLGNVCINCR QPFIFSASSY DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA
NNSSQILRLV ETKDSIGDED PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP
PLRWQYFRSL LPDASITMCP SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Position of stopcodon in wt / mu CDS

3402 / 3402

Position (AA) of stopcodon in wt / mu AA sequence

1134 / 1134

Position of stopcodon in wt / mu cDNA

3581 / 3581

Position of start ATG in wt / mu cDNA

180 / 180

Last intron/exon boundary

3491

Theoretical NMD boundary in CDS

3261

Length of CDS

3402

Coding sequence (CDS) position

21

cDNA position

200

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_19_ENST00000693233

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: 5utr
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.83, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000693233.1

Genbank transcript ID

NM_001280545 (by similarity), NM_001280546 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.132G>C
g.10745G>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MFNGIISIRN KNGEEKVKIE RPGGSLSPIW SICWNPSREE RNDILAVADW GQKVSFYQLS
GKQIGKDRAL NFDPCCISYF TKGEYILLGG SDKQVSLFTK DGVRLGTVGE QNSWVWTCQA
KPDSNYVVVG CQDGTISFYQ LIFSTVHGLY KDRYAYRDSM TDVIVQHLIT EQKVRIKCKE
LVKKIAIYRN RLAIQLPEKI LIYELYSEDL SDMHYRVKEK IIKKFECNLL VVCANHIILC
QEKRLQCLSF SGVKEREWQM ESLIRYIKVI GGPPGREGLL VGLKNGQILK IFVDNLFAIV
LLKQATAVRC LDMSASRKKL AVVDENDTCL VYDIDTKELL FQEPNANSVA WNTQCEDMLC
FSGGGYLNIK ASTFPVHRQK LQGFVVGYNG SKIFCLHVFS ISAVEVPQSA PMYQYLDRKL
FKEAYQIACL GVTDTDWREL AMEALEGLDF ETAKKAFIRV QDLRYLELIS SIEERKKRGE
TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL CMFEYAKDFL GSGDPKETKM
LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW VDMLIDIARK LDKAEREPLL
LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE AFALGEKHPE FKDDIYMPYA
QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES RFNDAAYYYW MLSMQCLDIA
QDPAQKDTML GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH RPETLFNISR FLLHSLPKDT
PSGISKVKIL FTLAKQSKAL GAYRLARHAY DKLRGLYIPA RFQKSIELGT LTIRAKPFHD
SEELVPLCYR CSTNNPLLNN LGNVCINCRQ PFIFSASSYD VLHLVEFYLE EGITDEEAIS
LIDLEVLRPK RDDRQLEIAN NSSQILRLVE TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS
RLVLRSMSRR DVLIKRWPPP LRWQYFRSLL PDASITMCPS CFQMFHSEDY ELLVLQHGCC
PYCRRCKDDP GP*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

254 / 254

Last intron/exon boundary

3262

Theoretical NMD boundary in CDS

2958

Length of CDS

3099

Coding sequence (CDS) position

N/A

cDNA position

132

gDNA position

10745

Chromosomal position

129440351

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_18_ENST00000693588

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000693588.1

Genbank transcript ID

NM_001410815 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EERKKRGETN NDLFLADVFS YQGKFHEAAK
LYKRSGHENL ALEMYTDLCM FEYAKDFLGS GDPKETKMLI TKQADWARNI KEPKAAVEMY
ISAGEHVKAI EICGDHGWVD MLIDIARKLD KAEREPLLLC ATYLKKLDSP GYAAETYLKM
GDLKSLVQLH VETQRWDEAF ALGEKHPEFK DDIYMPYAQW LAENDRFEEA QKAFHKAGRQ
REAVQVLEQL TNNAVAESRF NDAAYYYWML SMQCLDIAQD PAQKDTMLGK FYHFQRLAEL
YHGYHAIHRH TEDPFSVHRP ETLFNISRFL LHSLPKDTPS GISKVKILFT LAKQSKALGA
YRLARHAYDK LRGLYIPARF QKSIELGTLT IRAKPFHDSE ELVPLCYRCS TNNPLLNNLG
NVCINCRQPF IFSASSYDVL HLVEFYLEEG ITDEEAISLI DLEVLRPKRD DRQLEIANNS
SQILRLVETK DSIGDEDPFT AKLSFEQGGS EFVPVVVSRL VLRSMSRRDV LIKRWPPPLR
WQYFRSLLPD ASITMCPSCF QMFHSEDYEL LVLQHGCCPY CRRCKDDPGP *

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EERKKRGETN NDLFLADVFS YQGKFHEAAK
LYKRSGHENL ALEMYTDLCM FEYAKDFLGS GDPKETKMLI TKQADWARNI KEPKAAVEMY
ISAGEHVKAI EICGDHGWVD MLIDIARKLD KAEREPLLLC ATYLKKLDSP GYAAETYLKM
GDLKSLVQLH VETQRWDEAF ALGEKHPEFK DDIYMPYAQW LAENDRFEEA QKAFHKAGRQ
REAVQVLEQL TNNAVAESRF NDAAYYYWML SMQCLDIAQD PAQKDTMLGK FYHFQRLAEL
YHGYHAIHRH TEDPFSVHRP ETLFNISRFL LHSLPKDTPS GISKVKILFT LAKQSKALGA
YRLARHAYDK LRGLYIPARF QKSIELGTLT IRAKPFHDSE ELVPLCYRCS TNNPLLNNLG
NVCINCRQPF IFSASSYDVL HLVEFYLEEG ITDEEAISLI DLEVLRPKRD DRQLEIANNS
SQILRLVETK DSIGDEDPFT AKLSFEQGGS EFVPVVVSRL VLRSMSRRDV LIKRWPPPLR
WQYFRSLLPD ASITMCPSCF QMFHSEDYEL LVLQHGCCPY CRRCKDDPGP *

Position of stopcodon in wt / mu CDS

3393 / 3393

Position (AA) of stopcodon in wt / mu AA sequence

1131 / 1131

Position of stopcodon in wt / mu cDNA

3560 / 3560

Position of start ATG in wt / mu cDNA

168 / 168

Last intron/exon boundary

3470

Theoretical NMD boundary in CDS

3252

Length of CDS

3393

Coding sequence (CDS) position

21

cDNA position

188

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_21_ENST00000692901

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000692901.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	W	H	N	D	A	I
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	W	H	N	D	A	I	Q	C	V
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHWHNDAIQ CVSYNPITHQ LASCSSSDFG LWSPEQKSVS KHKSSSKIIC
CSWTNDGQYL ALGMFNGIIS IRNKNGEEKV KIERPGGSLS PIWSICWNPS REERNDILAV
ADWGQKVSFY QLSGKQIGKD RALNFDPCCI SYFTKGEYIL LGGSDKQVSL FTKDGVRLGT
VGEQNSWVWT CQAKPDSNYV VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH
LITEQKVRIK CKELVKKIAI YRNRLAIQLP EKILIYELYS EDLSDMHYRV KEKIIKKFEC
NLLVVCANHI ILCQEKRLQC LSFSGVKERE WQMESLIRYI KVIGGPPGRE GLLVGLKNGQ
ILKIFVDNLF AIVLLKQATA VRCLDMSASR KKLAVVDEND TCLVYDIDTK ELLFQEPNAN
SVAWNTQCED MLCFSGGGYL NIKASTFPVH RQKLQGFVVG YNGSKIFCLH VFSISAVEVP
QSAPMYQYLD RKLFKEAYQI ACLGVTDTDW RELAMEALEG LDFETAKKAF IRVQDLRYLE
LISSIEERKK RGETNNDLFL ADVFSYQGKF HEAAKLYKRS GHENLALEMY TDLCMFEYAK
DFLGSGDPKE TKMLITKQAD WARNIKEPKA AVEMYISAGE HVKAIEICGD HGWVDMLIDI
ARKLDKAERE PLLLCATYLK KLDSPGYAAE TYLKMGDLKS LVQLHVETQR WDEAFALGEK
HPEFKDDIYM PYAQWLAEND RFEEAQKAFH KAGRQREAVQ VLEQLTNNAV AESRFNDAAY
YYWMLSMQCL DIAQDPAQKD TMLGKFYHFQ RLAELYHGYH AIHRHTEDPF SVHRPETLFN
ISRFLLHSLP KDTPSGISKV KILFTLAKQS KALGAYRLAR HAYDKLRGLY IPARFQKSIE
LGTLTIRAKP FHDSEELVPL CYRCSTNNPL LNNLGNVCIN CRQPFIFSAS SYDVLHLVEF
YLEEGITDEE AISLIDLEVL RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF
EQGGSEFVPV VVSRLVLRSM SRRDVLIKRW PPPLRWQYFR SLLPDASITM CPSCFQMFHS
EDYELLVLQH GCCPYCRRCK DDPGP*

Mutated AA sequence

MRAVLTCRDK AEHWHNDAIQ CVSYNPITHQ LASCSSSDFG LWSPEQKSVS KHKSSSKIIC
CSWTNDGQYL ALGMFNGIIS IRNKNGEEKV KIERPGGSLS PIWSICWNPS REERNDILAV
ADWGQKVSFY QLSGKQIGKD RALNFDPCCI SYFTKGEYIL LGGSDKQVSL FTKDGVRLGT
VGEQNSWVWT CQAKPDSNYV VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH
LITEQKVRIK CKELVKKIAI YRNRLAIQLP EKILIYELYS EDLSDMHYRV KEKIIKKFEC
NLLVVCANHI ILCQEKRLQC LSFSGVKERE WQMESLIRYI KVIGGPPGRE GLLVGLKNGQ
ILKIFVDNLF AIVLLKQATA VRCLDMSASR KKLAVVDEND TCLVYDIDTK ELLFQEPNAN
SVAWNTQCED MLCFSGGGYL NIKASTFPVH RQKLQGFVVG YNGSKIFCLH VFSISAVEVP
QSAPMYQYLD RKLFKEAYQI ACLGVTDTDW RELAMEALEG LDFETAKKAF IRVQDLRYLE
LISSIEERKK RGETNNDLFL ADVFSYQGKF HEAAKLYKRS GHENLALEMY TDLCMFEYAK
DFLGSGDPKE TKMLITKQAD WARNIKEPKA AVEMYISAGE HVKAIEICGD HGWVDMLIDI
ARKLDKAERE PLLLCATYLK KLDSPGYAAE TYLKMGDLKS LVQLHVETQR WDEAFALGEK
HPEFKDDIYM PYAQWLAEND RFEEAQKAFH KAGRQREAVQ VLEQLTNNAV AESRFNDAAY
YYWMLSMQCL DIAQDPAQKD TMLGKFYHFQ RLAELYHGYH AIHRHTEDPF SVHRPETLFN
ISRFLLHSLP KDTPSGISKV KILFTLAKQS KALGAYRLAR HAYDKLRGLY IPARFQKSIE
LGTLTIRAKP FHDSEELVPL CYRCSTNNPL LNNLGNVCIN CRQPFIFSAS SYDVLHLVEF
YLEEGITDEE AISLIDLEVL RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF
EQGGSEFVPV VVSRLVLRSM SRRDVLIKRW PPPLRWQYFR SLLPDASITM CPSCFQMFHS
EDYELLVLQH GCCPYCRRCK DDPGP*

Position of stopcodon in wt / mu CDS

3318 / 3318

Position (AA) of stopcodon in wt / mu AA sequence

1106 / 1106

Position of stopcodon in wt / mu cDNA

3421 / 3421

Position of start ATG in wt / mu cDNA

104 / 104

Last intron/exon boundary

3331

Theoretical NMD boundary in CDS

3177

Length of CDS

3318

Coding sequence (CDS) position

21

cDNA position

124

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_22_ENST00000688020

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000688020.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSSRWES FWMNRENEDA EDVIVNRYIQ EIPSTLKSAV YSSQGSEAEE
EEPEEEDDSP RDDNLEERND ILAVADWGQK VSFYQLSGKQ IGKDRALNFD PCCISYFTKG
EYILLGGSDK QVSLFTKDGV RLGTVGEQNS WVWTCQAKPD SNYVVVGCQD GTISFYQLIF
STVHGLYKDR YAYRDSMTDV IVQHLITEQK VRIKCKELVK KIAIYRNRLA IQLPEKILIY
ELYSEDLSDM HYRVKEKIIK KFECNLLVVC ANHIILCQEK RLQCLSFSGV KEREWQMESL
IRYIKVIGGP PGREGLLVGL KNGQILKIFV DNLFAIVLLK QATAVRCLDM SASRKKLAVV
DENDTCLVYD IDTKELLFQE PNANSVAWNT QCEDMLCFSG GGYLNIKAST FPVHRQKLQG
FVVGYNGSKI FCLHVFSISA VEVPQSAPMY QYLDRKLFKE AYQIACLGVT DTDWRELAME
ALEGLDFETA KKAFIRVQDL RYLELISSIE ERKKRGETNN DLFLADVFSY QGKFHEAAKL
YKRSGHENLA LEMYTDLCMF EYAKDFLGSG DPKETKMLIT KQADWARNIK EPKAAVEMYI
SAGEHVKAIE ICGDHGWVDM LIDIARKLDK AEREPLLLCA TYLKKLDSPG YAAETYLKMG
DLKSLVQLHV ETQRWDEAFA LGEKHPEFKD DIYMPYAQWL AENDRFEEAQ KAFHKAGRQR
EAVQVLEQLT NNAVAESRFN DAAYYYWMLS MQCLDIAQDP AQKDTMLGKF YHFQRLAELY
HGYHAIHRHT EDPFSVHRPE TLFNISRFLL HSLPKDTPSG ISKVKILFTL AKQSKALGAY
RLARHAYDKL RGLYIPARFQ KSIELGTLTI RAKPFHDSEE LVPLCYRCST NNPLLNNLGN
VCINCRQPFI FSASSYDVLH LVEFYLEEGI TDEEAISLID LEVLRPKRDD RQLEIANNSS
QILRLVETKD SIGDEDPFTA KLSFEQGGSE FVPVVVSRLV LRSMSRRDVL IKRWPPPLRW
QYFRSLLPDA SITMCPSCFQ MFHSEDYELL VLQHGCCPYC RRCKDDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSSRWES FWMNRENEDA EDVIVNRYIQ EIPSTLKSAV YSSQGSEAEE
EEPEEEDDSP RDDNLEERND ILAVADWGQK VSFYQLSGKQ IGKDRALNFD PCCISYFTKG
EYILLGGSDK QVSLFTKDGV RLGTVGEQNS WVWTCQAKPD SNYVVVGCQD GTISFYQLIF
STVHGLYKDR YAYRDSMTDV IVQHLITEQK VRIKCKELVK KIAIYRNRLA IQLPEKILIY
ELYSEDLSDM HYRVKEKIIK KFECNLLVVC ANHIILCQEK RLQCLSFSGV KEREWQMESL
IRYIKVIGGP PGREGLLVGL KNGQILKIFV DNLFAIVLLK QATAVRCLDM SASRKKLAVV
DENDTCLVYD IDTKELLFQE PNANSVAWNT QCEDMLCFSG GGYLNIKAST FPVHRQKLQG
FVVGYNGSKI FCLHVFSISA VEVPQSAPMY QYLDRKLFKE AYQIACLGVT DTDWRELAME
ALEGLDFETA KKAFIRVQDL RYLELISSIE ERKKRGETNN DLFLADVFSY QGKFHEAAKL
YKRSGHENLA LEMYTDLCMF EYAKDFLGSG DPKETKMLIT KQADWARNIK EPKAAVEMYI
SAGEHVKAIE ICGDHGWVDM LIDIARKLDK AEREPLLLCA TYLKKLDSPG YAAETYLKMG
DLKSLVQLHV ETQRWDEAFA LGEKHPEFKD DIYMPYAQWL AENDRFEEAQ KAFHKAGRQR
EAVQVLEQLT NNAVAESRFN DAAYYYWMLS MQCLDIAQDP AQKDTMLGKF YHFQRLAELY
HGYHAIHRHT EDPFSVHRPE TLFNISRFLL HSLPKDTPSG ISKVKILFTL AKQSKALGAY
RLARHAYDKL RGLYIPARFQ KSIELGTLTI RAKPFHDSEE LVPLCYRCST NNPLLNNLGN
VCINCRQPFI FSASSYDVLH LVEFYLEEGI TDEEAISLID LEVLRPKRDD RQLEIANNSS
QILRLVETKD SIGDEDPFTA KLSFEQGGSE FVPVVVSRLV LRSMSRRDVL IKRWPPPLRW
QYFRSLLPDA SITMCPSCFQ MFHSEDYELL VLQHGCCPYC RRCKDDPGP*

Position of stopcodon in wt / mu CDS

3570 / 3570

Position (AA) of stopcodon in wt / mu AA sequence

1190 / 1190

Position of stopcodon in wt / mu cDNA

3671 / 3671

Position of start ATG in wt / mu cDNA

102 / 102

Last intron/exon boundary

3581

Theoretical NMD boundary in CDS

3429

Length of CDS

3570

Coding sequence (CDS) position

21

cDNA position

122

gDNA position

10745

Chromosomal position

129440351

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_20_ENST00000348417

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.69, misssense (oe): 0.88, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000348417.7

Genbank transcript ID

NM_052989 (exact from MANE)

UniProt / AlphaMissense peptide

IF122_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	all identical	7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Mmulatta	all identical	9			A	V	V	V	W	-	-	-	-	-	-	C	I	N	D	I	A	F	K	P
Fcatus	all identical	7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	Y	D	L	A	F	K	P
Mmusculus	all identical	7	M	R	A	V	L	T	W	R	D	K	A	E	Q	C	I	Y	D	L	A	F	K	P
Ggallus	all identical	7	M	R	A	A	L	T	W	R	D	R	A	E	H	C	I	Y	D	L	A	F	K	P
Trubripes	all identical	7	M	R	A	V	L	A	W	R	E	V	VR	E	E	C	V	Y	D	I	T	F	K	P
Drerio	no homologue
Dmelanogaster	all identical	7	M	R	G	V	L	K	W	L	E	R	I	E	FPNSKDNEI	S	V	H	N	V	C	Y	A	P
Celegans	all identical	7	M	R	P	N	L	L	W	V	D	KILDENNE	A	G	V	C	I	Y	D	L	A	F	K	P
Xtropicalis	no alignment	n/a

Protein features

Start (aa)	End (aa)	Feature	Details
1	1241	CHAIN		lost
3	10	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF SYQGKFHEAA KLYKRSGHEN
LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN IKEPKAAVEM YISAGEHVKA
IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL
HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAGR QREAVQVLEQ
LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ DPAQKDTMLG KFYHFQRLAE LYHGYHAIHR
HTEDPFSVHR PETLFNISRF LLHSLPKDTP SGISKVKILF TLAKQSKALG AYRLARHAYD
KLRGLYIPAR FQKSIELGTL TIRAKPFHDS EELVPLCYRC STNNPLLNNL GNVCINCRQP
FIFSASSYDV LHLVEFYLEE GITDEEAISL IDLEVLRPKR DDRQLEIANN SSQILRLVET
KDSIGDEDPF TAKLSFEQGG SEFVPVVVSR LVLRSMSRRD VLIKRWPPPL RWQYFRSLLP
DASITMCPSC FQMFHSEDYE LLVLQHGCCP YCRRCKDDPG P*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY THNDAIQCVS YNPITHQLAS CSSSDFGLWS
PEQKSVSKHK SSSKIICCSW TNDGQYLALG MFNGIISIRN KNGEEKVKIE RPGGSLSPIW
SICWNPSSRW ESFWMNRENE DAEDVIVNRY IQEIPSTLKS AVYSSQGSEA EEEEPEEEDD
SPRDDNLEER NDILAVADWG QKVSFYQLSG KQIGKDRALN FDPCCISYFT KGEYILLGGS
DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC QDGTISFYQL IFSTVHGLYK
DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR LAIQLPEKIL IYELYSEDLS
DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS GVKEREWQME SLIRYIKVIG
GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL DMSASRKKLA VVDENDTCLV
YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA STFPVHRQKL QGFVVGYNGS
KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG VTDTDWRELA MEALEGLDFE
TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF SYQGKFHEAA KLYKRSGHEN
LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN IKEPKAAVEM YISAGEHVKA
IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL
HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE AQKAFHKAGR QREAVQVLEQ
LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ DPAQKDTMLG KFYHFQRLAE LYHGYHAIHR
HTEDPFSVHR PETLFNISRF LLHSLPKDTP SGISKVKILF TLAKQSKALG AYRLARHAYD
KLRGLYIPAR FQKSIELGTL TIRAKPFHDS EELVPLCYRC STNNPLLNNL GNVCINCRQP
FIFSASSYDV LHLVEFYLEE GITDEEAISL IDLEVLRPKR DDRQLEIANN SSQILRLVET
KDSIGDEDPF TAKLSFEQGG SEFVPVVVSR LVLRSMSRRD VLIKRWPPPL RWQYFRSLLP
DASITMCPSC FQMFHSEDYE LLVLQHGCCP YCRRCKDDPG P*

Position of stopcodon in wt / mu CDS

3726 / 3726

Position (AA) of stopcodon in wt / mu AA sequence

1242 / 1242

Position of stopcodon in wt / mu cDNA

3833 / 3833

Position of start ATG in wt / mu cDNA

108 / 108

Last intron/exon boundary

3743

Theoretical NMD boundary in CDS

3585

Length of CDS

3726

Coding sequence (CDS) position

21

cDNA position

128

gDNA position

10745

Chromosomal position

129440351

Speed

0.08 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_23_ENST00000349441

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000349441.6

Genbank transcript ID

NM_052990 (by similarity)

UniProt / AlphaMissense peptide

IF122_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1241	CHAIN		lost
3	10	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EERKKRGETN NDLFLADVFS YQGKFHEAAK
LYKRSGHENL ALEMYTDLCM FEYAKDFLGS GDPKETKMLI TKQADWARNI KEPKAAVEMY
ISAGEHVKAI EICGDHGWVD MLIDIARKLD KAEREPLLLC ATYLKKLDSP GYAAETYLKM
GDLKSLVQLH VETQRWDEAF ALGEKHPEFK DDIYMPYAQW LAENDRFEEA QKAFHKAGRQ
REAVQVLEQL TNNAVAESRF NDAAYYYWML SMQCLDIAQA DPAQKDTMLG KFYHFQRLAE
LYHGYHAIHR HTEDPFSVHR PETLFNISRF LLHSLPKDTP SGISKVKILF TLAKQSKALG
AYRLARHAYD KLRGLYIPAR FQKSIELGTL TIRAKPFHDS EELVPLCYRC STNNPLLNNL
GNVCINCRQP FIFSASSYDV LHLVEFYLEE GITDEEAISL IDLEVLRPKR DDRQLEIANN
SSQILRLVET KDSIGDEDPF TAKLSFEQGG SEFVPVVVSR LVLRSMSRRD VLIKRWPPPL
RWQYFRSLLP DASITMCPSC FQMFHSEDYE LLVLQHGCCP YCRRCKDDPG P*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EERKKRGETN NDLFLADVFS YQGKFHEAAK
LYKRSGHENL ALEMYTDLCM FEYAKDFLGS GDPKETKMLI TKQADWARNI KEPKAAVEMY
ISAGEHVKAI EICGDHGWVD MLIDIARKLD KAEREPLLLC ATYLKKLDSP GYAAETYLKM
GDLKSLVQLH VETQRWDEAF ALGEKHPEFK DDIYMPYAQW LAENDRFEEA QKAFHKAGRQ
REAVQVLEQL TNNAVAESRF NDAAYYYWML SMQCLDIAQA DPAQKDTMLG KFYHFQRLAE
LYHGYHAIHR HTEDPFSVHR PETLFNISRF LLHSLPKDTP SGISKVKILF TLAKQSKALG
AYRLARHAYD KLRGLYIPAR FQKSIELGTL TIRAKPFHDS EELVPLCYRC STNNPLLNNL
GNVCINCRQP FIFSASSYDV LHLVEFYLEE GITDEEAISL IDLEVLRPKR DDRQLEIANN
SSQILRLVET KDSIGDEDPF TAKLSFEQGG SEFVPVVVSR LVLRSMSRRD VLIKRWPPPL
RWQYFRSLLP DASITMCPSC FQMFHSEDYE LLVLQHGCCP YCRRCKDDPG P*

Position of stopcodon in wt / mu CDS

3396 / 3396

Position (AA) of stopcodon in wt / mu AA sequence

1132 / 1132

Position of stopcodon in wt / mu cDNA

3483 / 3483

Position of start ATG in wt / mu cDNA

88 / 88

Last intron/exon boundary

3393

Theoretical NMD boundary in CDS

3255

Length of CDS

3396

Coding sequence (CDS) position

21

cDNA position

108

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_25_ENST00000689005

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000689005.1

Genbank transcript ID

UniProt / AlphaMissense peptide

IF122_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1241	CHAIN		lost
3	10	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCREER NDILAVADWG QKVSFYQLSG KQIGKDRALN
FDPCCISYFT KGEYILLGGS DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC
QDGTISFYQL IFSTVHGLYK DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR
LAIQLPEKIL IYELYSEDLS DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS
GVKEREWQME SLIRYIKVIG GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL
DMSASRKKLA VVDENDTCLV YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA
STFPVHRQKL QGFVVGYNGS KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG
VTDTDWRELA MEALEGLDFE TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF
SYQGKFHEAA KLYKRSGHEN LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN
IKEPKAAVEM YISAGEHVKA IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS
PGYAAETYLK MGDLKSLVQL HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE
AQKAFHKAGR QREAVQVLEQ LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ ADPAQKDTML
GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL
FTLAKQSKAL GAYRLARHAY DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR
CSTNNPLLNN LGNVCINCRQ PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK
RDDRQLEIAN NSSQILRLVE TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR
DVLIKRWPPP LRWQYFRSLL PDASITMCPS CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP
GP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCREER NDILAVADWG QKVSFYQLSG KQIGKDRALN
FDPCCISYFT KGEYILLGGS DKQVSLFTKD GVRLGTVGEQ NSWVWTCQAK PDSNYVVVGC
QDGTISFYQL IFSTVHGLYK DRYAYRDSMT DVIVQHLITE QKVRIKCKEL VKKIAIYRNR
LAIQLPEKIL IYELYSEDLS DMHYRVKEKI IKKFECNLLV VCANHIILCQ EKRLQCLSFS
GVKEREWQME SLIRYIKVIG GPPGREGLLV GLKNGQILKI FVDNLFAIVL LKQATAVRCL
DMSASRKKLA VVDENDTCLV YDIDTKELLF QEPNANSVAW NTQCEDMLCF SGGGYLNIKA
STFPVHRQKL QGFVVGYNGS KIFCLHVFSI SAVEVPQSAP MYQYLDRKLF KEAYQIACLG
VTDTDWRELA MEALEGLDFE TAKKAFIRVQ DLRYLELISS IEERKKRGET NNDLFLADVF
SYQGKFHEAA KLYKRSGHEN LALEMYTDLC MFEYAKDFLG SGDPKETKML ITKQADWARN
IKEPKAAVEM YISAGEHVKA IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS
PGYAAETYLK MGDLKSLVQL HVETQRWDEA FALGEKHPEF KDDIYMPYAQ WLAENDRFEE
AQKAFHKAGR QREAVQVLEQ LTNNAVAESR FNDAAYYYWM LSMQCLDIAQ ADPAQKDTML
GKFYHFQRLA ELYHGYHAIH RHTEDPFSVH RPETLFNISR FLLHSLPKDT PSGISKVKIL
FTLAKQSKAL GAYRLARHAY DKLRGLYIPA RFQKSIELGT LTIRAKPFHD SEELVPLCYR
CSTNNPLLNN LGNVCINCRQ PFIFSASSYD VLHLVEFYLE EGITDEEAIS LIDLEVLRPK
RDDRQLEIAN NSSQILRLVE TKDSIGDEDP FTAKLSFEQG GSEFVPVVVS RLVLRSMSRR
DVLIKRWPPP LRWQYFRSLL PDASITMCPS CFQMFHSEDY ELLVLQHGCC PYCRRCKDDP
GP*

Position of stopcodon in wt / mu CDS

3249 / 3249

Position (AA) of stopcodon in wt / mu AA sequence

1083 / 1083

Position of stopcodon in wt / mu cDNA

3333 / 3333

Position of start ATG in wt / mu cDNA

85 / 85

Last intron/exon boundary

3243

Theoretical NMD boundary in CDS

3108

Length of CDS

3249

Coding sequence (CDS) position

21

cDNA position

105

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_27_ENST00000515783

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.68, misssense (oe): 0.87, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000515783.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EDFLGSGDPK ETKMLITKQA DWARNIKEPK
AAVEMYISAG EHVKAIEICG DHGWVDMLID IARKLDKAER EPLLLCATYL KKLDSPGYAA
ETYLKMGDLK SLVQLHVETQ RWDEAFALGE KHPEFKDDIY MPYAQWLAEN DRFEEAQKAF
HKAGRQREAV QVLEQLTNNA VAESRFNDAA YYYWMLSMQC LDIAQDPAQK DTMLGKFYHF
QRLAELYHGY HAIHRHTEDP FSVHRPETLF NISRFLLHSL PKDTPSGISK VKILFTLAKQ
SKALGAYRLA RHAYDKLRGL YIPARFQKSI ELGTLTIRAK PFHDSEELVP LCYRCSTNNP
LLNNLGNVCI NCRQPFIFSA SSYDVLHLVE FYLEEGITDE EAISLIDLEV LRPKRDDRQL
EIANNSSQIL RLVETKDSIG DEDPFTAKLS FEQGGSEFVP VVVSRLVLRS MSRRDVLIKR
WPPPLRWQYF RSLLPDASIT MCPSCFQMFH SEDYELLVLQ HGCCPYCRRC KDDPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKAFIRVQD LRYLELISSI EDFLGSGDPK ETKMLITKQA DWARNIKEPK
AAVEMYISAG EHVKAIEICG DHGWVDMLID IARKLDKAER EPLLLCATYL KKLDSPGYAA
ETYLKMGDLK SLVQLHVETQ RWDEAFALGE KHPEFKDDIY MPYAQWLAEN DRFEEAQKAF
HKAGRQREAV QVLEQLTNNA VAESRFNDAA YYYWMLSMQC LDIAQDPAQK DTMLGKFYHF
QRLAELYHGY HAIHRHTEDP FSVHRPETLF NISRFLLHSL PKDTPSGISK VKILFTLAKQ
SKALGAYRLA RHAYDKLRGL YIPARFQKSI ELGTLTIRAK PFHDSEELVP LCYRCSTNNP
LLNNLGNVCI NCRQPFIFSA SSYDVLHLVE FYLEEGITDE EAISLIDLEV LRPKRDDRQL
EIANNSSQIL RLVETKDSIG DEDPFTAKLS FEQGGSEFVP VVVSRLVLRS MSRRDVLIKR
WPPPLRWQYF RSLLPDASIT MCPSCFQMFH SEDYELLVLQ HGCCPYCRRC KDDPGP*

Position of stopcodon in wt / mu CDS

3231 / 3231

Position (AA) of stopcodon in wt / mu AA sequence

1077 / 1077

Position of stopcodon in wt / mu cDNA

3333 / 3333

Position of start ATG in wt / mu cDNA

103 / 103

Last intron/exon boundary

3243

Theoretical NMD boundary in CDS

3090

Length of CDS

3231

Coding sequence (CDS) position

21

cDNA position

123

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_28_ENST00000504021

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.80, LOF (oe): 0.67, misssense (oe): 0.87, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000504021.6

Genbank transcript ID

NM_001410817 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL
CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW
VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE
AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES
RFNDAAYYYW MLSMQCLDIA QADPAQKDTM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV
HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP
ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY
DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED
PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP
SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGLWSPE QKSVSKHKSS SKIICCSWTN DGQYLALGMF NGIISIRNKN GEEKVKIERP
GGSLSPIWSI CWNPSREERN DILAVADWGQ KVSFYQLSGK QIGKDRALNF DPCCISYFTK
GEYILLGGSD KQVSLFTKDG VRLGTVGEQN SWVWTCQAKP DSNYVVVGCQ DGTISFYQLI
FSTVHGLYKD RYAYRDSMTD VIVQHLITEQ KVRIKCKELV KKIAIYRNRL AIQLPEKILI
YELYSEDLSD MHYRVKEKII KKFECNLLVV CANHIILCQE KRLQCLSFSG VKEREWQMES
LIRYIKVIGG PPGREGLLVG LKNGQILKIF VDNLFAIVLL KQATAVRCLD MSASRKKLAV
VDENDTCLVY DIDTKELLFQ EPNANSVAWN TQCEDMLCFS GGGYLNIKAS TFPVHRQKLQ
GFVVGYNGSK IFCLHVFSIS AVEVPQSAPM YQYLDRKLFK EAYQIACLGV TDTDWRELAM
EALEGLDFET AKKERKKRGE TNNDLFLADV FSYQGKFHEA AKLYKRSGHE NLALEMYTDL
CMFEYAKDFL GSGDPKETKM LITKQADWAR NIKEPKAAVE MYISAGEHVK AIEICGDHGW
VDMLIDIARK LDKAEREPLL LCATYLKKLD SPGYAAETYL KMGDLKSLVQ LHVETQRWDE
AFALGEKHPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES
RFNDAAYYYW MLSMQCLDIA QADPAQKDTM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV
HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP
ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY
DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED
PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP
SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Position of stopcodon in wt / mu CDS

3342 / 3342

Position (AA) of stopcodon in wt / mu AA sequence

1114 / 1114

Position of stopcodon in wt / mu cDNA

3453 / 3453

Position of start ATG in wt / mu cDNA

112 / 112

Last intron/exon boundary

3363

Theoretical NMD boundary in CDS

3201

Length of CDS

3342

Coding sequence (CDS) position

21

cDNA position

132

gDNA position

10745

Chromosomal position

129440351

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_29_ENST00000507564

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000507564.5

Genbank transcript ID

NM_001280541 (by similarity)

UniProt / AlphaMissense peptide

IF122_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1241	CHAIN		lost
3	10	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY TSWSVMSSLH LHLPFLGLHK TVRVTATDKA
PKGQGGRIDC LRPSVQNQPG QKHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH
KSSSKIICCS WTNDGQYLAL GMFNGIISIR NKNGEEKVKI ERPGGSLSPI WSICWNPSRE
ERNDILAVAD WGQKVSFYQL SGKQIGKDRA LNFDPCCISY FTKGEYILLG GSDKQVSLFT
KDGVRLGTVG EQNSWVWTCQ AKPDSNYVVV GCQDGTISFY QLIFSTVHGL YKDRYAYRDS
MTDVIVQHLI TEQKVRIKCK ELVKKIAIYR NRLAIQLPEK ILIYELYSED LSDMHYRVKE
KIIKKFECNL LVVCANHIIL CQEKRLQCLS FSGVKEREWQ MESLIRYIKV IGGPPGREGL
LVGLKNGQIL KIFVDNLFAI VLLKQATAVR CLDMSASRKK LAVVDENDTC LVYDIDTKEL
LFQEPNANSV AWNTQCEDML CFSGGGYLNI KASTFPVHRQ KLQGFVVGYN GSKIFCLHVF
SISAVEVPQS APMYQYLDRK LFKEAYQIAC LGVTDTDWRE LAMEALEGLD FETAKKAFIR
VQDLRYLELI SSIEERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD
LCMFEYAKDF LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG
WVDMLIDIAR KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD
EAFALGEKHP EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE
SRFNDAAYYY WMLSMQCLDI AQADPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS
VHRPETLFNI SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI
PARFQKSIEL GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS
YDVLHLVEFY LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE
DPFTAKLSFE QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC
PSCFQMFHSE DYELLVLQHG CCPYCRRCKD DPGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY TSWSVMSSLH LHLPFLGLHK TVRVTATDKA
PKGQGGRIDC LRPSVQNQPG QKHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH
KSSSKIICCS WTNDGQYLAL GMFNGIISIR NKNGEEKVKI ERPGGSLSPI WSICWNPSRE
ERNDILAVAD WGQKVSFYQL SGKQIGKDRA LNFDPCCISY FTKGEYILLG GSDKQVSLFT
KDGVRLGTVG EQNSWVWTCQ AKPDSNYVVV GCQDGTISFY QLIFSTVHGL YKDRYAYRDS
MTDVIVQHLI TEQKVRIKCK ELVKKIAIYR NRLAIQLPEK ILIYELYSED LSDMHYRVKE
KIIKKFECNL LVVCANHIIL CQEKRLQCLS FSGVKEREWQ MESLIRYIKV IGGPPGREGL
LVGLKNGQIL KIFVDNLFAI VLLKQATAVR CLDMSASRKK LAVVDENDTC LVYDIDTKEL
LFQEPNANSV AWNTQCEDML CFSGGGYLNI KASTFPVHRQ KLQGFVVGYN GSKIFCLHVF
SISAVEVPQS APMYQYLDRK LFKEAYQIAC LGVTDTDWRE LAMEALEGLD FETAKKAFIR
VQDLRYLELI SSIEERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD
LCMFEYAKDF LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG
WVDMLIDIAR KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD
EAFALGEKHP EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE
SRFNDAAYYY WMLSMQCLDI AQADPAQKDT MLGKFYHFQR LAELYHGYHA IHRHTEDPFS
VHRPETLFNI SRFLLHSLPK DTPSGISKVK ILFTLAKQSK ALGAYRLARH AYDKLRGLYI
PARFQKSIEL GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS
YDVLHLVEFY LEEGITDEEA ISLIDLEVLR PKRDDRQLEI ANNSSQILRL VETKDSIGDE
DPFTAKLSFE QGGSEFVPVV VSRLVLRSMS RRDVLIKRWP PPLRWQYFRS LLPDASITMC
PSCFQMFHSE DYELLVLQHG CCPYCRRCKD DPGP*

Position of stopcodon in wt / mu CDS

3705 / 3705

Position (AA) of stopcodon in wt / mu AA sequence

1235 / 1235

Position of stopcodon in wt / mu cDNA

3824 / 3824

Position of start ATG in wt / mu cDNA

120 / 120

Last intron/exon boundary

3734

Theoretical NMD boundary in CDS

3564

Length of CDS

3705

Coding sequence (CDS) position

21

cDNA position

140

gDNA position

10745

Chromosomal position

129440351

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

MutationT@ster 2025

Variant:

3:129440351G>C_32_ENST00000689313

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 4638 (pathogenic)

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr3:129440351G>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.81, LOF (oe): 0.69, misssense (oe): 0.87, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000689313.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.21G>C
g.10745G>C

AA changes

AAE:	W7C	?
Score:	215

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Cranioectodermal dysplasia 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA
Human		7	M	R	A	V	L	T	W	R	D	K	A	E	H	C	I	N	D	I	A
mutated	not conserved	7	M	R	A	V	L	T	C	R	D	K	A	E	H	C	I	N	D	I	A	F	K	P
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.068	1
	6.068	1
(flanking)	3.008	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

21

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered gDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Original cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGGAGAGATAAAGCCGAGCACTG

Altered cDNA sequence snippet

ATGAGGGCCGTGTTGACGTGCAGAGATAAAGCCGAGCACTG

Wildtype AA sequence

MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY TSWSVMSSLH LHLPFLGLHK TVRVTATDKA
PKGQGGRIDC LRPSVQNQPG QKHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH
KSSSKIICCS WTNDGQYLAL GMFNGIISIR NKNGEEKVKI ERPGGSLSPI WSICWNPSRE
ERNDILAVAD WGQKVSFYQL SGKQIGKDRA LNFDPCCISY FTKGEYILLG GSDKQVSLFT
KDGVRLGTVG EQNSWVWTCQ AKPDSNYVVV GCQDGTISFY QLIFSTVHGL YKDRYAYRDS
MTDVIVQHLI TEQKVRIKCK ELVKKIAIYR NRLAIQLPEK ILIYELYSED LSDMHYRVKE
KIIKKFECNL LVVCANHIIL CQEKRLQCLS FSGVKEREWQ MESLIRYIKV IGGPPGREGL
LVGLKNGQIL KIFVDNLFAI VLLKQATAVR CLDMSASRKK LAVVDENDTC LVYDIDTKEL
LFQEPNANSV AWNTQCEDML CFSGGGYLNI KASTFPVHRQ KLQGFVVGYN GSKIFCLHVF
SISAVEVPQS APMYQYLDRK LFKEAYQIAC LGVTDTDWRE LAMEALEGLD FETAKKAFIR
VQDLRYLELI SSIEERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD
LCMFEYAKDF LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG
WVDMLIDIAR KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD
EAFALGEKHP EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE
SRFNDAAYYY WMLSMQCLDI AQDPAQKDTM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV
HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP
ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY
DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED
PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP
SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Mutated AA sequence

MRAVLTCRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA
YAKDGKRFAS GSADKSVIIW TSKLEGILKY TSWSVMSSLH LHLPFLGLHK TVRVTATDKA
PKGQGGRIDC LRPSVQNQPG QKHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH
KSSSKIICCS WTNDGQYLAL GMFNGIISIR NKNGEEKVKI ERPGGSLSPI WSICWNPSRE
ERNDILAVAD WGQKVSFYQL SGKQIGKDRA LNFDPCCISY FTKGEYILLG GSDKQVSLFT
KDGVRLGTVG EQNSWVWTCQ AKPDSNYVVV GCQDGTISFY QLIFSTVHGL YKDRYAYRDS
MTDVIVQHLI TEQKVRIKCK ELVKKIAIYR NRLAIQLPEK ILIYELYSED LSDMHYRVKE
KIIKKFECNL LVVCANHIIL CQEKRLQCLS FSGVKEREWQ MESLIRYIKV IGGPPGREGL
LVGLKNGQIL KIFVDNLFAI VLLKQATAVR CLDMSASRKK LAVVDENDTC LVYDIDTKEL
LFQEPNANSV AWNTQCEDML CFSGGGYLNI KASTFPVHRQ KLQGFVVGYN GSKIFCLHVF
SISAVEVPQS APMYQYLDRK LFKEAYQIAC LGVTDTDWRE LAMEALEGLD FETAKKAFIR
VQDLRYLELI SSIEERKKRG ETNNDLFLAD VFSYQGKFHE AAKLYKRSGH ENLALEMYTD
LCMFEYAKDF LGSGDPKETK MLITKQADWA RNIKEPKAAV EMYISAGEHV KAIEICGDHG
WVDMLIDIAR KLDKAEREPL LLCATYLKKL DSPGYAAETY LKMGDLKSLV QLHVETQRWD
EAFALGEKHP EFKDDIYMPY AQWLAENDRF EEAQKAFHKA GRQREAVQVL EQLTNNAVAE
SRFNDAAYYY WMLSMQCLDI AQDPAQKDTM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV
HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLARHA YDKLRGLYIP
ARFQKSIELG TLTIRAKPFH DSEELVPLCY RCSTNNPLLN NLGNVCINCR QPFIFSASSY
DVLHLVEFYL EEGITDEEAI SLIDLEVLRP KRDDRQLEIA NNSSQILRLV ETKDSIGDED
PFTAKLSFEQ GGSEFVPVVV SRLVLRSMSR RDVLIKRWPP PLRWQYFRSL LPDASITMCP
SCFQMFHSED YELLVLQHGC CPYCRRCKDD PGP*

Position of stopcodon in wt / mu CDS

3702 / 3702

Position (AA) of stopcodon in wt / mu AA sequence

1234 / 1234

Position of stopcodon in wt / mu cDNA

3928 / 3928

Position of start ATG in wt / mu cDNA

227 / 227

Last intron/exon boundary

3838

Theoretical NMD boundary in CDS

3561

Length of CDS

3702

Coding sequence (CDS) position

21

cDNA position

247

gDNA position

10745

Chromosomal position

129440351

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project