MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000272238
Querying Taster for transcript #2: ENST00000381661
Querying Taster for transcript #3: ENST00000635370
MT speed 0.07 s - this script 2.422033 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length
ENST00000272238(MANE Select)	ATP6V1C2	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000381661	ATP6V1C2	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000635370	ATP6V1C2	Benign	0\|200	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

2:10782201C>T_1_ENST00000272238

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:10782201C>T (GRCh38)

Gene symbol

ATP6V1C2

Gene constraints

LOEUF: 1.01, LOF (oe): 0.78, misssense (oe): 0.86, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000272238.9

Genbank transcript ID

NM_001039362 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1062-42C>T
g.61102C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs780223216
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	79	79

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.048	0
	-0.489	0
(flanking)	-1.649	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

1

Original gDNA sequence snippet

GTTCCTTCTATCCGTGTTTGCATTTGGAGCAGTGAACTGAC

Altered gDNA sequence snippet

GTTCCTTCTATCCGTGTTTGTATTTGGAGCAGTGAACTGAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSEFWLISAP GDKENLQALE RMNTVTSKSN LSYNTKFAIP DFKVGTLDSL VGLSDELGKL
DTFAESLIRR MAQSVVEVME DSKGKVQEHL LANGVDLTSF VTHFEWDMAK YPVKQPLVSV
VDTIAKQLAQ IEMDLKSRTA AYNTLKTNLE NLEKKSMGNL FTRTLSDIVS KEDFVLDSEY
LVTLLVIVPK PNYSQWQKTY ESLSDMVVPR STKLITEDKE GGLFTVTLFR KVIEDFKTKA
KENKFTVREF YYDEKEIERE REEMARLLSD KKQQYQTSCV ALKKGSSTFP DHKVKVTPLG
NPDRPAAGQT DRERESEGEG EGPLLRWLKV NFSEAFIAWI HIKALRVFVE SVLRYGLPVN
FQAVLLQPHK KSSTKRLREV LNSVFRHLDE VAATSILDAS VEIPGLQLNN QDYFPYVYFH
IDLSLLD*

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

129 / 129

Last intron/exon boundary

1322

Theoretical NMD boundary in CDS

1143

Length of CDS

1284

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

61102

Chromosomal position

10782201

Speed

0.03 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:

2:10782201C>T_2_ENST00000381661

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:10782201C>T (GRCh38)

Gene symbol

ATP6V1C2

Gene constraints

LOEUF: 1.05, LOF (oe): 0.80, misssense (oe): 0.85, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000381661.3

Genbank transcript ID

NM_144583 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.924-42C>T
g.61102C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs780223216
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	79	79

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.048	0
	-0.489	0
(flanking)	-1.649	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

1

Original gDNA sequence snippet

GTTCCTTCTATCCGTGTTTGCATTTGGAGCAGTGAACTGAC

Altered gDNA sequence snippet

GTTCCTTCTATCCGTGTTTGTATTTGGAGCAGTGAACTGAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSEFWLISAP GDKENLQALE RMNTVTSKSN LSYNTKFAIP DFKVGTLDSL VGLSDELGKL
DTFAESLIRR MAQSVVEVME DSKGKVQEHL LANGVDLTSF VTHFEWDMAK YPVKQPLVSV
VDTIAKQLAQ IEMDLKSRTA AYNTLKTNLE NLEKKSMGNL FTRTLSDIVS KEDFVLDSEY
LVTLLVIVPK PNYSQWQKTY ESLSDMVVPR STKLITEDKE GGLFTVTLFR KVIEDFKTKA
KENKFTVREF YYDEKEIERE REEMARLLSD KKQQYGPLLR WLKVNFSEAF IAWIHIKALR
VFVESVLRYG LPVNFQAVLL QPHKKSSTKR LREVLNSVFR HLDEVAATSI LDASVEIPGL
QLNNQDYFPY VYFHIDLSLL D*

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

110 / 110

Last intron/exon boundary

1165

Theoretical NMD boundary in CDS

1005

Length of CDS

1146

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

61102

Chromosomal position

10782201

Speed

0.02 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:

2:10782201C>T_3_ENST00000635370

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:10782201C>T (GRCh38)

Gene symbol

ATP6V1C2

Gene constraints

LOEUF: 1.01, LOF (oe): 0.78, misssense (oe): 0.86, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000635370.1

Genbank transcript ID

NM_001410707 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1092-42C>T
g.61102C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs780223216
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	79	79

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.048	0
	-0.489	0
(flanking)	-1.649	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

1

Original gDNA sequence snippet

GTTCCTTCTATCCGTGTTTGCATTTGGAGCAGTGAACTGAC

Altered gDNA sequence snippet

GTTCCTTCTATCCGTGTTTGTATTTGGAGCAGTGAACTGAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSEFWLISAP GDKENLQALE RMNTVTSKSN LSYNTKFAIP DFKVGTLDSL VGLSDELGKL
DTFAESLIRR MAQSVVEVME DSKGKVQEHL LANGGLKGKM KCLKIDLTSF VTHFEWDMAK
YPVKQPLVSV VDTIAKQLAQ IEMDLKSRTA AYNTLKTNLE NLEKKSMGNL FTRTLSDIVS
KEDFVLDSEY LVTLLVIVPK PNYSQWQKTY ESLSDMVVPR STKLITEDKE GGLFTVTLFR
KVIEDFKTKA KENKFTVREF YYDEKEIERE REEMARLLSD KKQQYQTSCV ALKKGSSTFP
DHKVKVTPLG NPDRPAAGQT DRERESEGEG EGPLLRWLKV NFSEAFIAWI HIKALRVFVE
SVLRYGLPVN FQAVLLQPHK KSSTKRLREV LNSVFRHLDE VAATSILDAS VEIPGLQLNN
QDYFPYVYFH IDLSLLD*

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

79 / 79

Last intron/exon boundary

1302

Theoretical NMD boundary in CDS

1173

Length of CDS

1314

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

61102

Chromosomal position

10782201

Speed

0.02 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