MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000380518
Querying Taster for transcript #2: ENST00000337299
MT speed 0.1 s - this script 2.531713 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000337299	COL2A1	Deleterious	95\|5	simple_aae		No	Yes			Single base exchange		Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 17377 (pathogenic) Protein features (might be) affected
ENST00000380518(MANE Select)	COL2A1	Deleterious	98\|2	simple_aae		No	Yes			Single base exchange		Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 17377 (pathogenic) Protein features (might be) affected

MutationT@ster 2025

Variant:

12:47986353C>A_2_ENST00000337299

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 17377 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr12:47986353C>A (GRCh38)

Gene symbol

COL2A1

Gene constraints

LOEUF: 0.19, LOF (oe): 0.14, misssense (oe): 0.68, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000337299.7

Genbank transcript ID

NM_033150 (by similarity)

UniProt / AlphaMissense peptide

CO2A1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1303G>T
g.18202G>T

AA changes

AAE:	G435C	?
Score:	159

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Spondyloepimetaphyseal dysplasia, Strudwick type

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs121912880
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		435	A	R	G	E	P	G	G	V	G	P	I	G	P	P	G	E	R	G	A	P	G	N	R	G
mutated	not conserved	435	A	R	G	E	P	G	G	V	G	P	I	C	P	P	G	E	R	G	A	P	G	N	R
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
97	1237	REGION		lost
182	1241	CHAIN		lost
201	1214	REGION	Triple-helical region	lost
432	446	COMPBIAS	Pro residues	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.164	1
	7.905	1
(flanking)	-5.695	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

18

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTGGTGGCGTTGGGCCCATCGGTCCCCCTGGAGAAAGAGTT

Altered gDNA sequence snippet

CTGGTGGCGTTGGGCCCATCTGTCCCCCTGGAGAAAGAGTT

Original cDNA sequence snippet

CTGGTGGCGTTGGGCCCATCGGTCCCCCTGGAGAAAGAGGT

Altered cDNA sequence snippet

CTGGTGGCGTTGGGCCCATCTGTCCCCCTGGAGAAAGAGGT

Wildtype AA sequence

MIRLGAPQTL VLLTLLVAAV LRCQGQDVRQ PGPKGQKGEP GDIKDIVGPK GPPGPQGPAG
EQGPRGDRGD KGEKGAPGPR GRDGEPGTPG NPGPPGPPGP PGPPGLGGNF AAQMAGGFDE
KAGGAQLGVM QGPMGPMGPR GPPGPAGAPG PQGFQGNPGE PGEPGVSGPM GPRGPPGPPG
KPGDDGEAGK PGKAGERGPP GPQGARGFPG TPGLPGVKGH RGYPGLDGAK GEAGAPGVKG
ESGSPGENGS PGPMGPRGLP GERGRTGPAG AAGARGNDGQ PGPAGPPGPV GPAGGPGFPG
APGAKGEAGP TGARGPEGAQ GPRGEPGTPG SPGPAGASGN PGTDGIPGAK GSAGAPGIAG
APGFPGPRGP PGPQGATGPL GPKGQTGEPG IAGFKGEQGP KGEPGPAGPQ GAPGPAGEEG
KRGARGEPGG VGPIGPPGER GAPGNRGFPG QDGLAGPKGA PGERGPSGLA GPKGANGDPG
RPGEPGLPGA RGLTGRPGDA GPQGKVGPSG APGEDGRPGP PGPQGARGQP GVMGFPGPKG
ANGEPGKAGE KGLPGAPGLR GLPGKDGETG AAGPPGPAGP AGERGEQGAP GPSGFQGLPG
PPGPPGEGGK PGDQGVPGEA GAPGLVGPRG ERGFPGERGS PGAQGLQGPR GLPGTPGTDG
PKGASGPAGP PGAQGPPGLQ GMPGERGAAG IAGPKGDRGD VGEKGPEGAP GKDGGRGLTG
PIGPPGPAGA NGEKGEVGPP GPAGSAGARG APGERGETGP PGPAGFAGPP GADGQPGAKG
EQGEAGQKGD AGAPGPQGPS GAPGPQGPTG VTGPKGARGA QGPPGATGFP GAAGRVGPPG
SNGNPGPPGP PGPSGKDGPK GARGDSGPPG RAGEPGLQGP AGPPGEKGEP GDDGPSGAEG
PPGPQGLAGQ RGIVGLPGQR GERGFPGLPG PSGEPGKQGA PGASGDRGPP GPVGPPGLTG
PAGEPGREGS PGADGPPGRD GAAGVKGDRG ETGAVGAPGA PGPPGSPGPA GPTGKQGDRG
EAGAQGPMGP SGPAGARGIQ GPQGPRGDKG EAGEPGERGL KGHRGFTGLQ GLPGPPGPSG
DQGASGPAGP SGPRGPPGPV GPSGKDGANG IPGPIGPPGP RGRSGETGPA GPPGNPGPPG
PPGPPGPGID MSAFAGLGPR EKGPDPLQYM RADQAAGGLR QHDAEVDATL KSLNNQIESI
RSPEGSRKNP ARTCRDLKLC HPEWKSGDYW IDPNQGCTLD AMKVFCNMET GETCVYPNPA
NVPKKNWWSS KSKEKKHIWF GETINGGFHF SYGDDNLAPN TANVQMTFLR LLSTEGSQNI
TYHCKNSIAY LDEAAGNLKK ALLIQGSNDV EIRAEGNSRF TYTALKDGCT KHTGKWGKTV
IEYRSQKTSR LPIIDIAPMD IGGPEQEFGV DIGPVCFL*

Mutated AA sequence

MIRLGAPQTL VLLTLLVAAV LRCQGQDVRQ PGPKGQKGEP GDIKDIVGPK GPPGPQGPAG
EQGPRGDRGD KGEKGAPGPR GRDGEPGTPG NPGPPGPPGP PGPPGLGGNF AAQMAGGFDE
KAGGAQLGVM QGPMGPMGPR GPPGPAGAPG PQGFQGNPGE PGEPGVSGPM GPRGPPGPPG
KPGDDGEAGK PGKAGERGPP GPQGARGFPG TPGLPGVKGH RGYPGLDGAK GEAGAPGVKG
ESGSPGENGS PGPMGPRGLP GERGRTGPAG AAGARGNDGQ PGPAGPPGPV GPAGGPGFPG
APGAKGEAGP TGARGPEGAQ GPRGEPGTPG SPGPAGASGN PGTDGIPGAK GSAGAPGIAG
APGFPGPRGP PGPQGATGPL GPKGQTGEPG IAGFKGEQGP KGEPGPAGPQ GAPGPAGEEG
KRGARGEPGG VGPICPPGER GAPGNRGFPG QDGLAGPKGA PGERGPSGLA GPKGANGDPG
RPGEPGLPGA RGLTGRPGDA GPQGKVGPSG APGEDGRPGP PGPQGARGQP GVMGFPGPKG
ANGEPGKAGE KGLPGAPGLR GLPGKDGETG AAGPPGPAGP AGERGEQGAP GPSGFQGLPG
PPGPPGEGGK PGDQGVPGEA GAPGLVGPRG ERGFPGERGS PGAQGLQGPR GLPGTPGTDG
PKGASGPAGP PGAQGPPGLQ GMPGERGAAG IAGPKGDRGD VGEKGPEGAP GKDGGRGLTG
PIGPPGPAGA NGEKGEVGPP GPAGSAGARG APGERGETGP PGPAGFAGPP GADGQPGAKG
EQGEAGQKGD AGAPGPQGPS GAPGPQGPTG VTGPKGARGA QGPPGATGFP GAAGRVGPPG
SNGNPGPPGP PGPSGKDGPK GARGDSGPPG RAGEPGLQGP AGPPGEKGEP GDDGPSGAEG
PPGPQGLAGQ RGIVGLPGQR GERGFPGLPG PSGEPGKQGA PGASGDRGPP GPVGPPGLTG
PAGEPGREGS PGADGPPGRD GAAGVKGDRG ETGAVGAPGA PGPPGSPGPA GPTGKQGDRG
EAGAQGPMGP SGPAGARGIQ GPQGPRGDKG EAGEPGERGL KGHRGFTGLQ GLPGPPGPSG
DQGASGPAGP SGPRGPPGPV GPSGKDGANG IPGPIGPPGP RGRSGETGPA GPPGNPGPPG
PPGPPGPGID MSAFAGLGPR EKGPDPLQYM RADQAAGGLR QHDAEVDATL KSLNNQIESI
RSPEGSRKNP ARTCRDLKLC HPEWKSGDYW IDPNQGCTLD AMKVFCNMET GETCVYPNPA
NVPKKNWWSS KSKEKKHIWF GETINGGFHF SYGDDNLAPN TANVQMTFLR LLSTEGSQNI
TYHCKNSIAY LDEAAGNLKK ALLIQGSNDV EIRAEGNSRF TYTALKDGCT KHTGKWGKTV
IEYRSQKTSR LPIIDIAPMD IGGPEQEFGV DIGPVCFL*

Position of stopcodon in wt / mu CDS

4257 / 4257

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

1419 / 1419

Position of stopcodon in wt / mu cDNA

4442 / 4442

Position of start ATG in wt / mu cDNA

186 / 186

Last intron/exon boundary

4295

Theoretical NMD boundary in CDS

4059

Length of CDS

4257

Coding sequence (CDS) position

1303

cDNA position

1488

gDNA position

18202

Chromosomal position

47986353

Speed

0.05 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

Back to summary table

MutationT@ster 2025

Variant:

12:47986353C>A_1_ENST00000380518

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 17377 (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

Chr12:47986353C>A (GRCh38)

Gene symbol

COL2A1

Gene constraints

LOEUF: 0.18, LOF (oe): 0.13, misssense (oe): 0.67, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000380518.8

Genbank transcript ID

NM_001844 (exact from MANE)

UniProt / AlphaMissense peptide

CO2A1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1510G>T
g.18202G>T

AA changes

AAE:	G504C	?
Score:	159

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Spondyloepimetaphyseal dysplasia, Strudwick type

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs121912880
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		504	A	R	G	E	P	G	G	V	G	P	I	G	P	P	G	E	R	G	A	P	G	N	R	G
mutated	not conserved	504	A	R	G	E	P	G	G	V	G	P	I	C	P	P	G	E	R	G	A	P	G	N	R
Ptroglodytes	all identical	504	A	R	G	E	P	G	G	V	G	P	I	G	P	P	G	E	R	G	A	P	G	N	R
Mmulatta	all identical	504	A	R	G	E	P	G	G	V	G	P	I	G	P	P	G	E	R	G	A	P	G	N	R
Fcatus	all identical	504	A	R	G	E	P	G	G	A	G	P	V	G	P	P	G	E	R	G	A	P	G	N	R
Mmusculus	all identical	504	A	R	G	E	P	G	G	A	G	P	I	G	P	P	G	E	R	G	A	P	G	N	R
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	506	A	R	G	E	P	G	A	A	G	P	L	G	P	P	G	E	R	G	A	P	G	N	R

Protein features

Start (aa)	End (aa)	Feature	Details
97	1237	REGION		lost
182	1241	CHAIN		lost
201	1214	REGION	Triple-helical region	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.164	1
	7.905	1
(flanking)	-5.695	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

18

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

CTGGTGGCGTTGGGCCCATCGGTCCCCCTGGAGAAAGAGTT

Altered gDNA sequence snippet

CTGGTGGCGTTGGGCCCATCTGTCCCCCTGGAGAAAGAGTT

Original cDNA sequence snippet

CTGGTGGCGTTGGGCCCATCGGTCCCCCTGGAGAAAGAGGT

Altered cDNA sequence snippet

CTGGTGGCGTTGGGCCCATCTGTCCCCCTGGAGAAAGAGGT

Wildtype AA sequence

MIRLGAPQTL VLLTLLVAAV LRCQGQDVQE AGSCVQDGQR YNDKDVWKPE PCRICVCDTG
TVLCDDIICE DVKDCLSPEI PFGECCPICP TDLATASGQP GPKGQKGEPG DIKDIVGPKG
PPGPQGPAGE QGPRGDRGDK GEKGAPGPRG RDGEPGTPGN PGPPGPPGPP GPPGLGGNFA
AQMAGGFDEK AGGAQLGVMQ GPMGPMGPRG PPGPAGAPGP QGFQGNPGEP GEPGVSGPMG
PRGPPGPPGK PGDDGEAGKP GKAGERGPPG PQGARGFPGT PGLPGVKGHR GYPGLDGAKG
EAGAPGVKGE SGSPGENGSP GPMGPRGLPG ERGRTGPAGA AGARGNDGQP GPAGPPGPVG
PAGGPGFPGA PGAKGEAGPT GARGPEGAQG PRGEPGTPGS PGPAGASGNP GTDGIPGAKG
SAGAPGIAGA PGFPGPRGPP GPQGATGPLG PKGQTGEPGI AGFKGEQGPK GEPGPAGPQG
APGPAGEEGK RGARGEPGGV GPIGPPGERG APGNRGFPGQ DGLAGPKGAP GERGPSGLAG
PKGANGDPGR PGEPGLPGAR GLTGRPGDAG PQGKVGPSGA PGEDGRPGPP GPQGARGQPG
VMGFPGPKGA NGEPGKAGEK GLPGAPGLRG LPGKDGETGA AGPPGPAGPA GERGEQGAPG
PSGFQGLPGP PGPPGEGGKP GDQGVPGEAG APGLVGPRGE RGFPGERGSP GAQGLQGPRG
LPGTPGTDGP KGASGPAGPP GAQGPPGLQG MPGERGAAGI AGPKGDRGDV GEKGPEGAPG
KDGGRGLTGP IGPPGPAGAN GEKGEVGPPG PAGSAGARGA PGERGETGPP GPAGFAGPPG
ADGQPGAKGE QGEAGQKGDA GAPGPQGPSG APGPQGPTGV TGPKGARGAQ GPPGATGFPG
AAGRVGPPGS NGNPGPPGPP GPSGKDGPKG ARGDSGPPGR AGEPGLQGPA GPPGEKGEPG
DDGPSGAEGP PGPQGLAGQR GIVGLPGQRG ERGFPGLPGP SGEPGKQGAP GASGDRGPPG
PVGPPGLTGP AGEPGREGSP GADGPPGRDG AAGVKGDRGE TGAVGAPGAP GPPGSPGPAG
PTGKQGDRGE AGAQGPMGPS GPAGARGIQG PQGPRGDKGE AGEPGERGLK GHRGFTGLQG
LPGPPGPSGD QGASGPAGPS GPRGPPGPVG PSGKDGANGI PGPIGPPGPR GRSGETGPAG
PPGNPGPPGP PGPPGPGIDM SAFAGLGPRE KGPDPLQYMR ADQAAGGLRQ HDAEVDATLK
SLNNQIESIR SPEGSRKNPA RTCRDLKLCH PEWKSGDYWI DPNQGCTLDA MKVFCNMETG
ETCVYPNPAN VPKKNWWSSK SKEKKHIWFG ETINGGFHFS YGDDNLAPNT ANVQMTFLRL
LSTEGSQNIT YHCKNSIAYL DEAAGNLKKA LLIQGSNDVE IRAEGNSRFT YTALKDGCTK
HTGKWGKTVI EYRSQKTSRL PIIDIAPMDI GGPEQEFGVD IGPVCFL*

Mutated AA sequence

MIRLGAPQTL VLLTLLVAAV LRCQGQDVQE AGSCVQDGQR YNDKDVWKPE PCRICVCDTG
TVLCDDIICE DVKDCLSPEI PFGECCPICP TDLATASGQP GPKGQKGEPG DIKDIVGPKG
PPGPQGPAGE QGPRGDRGDK GEKGAPGPRG RDGEPGTPGN PGPPGPPGPP GPPGLGGNFA
AQMAGGFDEK AGGAQLGVMQ GPMGPMGPRG PPGPAGAPGP QGFQGNPGEP GEPGVSGPMG
PRGPPGPPGK PGDDGEAGKP GKAGERGPPG PQGARGFPGT PGLPGVKGHR GYPGLDGAKG
EAGAPGVKGE SGSPGENGSP GPMGPRGLPG ERGRTGPAGA AGARGNDGQP GPAGPPGPVG
PAGGPGFPGA PGAKGEAGPT GARGPEGAQG PRGEPGTPGS PGPAGASGNP GTDGIPGAKG
SAGAPGIAGA PGFPGPRGPP GPQGATGPLG PKGQTGEPGI AGFKGEQGPK GEPGPAGPQG
APGPAGEEGK RGARGEPGGV GPICPPGERG APGNRGFPGQ DGLAGPKGAP GERGPSGLAG
PKGANGDPGR PGEPGLPGAR GLTGRPGDAG PQGKVGPSGA PGEDGRPGPP GPQGARGQPG
VMGFPGPKGA NGEPGKAGEK GLPGAPGLRG LPGKDGETGA AGPPGPAGPA GERGEQGAPG
PSGFQGLPGP PGPPGEGGKP GDQGVPGEAG APGLVGPRGE RGFPGERGSP GAQGLQGPRG
LPGTPGTDGP KGASGPAGPP GAQGPPGLQG MPGERGAAGI AGPKGDRGDV GEKGPEGAPG
KDGGRGLTGP IGPPGPAGAN GEKGEVGPPG PAGSAGARGA PGERGETGPP GPAGFAGPPG
ADGQPGAKGE QGEAGQKGDA GAPGPQGPSG APGPQGPTGV TGPKGARGAQ GPPGATGFPG
AAGRVGPPGS NGNPGPPGPP GPSGKDGPKG ARGDSGPPGR AGEPGLQGPA GPPGEKGEPG
DDGPSGAEGP PGPQGLAGQR GIVGLPGQRG ERGFPGLPGP SGEPGKQGAP GASGDRGPPG
PVGPPGLTGP AGEPGREGSP GADGPPGRDG AAGVKGDRGE TGAVGAPGAP GPPGSPGPAG
PTGKQGDRGE AGAQGPMGPS GPAGARGIQG PQGPRGDKGE AGEPGERGLK GHRGFTGLQG
LPGPPGPSGD QGASGPAGPS GPRGPPGPVG PSGKDGANGI PGPIGPPGPR GRSGETGPAG
PPGNPGPPGP PGPPGPGIDM SAFAGLGPRE KGPDPLQYMR ADQAAGGLRQ HDAEVDATLK
SLNNQIESIR SPEGSRKNPA RTCRDLKLCH PEWKSGDYWI DPNQGCTLDA MKVFCNMETG
ETCVYPNPAN VPKKNWWSSK SKEKKHIWFG ETINGGFHFS YGDDNLAPNT ANVQMTFLRL
LSTEGSQNIT YHCKNSIAYL DEAAGNLKKA LLIQGSNDVE IRAEGNSRFT YTALKDGCTK
HTGKWGKTVI EYRSQKTSRL PIIDIAPMDI GGPEQEFGVD IGPVCFL*

Position of stopcodon in wt / mu CDS

4464 / 4464

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

1488 / 1488

Position of stopcodon in wt / mu cDNA

4619 / 4619

Position of start ATG in wt / mu cDNA

156 / 156

Last intron/exon boundary

4472

Theoretical NMD boundary in CDS

4266

Length of CDS

4464

Coding sequence (CDS) position

1510

cDNA position

1665

gDNA position

18202

Chromosomal position

47986353

Speed

0.05 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

Back to summary table