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: ENST00000265631
Querying Taster for transcript #2: ENST00000416240
MT speed 0.09 s - this script 2.523555 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
ENST00000265631(MANE Select)	SLC25A13	Deleterious	88\|12	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000416240	SLC25A13	Deleterious	92\|8	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

7:96121309A>G_1_ENST00000265631

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 88|12 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:96121309A>G (GRCh38)

Gene symbol

SLC25A13

Gene constraints

LOEUF: 0.94, LOF (oe): 0.77, misssense (oe): 0.89, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000265631.10

Genbank transcript ID

NM_014251 (exact from MANE)

UniProt / AlphaMissense peptide

S2513_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1910T>C
g.200839T>C

AA changes

AAE:	V637A	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs148962110
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	1	417	418

Protein conservation

Species	Match	AA	Alignment
Human		637	R	I	N	L	P	A	P	N	P	D	H	V	G	G	Y	K	L	A	V	A	T	F	A	G
mutated	not conserved	637	R	I	N	L	P	A	P	N	P	D	H	A	G	G	Y	K	L	A	V	A	T	F	A
Ptroglodytes	all identical	637	R	I	N	L	P	A	P	N	P	D	H	V	G	G	Y	K	L	A	V	A	T	F	A
Mmulatta	all identical	642	R	I	N	L	P	A	P	N	P	D	H	V	G	G	Y	K	L	A	V	A	T	F	A
Fcatus	all identical	638	R	I	V	L	P	A	P	N	P	D	H	V	G	G	Y	R	L	A	V	A	T	F	A
Mmusculus	all identical	638	R	I	T	L	P	A	P	N	P	D	H	V	G	G	Y	K	L	A	V	A	T	F	A
Ggallus	all identical	643	R	I	T	L	P	A	P	N	P	D	H	V	G	G	Y	K	L	A	V	A	T	F	A
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	637	R	I	T	L	P	A	P	N	P	D	H	V	G	G	Y	R	L	A	V	A	T	F	A

Protein features

Start (aa)	End (aa)	Feature	Details
2	675	CHAIN		lost
601	675	TOPO_DOM	Mitochondrial intermembrane	lost
613	675	REGION	C-terminal	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.426	0
	9.156	1
(flanking)	0.594	0.972

?

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

7

Strand

-1

Original gDNA sequence snippet

TGCCCCGAATCCTGATCACGTTGGGGGCTACAAACTGGCAG

Altered gDNA sequence snippet

TGCCCCGAATCCTGATCACGCTGGGGGCTACAAACTGGCAG

Original cDNA sequence snippet

TGCCCCGAATCCTGATCACGTTGGGGGCTACAAACTGGCAG

Altered cDNA sequence snippet

TGCCCCGAATCCTGATCACGCTGGGGGCTACAAACTGGCAG

Wildtype AA sequence

MAAAKVALTK RADPAELRTI FLKYASIEKN GEFFMSPNDF VTRYLNIFGE SQPNPKTVEL
LSGVVDQTKD GLISFQEFVA FESVLCAPDA LFMVAFQLFD KAGKGEVTFE DVKQVFGQTT
IHQHIPFNWD SEFVQLHFGK ERKRHLTYAE FTQFLLEIQL EHAKQAFVQR DNARTGRVTA
IDFRDIMVTI RPHVLTPFVE ECLVAAAGGT TSHQVSFSYF NGFNSLLNNM ELIRKIYSTL
AGTRKDVEVT KEEFVLAAQK FGQVTPMEVD ILFQLADLYE PRGRMTLADI ERIAPLEEGT
LPFNLAEAQR QKASGDSARP VLLQVAESAY RFGLGSVAGA VGATAVYPID LVKTRMQNQR
STGSFVGELM YKNSFDCFKK VLRYEGFFGL YRGLLPQLLG VAPEKAIKLT VNDFVRDKFM
HKDGSVPLAA EILAGGCAGG SQVIFTNPLE IVKIRLQVAG EITTGPRVSA LSVVRDLGFF
GIYKGAKACF LRDIPFSAIY FPCYAHVKAS FANEDGQVSP GSLLLAGAIA GMPAASLVTP
ADVIKTRLQV AARAGQTTYS GVIDCFRKIL REEGPKALWK GAGARVFRSS PQFGVTLLTY
ELLQRWFYID FGGVKPMGSE PVPKSRINLP APNPDHVGGY KLAVATFAGI ENKFGLYLPL
FKPSVSTSKA IGGGP*

Mutated AA sequence

MAAAKVALTK RADPAELRTI FLKYASIEKN GEFFMSPNDF VTRYLNIFGE SQPNPKTVEL
LSGVVDQTKD GLISFQEFVA FESVLCAPDA LFMVAFQLFD KAGKGEVTFE DVKQVFGQTT
IHQHIPFNWD SEFVQLHFGK ERKRHLTYAE FTQFLLEIQL EHAKQAFVQR DNARTGRVTA
IDFRDIMVTI RPHVLTPFVE ECLVAAAGGT TSHQVSFSYF NGFNSLLNNM ELIRKIYSTL
AGTRKDVEVT KEEFVLAAQK FGQVTPMEVD ILFQLADLYE PRGRMTLADI ERIAPLEEGT
LPFNLAEAQR QKASGDSARP VLLQVAESAY RFGLGSVAGA VGATAVYPID LVKTRMQNQR
STGSFVGELM YKNSFDCFKK VLRYEGFFGL YRGLLPQLLG VAPEKAIKLT VNDFVRDKFM
HKDGSVPLAA EILAGGCAGG SQVIFTNPLE IVKIRLQVAG EITTGPRVSA LSVVRDLGFF
GIYKGAKACF LRDIPFSAIY FPCYAHVKAS FANEDGQVSP GSLLLAGAIA GMPAASLVTP
ADVIKTRLQV AARAGQTTYS GVIDCFRKIL REEGPKALWK GAGARVFRSS PQFGVTLLTY
ELLQRWFYID FGGVKPMGSE PVPKSRINLP APNPDHAGGY KLAVATFAGI ENKFGLYLPL
FKPSVSTSKA IGGGP*

Position of stopcodon in wt / mu CDS

2028 / 2028

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

676 / 676

Position of stopcodon in wt / mu cDNA

2170 / 2170

Position of start ATG in wt / mu cDNA

143 / 143

Last intron/exon boundary

1983

Theoretical NMD boundary in CDS

1790

Length of CDS

2028

Coding sequence (CDS) position

1910

cDNA position

2052

gDNA position

200839

Chromosomal position

96121309

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:

7:96121309A>G_2_ENST00000416240

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 92|8 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr7:96121309A>G (GRCh38)

Gene symbol

SLC25A13

Gene constraints

LOEUF: 0.93, LOF (oe): 0.76, misssense (oe): 0.89, synonymous (oe): 0.84 ? (gnomAD)

Ensembl transcript ID

ENST00000416240.6

Genbank transcript ID

NM_001160210 (by similarity)

UniProt / AlphaMissense peptide

S2513_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1913T>C
g.200839T>C

AA changes

AAE:	V638A	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs148962110
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	1	417	418

Protein conservation

Species	Match	AA	Alignment
Human		638	R	I	N	L	P	A	P	N	P	D	H	V	G	G	Y	K	L	A	V	A	T	F	A	G
mutated	not conserved	638	R	I	N	L	P	A	P	N	P	D	H	A	G	G	Y	K	L	A	V	A	T	F	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
2	675	CHAIN		lost
601	675	TOPO_DOM	Mitochondrial intermembrane	lost
613	675	REGION	C-terminal	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.426	0
	9.156	1
(flanking)	0.594	0.972

?

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

7

Strand

-1

Original gDNA sequence snippet

TGCCCCGAATCCTGATCACGTTGGGGGCTACAAACTGGCAG

Altered gDNA sequence snippet

TGCCCCGAATCCTGATCACGCTGGGGGCTACAAACTGGCAG

Original cDNA sequence snippet

TGCCCCGAATCCTGATCACGTTGGGGGCTACAAACTGGCAG

Altered cDNA sequence snippet

TGCCCCGAATCCTGATCACGCTGGGGGCTACAAACTGGCAG

Wildtype AA sequence

MAAAKVALTK RADPAELRTI FLKYASIEKN GEFFMSPNDF VTRYLNIFGE SQPNPKTVEL
LSGVVDQTKD GLISFQEFVA FESVLCAPDA LFMVAFQLFD KAGKGEVTFE DVKQVFGQTT
IHQHIPFNWD SEFVQLHFGK ERKRHLTYAE FTQFLLEIQL EHAKQAFVQR DNARTGRVTA
IDFRDIMVTI RPHVLTPFVE ECLVAAAGGT TSHQVSFSYF NGFNSLLNNM ELIRKIYSTL
AGTRKDVEVT KEEFVLAAQK FGQVTPMEVD ILFQLADLYE PRGRMTLADI ERIAPLEEGT
LPFNLAEAQR QQKASGDSAR PVLLQVAESA YRFGLGSVAG AVGATAVYPI DLVKTRMQNQ
RSTGSFVGEL MYKNSFDCFK KVLRYEGFFG LYRGLLPQLL GVAPEKAIKL TVNDFVRDKF
MHKDGSVPLA AEILAGGCAG GSQVIFTNPL EIVKIRLQVA GEITTGPRVS ALSVVRDLGF
FGIYKGAKAC FLRDIPFSAI YFPCYAHVKA SFANEDGQVS PGSLLLAGAI AGMPAASLVT
PADVIKTRLQ VAARAGQTTY SGVIDCFRKI LREEGPKALW KGAGARVFRS SPQFGVTLLT
YELLQRWFYI DFGGVKPMGS EPVPKSRINL PAPNPDHVGG YKLAVATFAG IENKFGLYLP
LFKPSVSTSK AIGGGP*

Mutated AA sequence

MAAAKVALTK RADPAELRTI FLKYASIEKN GEFFMSPNDF VTRYLNIFGE SQPNPKTVEL
LSGVVDQTKD GLISFQEFVA FESVLCAPDA LFMVAFQLFD KAGKGEVTFE DVKQVFGQTT
IHQHIPFNWD SEFVQLHFGK ERKRHLTYAE FTQFLLEIQL EHAKQAFVQR DNARTGRVTA
IDFRDIMVTI RPHVLTPFVE ECLVAAAGGT TSHQVSFSYF NGFNSLLNNM ELIRKIYSTL
AGTRKDVEVT KEEFVLAAQK FGQVTPMEVD ILFQLADLYE PRGRMTLADI ERIAPLEEGT
LPFNLAEAQR QQKASGDSAR PVLLQVAESA YRFGLGSVAG AVGATAVYPI DLVKTRMQNQ
RSTGSFVGEL MYKNSFDCFK KVLRYEGFFG LYRGLLPQLL GVAPEKAIKL TVNDFVRDKF
MHKDGSVPLA AEILAGGCAG GSQVIFTNPL EIVKIRLQVA GEITTGPRVS ALSVVRDLGF
FGIYKGAKAC FLRDIPFSAI YFPCYAHVKA SFANEDGQVS PGSLLLAGAI AGMPAASLVT
PADVIKTRLQ VAARAGQTTY SGVIDCFRKI LREEGPKALW KGAGARVFRS SPQFGVTLLT
YELLQRWFYI DFGGVKPMGS EPVPKSRINL PAPNPDHAGG YKLAVATFAG IENKFGLYLP
LFKPSVSTSK AIGGGP*

Position of stopcodon in wt / mu CDS

2031 / 2031

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

677 / 677

Position of stopcodon in wt / mu cDNA

2222 / 2222

Position of start ATG in wt / mu cDNA

192 / 192

Last intron/exon boundary

2035

Theoretical NMD boundary in CDS

1793

Length of CDS

2031

Coding sequence (CDS) position

1913

cDNA position

2104

gDNA position

200839

Chromosomal position

96121309

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