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: ENST00000451604
Querying Taster for transcript #2: ENST00000537393
Querying Taster for transcript #3: ENST00000646273
Querying Taster for transcript #4: ENST00000704296
Querying Taster for transcript #5: ENST00000704299
Querying Taster for transcript #6: ENST00000396007
Querying Taster for transcript #7: ENST00000545921
MT speed 0.34 s - this script 2.787261 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000451604(MANE Select)	SOX5	Deleterious	70\|30	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000545921	SOX5	Deleterious	93\|7	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000537393	SOX5	Deleterious	97\|3	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000646273	SOX5	Deleterious	97\|3	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000704296	SOX5	Deleterious	100\|0	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000704299	SOX5	Deleterious	100\|0	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000396007	SOX5	Deleterious	100\|0	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

12:23534259C>A_1_ENST00000451604

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 70|30 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

LOEUF: 0.20, LOF (oe): 0.11, misssense (oe): 0.65, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000451604.7

Genbank transcript ID

NM_006940 (exact from MANE)

UniProt / AlphaMissense peptide

SOX5_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2252G>T
g.1028286G>T

AA changes

AAE:	G751V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		751	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	751	D	E	E	E	D	D	P	D	V	D	Y	V	S	D	S	E	N	H	I	A	G	Q	A
Ptroglodytes	all identical	753	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A
Mmulatta	all identical	815	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A
Fcatus	all identical	775	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A
Mmusculus	all identical	751	D	E	E	E	E	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A
Ggallus	all identical	739	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	805	D	-	E	D	D	D	P	D	V	D	Y	A	S	D	S	E	N	L	S	A	E	Q	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	763	CHAIN		lost
714	763	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MLTDPDLPQE FERMSSKRPA SPYGEADGEV AMVTSRQKVE EEESDGLPAF HLPLHVSFPN
KPHSEEFQPV SLLTQETCGH RTPTSQHNTM EVDGNKVMSS FAPHNSSTSP QKAEEGGRQS
GESLSSTALG TPERRKGSLA DVVDTLKQRK MEELIKNEPE ETPSIEKLLS KDWKDKLLAM
GSGNFGEIKG TPESLAEKER QLMGMINQLT SLREQLLAAH DEQKKLAASQ IEKQRQQMEL
AKQQQEQIAR QQQQLLQQQH KINLLQQQIQ VQGQLPPLMI PVFPPDQRTL AAAAQQGFLL
PPGFSYKAGC SDPYPVQLIP TTMAAAAAAT PGLGPLQLQQ LYAAQLAAMQ VSPGGKLPGI
PQGNLGAAVS PTSIHTDKST NSPPPKSKDE VAQPLNLSAK PKTSDGKSPT SPTSPHMPAL
RINSGAGPLK ASVPAALASP SARVSTIGYL NDHDAVTKAI QEARQMKEQL RREQQVLDGK
VAVVNSLGLN NCRTEKEKTT LESLTQQLAV KQNEEGKFSH AMMDFNLSGD SDGSAGVSES
RIYRESRGRG SNEPHIKRPM NAFMVWAKDE RRKILQAFPD MHNSNISKIL GSRWKAMTNL
EKQPYYEEQA RLSKQHLEKY PDYKYKPRPK RTCLVDGKKL RIGEYKAIMR NRRQEMRQYF
NVGQQAQIPI ATAGVVYPGA IAMAGMPSPH LPSEHSSVSS SPEPGMPVIQ STYGVKGEEP
HIKEEIQAED INGEIYDEYD EEEDDPDVDY GSDSENHIAG QAN*

Mutated AA sequence

MLTDPDLPQE FERMSSKRPA SPYGEADGEV AMVTSRQKVE EEESDGLPAF HLPLHVSFPN
KPHSEEFQPV SLLTQETCGH RTPTSQHNTM EVDGNKVMSS FAPHNSSTSP QKAEEGGRQS
GESLSSTALG TPERRKGSLA DVVDTLKQRK MEELIKNEPE ETPSIEKLLS KDWKDKLLAM
GSGNFGEIKG TPESLAEKER QLMGMINQLT SLREQLLAAH DEQKKLAASQ IEKQRQQMEL
AKQQQEQIAR QQQQLLQQQH KINLLQQQIQ VQGQLPPLMI PVFPPDQRTL AAAAQQGFLL
PPGFSYKAGC SDPYPVQLIP TTMAAAAAAT PGLGPLQLQQ LYAAQLAAMQ VSPGGKLPGI
PQGNLGAAVS PTSIHTDKST NSPPPKSKDE VAQPLNLSAK PKTSDGKSPT SPTSPHMPAL
RINSGAGPLK ASVPAALASP SARVSTIGYL NDHDAVTKAI QEARQMKEQL RREQQVLDGK
VAVVNSLGLN NCRTEKEKTT LESLTQQLAV KQNEEGKFSH AMMDFNLSGD SDGSAGVSES
RIYRESRGRG SNEPHIKRPM NAFMVWAKDE RRKILQAFPD MHNSNISKIL GSRWKAMTNL
EKQPYYEEQA RLSKQHLEKY PDYKYKPRPK RTCLVDGKKL RIGEYKAIMR NRRQEMRQYF
NVGQQAQIPI ATAGVVYPGA IAMAGMPSPH LPSEHSSVSS SPEPGMPVIQ STYGVKGEEP
HIKEEIQAED INGEIYDEYD EEEDDPDVDY VSDSENHIAG QAN*

Position of stopcodon in wt / mu CDS

2292 / 2292

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

764 / 764

Position of stopcodon in wt / mu cDNA

2361 / 2361

Position of start ATG in wt / mu cDNA

70 / 70

Last intron/exon boundary

2057

Theoretical NMD boundary in CDS

1937

Length of CDS

2292

Coding sequence (CDS) position

2252

cDNA position

2321

gDNA position

1028286

Chromosomal position

23534259

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

Back to summary table

MutationT@ster 2025

Variant:

12:23534259C>A_7_ENST00000545921

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 93|7 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

LOEUF: 0.19, LOF (oe): 0.10, misssense (oe): 0.64, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000545921.5

Genbank transcript ID

NM_001261415 (by similarity)

UniProt / AlphaMissense peptide

SOX5_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2222G>T
g.1028286G>T

AA changes

AAE:	G741V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		741	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	741	D	E	E	E	D	D	P	D	V	D	Y	V	S	D	S	E	N	H	I	A	G	Q	A
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	763	CHAIN		lost
714	763	REGION		lost
731	750	COMPBIAS	Acidic residues	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MSVMSSKRPA SPYGEADGEV AMVTSRQKVE EEESDGLPAF HLPLHVSFPN KPHSEEFQPV
SLLTQETCGH RTPTSQHNTM EVDGNKVMSS FAPHNSSTSP QKAEEGGRQS GESLSSTALG
TPERRKGSLA DVVDTLKQRK MEELIKNEPE ETPSIEKLLS KDWKDKLLAM GSGNFGEIKG
TPESLAEKER QLMGMINQLT SLREQLLAAH DEQKKLAASQ IEKQRQQMEL AKQQQEQIAR
QQQQLLQQQH KINLLQQQIQ VQGQLPPLMI PVFPPDQRTL AAAAQQGFLL PPGFSYKAGC
SDPYPVQLIP TTMAAAAAAT PGLGPLQLQQ LYAAQLAAMQ VSPGGKLPGI PQGNLGAAVS
PTSIHTDKST NSPPPKSKDE VAQPLNLSAK PKTSDGKSPT SPTSPHMPAL RINSGAGPLK
ASVPAALASP SARVSTIGYL NDHDAVTKAI QEARQMKEQL RREQQVLDGK VAVVNSLGLN
NCRTEKEKTT LESLTQQLAV KQNEEGKFSH AMMDFNLSGD SDGSAGVSES RIYRESRGRG
SNEPHIKRPM NAFMVWAKDE RRKILQAFPD MHNSNISKIL GSRWKAMTNL EKQPYYEEQA
RLSKQHLEKY PDYKYKPRPK RTCLVDGKKL RIGEYKAIMR NRRQEMRQYF NVGQQAQIPI
ATAGVVYPGA IAMAGMPSPH LPSEHSSVSS SPEPGMPVIQ STYGVKGEEP HIKEEIQAED
INGEIYDEYD EEEDDPDVDY GSDSENHIAG QAN*

Mutated AA sequence

MSVMSSKRPA SPYGEADGEV AMVTSRQKVE EEESDGLPAF HLPLHVSFPN KPHSEEFQPV
SLLTQETCGH RTPTSQHNTM EVDGNKVMSS FAPHNSSTSP QKAEEGGRQS GESLSSTALG
TPERRKGSLA DVVDTLKQRK MEELIKNEPE ETPSIEKLLS KDWKDKLLAM GSGNFGEIKG
TPESLAEKER QLMGMINQLT SLREQLLAAH DEQKKLAASQ IEKQRQQMEL AKQQQEQIAR
QQQQLLQQQH KINLLQQQIQ VQGQLPPLMI PVFPPDQRTL AAAAQQGFLL PPGFSYKAGC
SDPYPVQLIP TTMAAAAAAT PGLGPLQLQQ LYAAQLAAMQ VSPGGKLPGI PQGNLGAAVS
PTSIHTDKST NSPPPKSKDE VAQPLNLSAK PKTSDGKSPT SPTSPHMPAL RINSGAGPLK
ASVPAALASP SARVSTIGYL NDHDAVTKAI QEARQMKEQL RREQQVLDGK VAVVNSLGLN
NCRTEKEKTT LESLTQQLAV KQNEEGKFSH AMMDFNLSGD SDGSAGVSES RIYRESRGRG
SNEPHIKRPM NAFMVWAKDE RRKILQAFPD MHNSNISKIL GSRWKAMTNL EKQPYYEEQA
RLSKQHLEKY PDYKYKPRPK RTCLVDGKKL RIGEYKAIMR NRRQEMRQYF NVGQQAQIPI
ATAGVVYPGA IAMAGMPSPH LPSEHSSVSS SPEPGMPVIQ STYGVKGEEP HIKEEIQAED
INGEIYDEYD EEEDDPDVDY VSDSENHIAG QAN*

Position of stopcodon in wt / mu CDS

2262 / 2262

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

754 / 754

Position of stopcodon in wt / mu cDNA

2418 / 2418

Position of start ATG in wt / mu cDNA

157 / 157

Last intron/exon boundary

2114

Theoretical NMD boundary in CDS

1907

Length of CDS

2262

Coding sequence (CDS) position

2222

cDNA position

2378

gDNA position

1028286

Chromosomal position

23534259

Speed

0.04 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:

12:23534259C>A_2_ENST00000537393

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

LOEUF: 0.20, LOF (oe): 0.11, misssense (oe): 0.63, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000537393.5

Genbank transcript ID

NM_001330785 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2147G>T
g.1028286G>T

AA changes

AAE:	G716V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		716	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	716	D	E	E	E	D	D	P	D	V	D	Y	V	S	D	S	E
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)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MLTDPDLPQE FERMSSKRPA SPYGEADGEV AMVTSRQKVE EEESDGLPAF HLPLHEVDGN
KVMSSFAPHN SSTSPQKAEE GGRQSGESLS STALGTPERR KGSLADVVDT LKQRKMEELI
KNEPEETPSI EKLLSKDWKD KLLAMGSGNF GEIKGTPESL AEKERQLMGM INQLTSLREQ
LLAAHDEQKK LAASQIEKQR QQMELAKQQQ EQIARQQQQL LQQQHKINLL QQQIQVQGQL
PPLMIPVFPP DQRTLAAAAQ QGFLLPPGFS YKAGCSDPYP VQLIPTTMAA AAAATPGLGP
LQLQQLYAAQ LAAMQVSPGG KLPGIPQGNL GAAVSPTSIH TDKSTNSPPP KSKDEVAQPL
NLSAKPKTSD GKSPTSPTSP HMPALRINSG AGPLKASVPA ALASPSARVS TIGYLNDHDA
VTKAIQEARQ MKEQLRREQQ VLDGKVAVVN SLGLNNCRTE KEKTTLESLT QQLAVKQNEE
GKFSHAMMDF NLSGDSDGSA GVSESRIYRE SRGRGSNEPH IKRPMNAFMV WAKDERRKIL
QAFPDMHNSN ISKILGSRWK AMTNLEKQPY YEEQARLSKQ HLEKYPDYKY KPRPKRTCLV
DGKKLRIGEY KAIMRNRRQE MRQYFNVGQQ AQIPIATAGV VYPGAIAMAG MPSPHLPSEH
SSVSSSPEPG MPVIQSTYGV KGEEPHIKEE IQAEDINGEI YDEYDEEEDD PDVDYGSDSE
NHIAGQAN*

Mutated AA sequence

MLTDPDLPQE FERMSSKRPA SPYGEADGEV AMVTSRQKVE EEESDGLPAF HLPLHEVDGN
KVMSSFAPHN SSTSPQKAEE GGRQSGESLS STALGTPERR KGSLADVVDT LKQRKMEELI
KNEPEETPSI EKLLSKDWKD KLLAMGSGNF GEIKGTPESL AEKERQLMGM INQLTSLREQ
LLAAHDEQKK LAASQIEKQR QQMELAKQQQ EQIARQQQQL LQQQHKINLL QQQIQVQGQL
PPLMIPVFPP DQRTLAAAAQ QGFLLPPGFS YKAGCSDPYP VQLIPTTMAA AAAATPGLGP
LQLQQLYAAQ LAAMQVSPGG KLPGIPQGNL GAAVSPTSIH TDKSTNSPPP KSKDEVAQPL
NLSAKPKTSD GKSPTSPTSP HMPALRINSG AGPLKASVPA ALASPSARVS TIGYLNDHDA
VTKAIQEARQ MKEQLRREQQ VLDGKVAVVN SLGLNNCRTE KEKTTLESLT QQLAVKQNEE
GKFSHAMMDF NLSGDSDGSA GVSESRIYRE SRGRGSNEPH IKRPMNAFMV WAKDERRKIL
QAFPDMHNSN ISKILGSRWK AMTNLEKQPY YEEQARLSKQ HLEKYPDYKY KPRPKRTCLV
DGKKLRIGEY KAIMRNRRQE MRQYFNVGQQ AQIPIATAGV VYPGAIAMAG MPSPHLPSEH
SSVSSSPEPG MPVIQSTYGV KGEEPHIKEE IQAEDINGEI YDEYDEEEDD PDVDYVSDSE
NHIAGQAN*

Position of stopcodon in wt / mu CDS

2187 / 2187

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

729 / 729

Position of stopcodon in wt / mu cDNA

2233 / 2233

Position of start ATG in wt / mu cDNA

47 / 47

Last intron/exon boundary

1929

Theoretical NMD boundary in CDS

1832

Length of CDS

2187

Coding sequence (CDS) position

2147

cDNA position

2193

gDNA position

1028286

Chromosomal position

23534259

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:

12:23534259C>A_3_ENST00000646273

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

LOEUF: 0.21, LOF (oe): 0.10, misssense (oe): 0.64, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000646273.1

Genbank transcript ID

NM_001261414 (by similarity)

UniProt / AlphaMissense peptide

SOX5_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1889G>T
g.1028286G>T

AA changes

AAE:	G630V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		630	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	630	D	E	E	E	D	D	P	D	V	D	Y	V	S	D	S	E	N	H	I	A	G	Q	A
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	763	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MSSKRPASPY GEADGEVAMV TSRQKVEEEE SDGLPAFHLP LHVSFPNKPH SEEFQPVSLL
TQETCGHRTP TSQHNTMEVD GNKVMSSFAP HNSSTSPQKA EEGGRQSGES LSSTALGTPE
RRKGSLADVV DTLKQRKMEE LIKNEPEETP SIEKLLSKDW KDKLLAMGSG NFGEIKGTPE
SLAEKERQLM GMINQLTSLR EQLLAAHDEQ KKLAASQIEK QRQQMELAKQ QQEQIARQQQ
QLLQQQHKIN LLQQQIQVQG QLPPLMIPVF PPDQRTLAAA AQQGFLLPPG FSYKAGCSDP
YPVQLIPTTM AAAAAATPGL GPLQLQQLYA AQLAAMQVSP GGKLPGIPQG NLGAAVSPTS
IHTDKSTNSP PPKSKEKTTL ESLTQQLAVK QNEEGKFSHA MMDFNLSGDS DGSAGVSESR
IYRESRGRGS NEPHIKRPMN AFMVWAKDER RKILQAFPDM HNSNISKILG SRWKAMTNLE
KQPYYEEQAR LSKQHLEKYP DYKYKPRPKR TCLVDGKKLR IGEYKAIMRN RRQEMRQYFN
VGQQAQIPIA TAGVVYPGAI AMAGMPSPHL PSEHSSVSSS PEPGMPVIQS TYGVKGEEPH
IKEEIQAEDI NGEIYDEYDE EEDDPDVDYG SDSENHIAGQ AN*

Mutated AA sequence

MSSKRPASPY GEADGEVAMV TSRQKVEEEE SDGLPAFHLP LHVSFPNKPH SEEFQPVSLL
TQETCGHRTP TSQHNTMEVD GNKVMSSFAP HNSSTSPQKA EEGGRQSGES LSSTALGTPE
RRKGSLADVV DTLKQRKMEE LIKNEPEETP SIEKLLSKDW KDKLLAMGSG NFGEIKGTPE
SLAEKERQLM GMINQLTSLR EQLLAAHDEQ KKLAASQIEK QRQQMELAKQ QQEQIARQQQ
QLLQQQHKIN LLQQQIQVQG QLPPLMIPVF PPDQRTLAAA AQQGFLLPPG FSYKAGCSDP
YPVQLIPTTM AAAAAATPGL GPLQLQQLYA AQLAAMQVSP GGKLPGIPQG NLGAAVSPTS
IHTDKSTNSP PPKSKEKTTL ESLTQQLAVK QNEEGKFSHA MMDFNLSGDS DGSAGVSESR
IYRESRGRGS NEPHIKRPMN AFMVWAKDER RKILQAFPDM HNSNISKILG SRWKAMTNLE
KQPYYEEQAR LSKQHLEKYP DYKYKPRPKR TCLVDGKKLR IGEYKAIMRN RRQEMRQYFN
VGQQAQIPIA TAGVVYPGAI AMAGMPSPHL PSEHSSVSSS PEPGMPVIQS TYGVKGEEPH
IKEEIQAEDI NGEIYDEYDE EEDDPDVDYV SDSENHIAGQ AN*

Position of stopcodon in wt / mu CDS

1929 / 1929

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

643 / 643

Position of stopcodon in wt / mu cDNA

2378 / 2378

Position of start ATG in wt / mu cDNA

450 / 450

Last intron/exon boundary

2074

Theoretical NMD boundary in CDS

1574

Length of CDS

1929

Coding sequence (CDS) position

1889

cDNA position

2338

gDNA position

1028286

Chromosomal position

23534259

Speed

0.04 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

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MutationT@ster 2025

Variant:

12:23534259C>A_4_ENST00000704296

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

no data

Ensembl transcript ID

ENST00000704296.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1004G>T
g.1028286G>T

AA changes

AAE:	G335V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		335	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	335	D	E	E	E	D	D	P	D	V	D	Y	V	S	D	S	E	N	H	I	A	G	Q	A
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)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MPALRINSGA GPLKASVPAA LASPSARVST IGYLNDHDAV TKAIQEARQM KEQLRREQQV
LDGKVAVVNS LGLNNCRTEK EKTTLESLTQ QLAVKQNEEG KFSHAMMDFN LSGDSDGSAG
VSESRIYRES RGRGSNEPHI KRPMNAFMVW AKDERRKILQ AFPDMHNSNI SKILGSRWKA
MTNLEKQPYY EEQARLSKQH LEKYPDYKYK PRPKRTCLVD GKKLRIGEYK AIMRNRRQEM
RQYFNVGQQA QIPIATAGVV YPGAIAMAGM PSPHLPSEHS SVSSSPEPGM PVIQSTYGVK
GEEPHIKEEI QAEDINGEIY DEYDEEEDDP DVDYGSDSEN HIAGQAN*

Mutated AA sequence

MPALRINSGA GPLKASVPAA LASPSARVST IGYLNDHDAV TKAIQEARQM KEQLRREQQV
LDGKVAVVNS LGLNNCRTEK EKTTLESLTQ QLAVKQNEEG KFSHAMMDFN LSGDSDGSAG
VSESRIYRES RGRGSNEPHI KRPMNAFMVW AKDERRKILQ AFPDMHNSNI SKILGSRWKA
MTNLEKQPYY EEQARLSKQH LEKYPDYKYK PRPKRTCLVD GKKLRIGEYK AIMRNRRQEM
RQYFNVGQQA QIPIATAGVV YPGAIAMAGM PSPHLPSEHS SVSSSPEPGM PVIQSTYGVK
GEEPHIKEEI QAEDINGEIY DEYDEEEDDP DVDYVSDSEN HIAGQAN*

Position of stopcodon in wt / mu CDS

1044 / 1044

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

348 / 348

Position of stopcodon in wt / mu cDNA

1297 / 1297

Position of start ATG in wt / mu cDNA

254 / 254

Last intron/exon boundary

993

Theoretical NMD boundary in CDS

689

Length of CDS

1044

Coding sequence (CDS) position

1004

cDNA position

1257

gDNA position

1028286

Chromosomal position

23534259

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

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MutationT@ster 2025

Variant:

12:23534259C>A_5_ENST00000704299

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

no data

Ensembl transcript ID

ENST00000704299.1

Genbank transcript ID

NM_152989 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2108G>T
g.1028286G>T

AA changes

AAE:	G703V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		703	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	703	D	E	E	E	D	D	P	D	V	D	Y	V	S	D	S	E	N	H	I	A	G	Q	A
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)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MSSKRPASPY GEADGEVAMV TSRQKVEEEE SDGLPAFHLP LHEVDGNKVM SSFAPHNSST
SPQKAEEGGR QSGESLSSTA LGTPERRKGS LADVVDTLKQ RKMEELIKNE PEETPSIEKL
LSKDWKDKLL AMGSGNFGEI KGTPESLAEK ERQLMGMINQ LTSLREQLLA AHDEQKKLAA
SQIEKQRQQM ELAKQQQEQI ARQQQQLLQQ QHKINLLQQQ IQVQGQLPPL MIPVFPPDQR
TLAAAAQQGF LLPPGFSYKA GCSDPYPVQL IPTTMAAAAA ATPGLGPLQL QQLYAAQLAA
MQVSPGGKLP GIPQGNLGAA VSPTSIHTDK STNSPPPKSK DEVAQPLNLS AKPKTSDGKS
PTSPTSPHMP ALRINSGAGP LKASVPAALA SPSARVSTIG YLNDHDAVTK AIQEARQMKE
QLRREQQVLD GKVAVVNSLG LNNCRTEKEK TTLESLTQQL AVKQNEEGKF SHAMMDFNLS
GDSDGSAGVS ESRIYRESRG RGSNEPHIKR PMNAFMVWAK DERRKILQAF PDMHNSNISK
ILGSRWKAMT NLEKQPYYEE QARLSKQHLE KYPDYKYKPR PKRTCLVDGK KLRIGEYKAI
MRNRRQEMRQ YFNVGQQAQI PIATAGVVYP GAIAMAGMPS PHLPSEHSSV SSSPEPGMPV
IQSTYGVKGE EPHIKEEIQA EDINGEIYDE YDEEEDDPDV DYGSDSENHI AGQAN*

Mutated AA sequence

MSSKRPASPY GEADGEVAMV TSRQKVEEEE SDGLPAFHLP LHEVDGNKVM SSFAPHNSST
SPQKAEEGGR QSGESLSSTA LGTPERRKGS LADVVDTLKQ RKMEELIKNE PEETPSIEKL
LSKDWKDKLL AMGSGNFGEI KGTPESLAEK ERQLMGMINQ LTSLREQLLA AHDEQKKLAA
SQIEKQRQQM ELAKQQQEQI ARQQQQLLQQ QHKINLLQQQ IQVQGQLPPL MIPVFPPDQR
TLAAAAQQGF LLPPGFSYKA GCSDPYPVQL IPTTMAAAAA ATPGLGPLQL QQLYAAQLAA
MQVSPGGKLP GIPQGNLGAA VSPTSIHTDK STNSPPPKSK DEVAQPLNLS AKPKTSDGKS
PTSPTSPHMP ALRINSGAGP LKASVPAALA SPSARVSTIG YLNDHDAVTK AIQEARQMKE
QLRREQQVLD GKVAVVNSLG LNNCRTEKEK TTLESLTQQL AVKQNEEGKF SHAMMDFNLS
GDSDGSAGVS ESRIYRESRG RGSNEPHIKR PMNAFMVWAK DERRKILQAF PDMHNSNISK
ILGSRWKAMT NLEKQPYYEE QARLSKQHLE KYPDYKYKPR PKRTCLVDGK KLRIGEYKAI
MRNRRQEMRQ YFNVGQQAQI PIATAGVVYP GAIAMAGMPS PHLPSEHSSV SSSPEPGMPV
IQSTYGVKGE EPHIKEEIQA EDINGEIYDE YDEEEDDPDV DYVSDSENHI AGQAN*

Position of stopcodon in wt / mu CDS

2148 / 2148

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

716 / 716

Position of stopcodon in wt / mu cDNA

2276 / 2276

Position of start ATG in wt / mu cDNA

129 / 129

Last intron/exon boundary

1972

Theoretical NMD boundary in CDS

1793

Length of CDS

2148

Coding sequence (CDS) position

2108

cDNA position

2236

gDNA position

1028286

Chromosomal position

23534259

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:

12:23534259C>A_6_ENST00000396007

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:23534259C>A (GRCh38)

Gene symbol

SOX5

Gene constraints

LOEUF: 0.13, LOF (oe): 0.03, misssense (oe): 0.59, synonymous (oe): 0.83 ? (gnomAD)

Ensembl transcript ID

ENST00000396007.6

Genbank transcript ID

NM_178010 (by similarity)

UniProt / AlphaMissense peptide

SOX5_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1094G>T
g.1028286G>T

AA changes

AAE:	G365V	?
Score:	109

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs769351289
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		365	D	E	E	E	D	D	P	D	V	D	Y	G	S	D	S	E	N	H	I	A	G	Q	A	N
mutated	not conserved	365								D	V	D	Y	V	S	D	S	E	N	H	I	A	G	Q	A
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	763	CHAIN		lost
359	426	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.999	1
	5.108	1
(flanking)	4.106	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered gDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Original cDNA sequence snippet

TGATCCAGATGTAGATTATGGGAGTGACAGTGAAAACCATA

Altered cDNA sequence snippet

TGATCCAGATGTAGATTATGTGAGTGACAGTGAAAACCATA

Wildtype AA sequence

MHDEVAQPLN LSAKPKTSDG KSPTSPTSPH MPALRINSGA GPLKASVPAA LASPSARVST
IGYLNDHDAV TKAIQEARQM KEQLRREQQV LDGKVAVVNS LGLNNCRTEK EKTTLESLTQ
QLAVKQNEEG KFSHAMMDFN LSGDSDGSAG VSESRIYRES RGRGSNEPHI KRPMNAFMVW
AKDERRKILQ AFPDMHNSNI SKILGSRWKA MTNLEKQPYY EEQARLSKQH LEKYPDYKYK
PRPKRTCLVD GKKLRIGEYK AIMRNRRQEM RQYFNVGQQA QIPIATAGVV YPGAIAMAGM
PSPHLPSEHS SVSSSPEPGM PVIQSTYGVK GEEPHIKEEI QAEDINGEIY DEYDEEEDDP
DVDYGSDSEN HIAGQAN*

Mutated AA sequence

MHDEVAQPLN LSAKPKTSDG KSPTSPTSPH MPALRINSGA GPLKASVPAA LASPSARVST
IGYLNDHDAV TKAIQEARQM KEQLRREQQV LDGKVAVVNS LGLNNCRTEK EKTTLESLTQ
QLAVKQNEEG KFSHAMMDFN LSGDSDGSAG VSESRIYRES RGRGSNEPHI KRPMNAFMVW
AKDERRKILQ AFPDMHNSNI SKILGSRWKA MTNLEKQPYY EEQARLSKQH LEKYPDYKYK
PRPKRTCLVD GKKLRIGEYK AIMRNRRQEM RQYFNVGQQA QIPIATAGVV YPGAIAMAGM
PSPHLPSEHS SVSSSPEPGM PVIQSTYGVK GEEPHIKEEI QAEDINGEIY DEYDEEEDDP
DVDYVSDSEN HIAGQAN*

Position of stopcodon in wt / mu CDS

1134 / 1134

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

378 / 378

Position of stopcodon in wt / mu cDNA

1194 / 1194

Position of start ATG in wt / mu cDNA

61 / 61

Last intron/exon boundary

890

Theoretical NMD boundary in CDS

779

Length of CDS

1134

Coding sequence (CDS) position

1094

cDNA position

1154

gDNA position

1028286

Chromosomal position

23534259

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