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: ENST00000337195
Querying Taster for transcript #2: ENST00000309035
Querying Taster for transcript #3: ENST00000411419
Querying Taster for transcript #4: ENST00000531469
Querying Taster for transcript #5: ENST00000494626
MT speed 0.1 s - this script 2.503004 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000337195(MANE Select)	CTBP2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000309035	CTBP2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000411419	CTBP2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000531469	CTBP2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000494626	CTBP2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

10:125008303T>C_1_ENST00000337195

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:125008303T>C (GRCh38)

Gene symbol

CTBP2

Gene constraints

LOEUF: 0.14, LOF (oe): 0.04, misssense (oe): 0.61, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000337195.11

Genbank transcript ID

NM_001329 (exact from MANE), NM_001321012 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.59-4811A>G
g.152868A>G

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	rs4962416
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	4414	25903	30317

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.326	0
	-1.084	0
(flanking)	0.019	0.005

?

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

10

Strand

-1

Original gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTACGGTGTCAGGAAACTTCCAT

Altered gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTGCGGTGTCAGGAAACTTCCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALVDKHKVK RQRLDRICEG IRPQIMNGPL HPRPLVALLD GRDCTVEMPI LKDLATVAFC
DAQSTQEIHE KVLNEAVGAM MYHTITLTRE DLEKFKALRV IVRIGSGYDN VDIKAAGELG
IAVCNIPSAA VEETADSTIC HILNLYRRNT WLYQALREGT RVQSVEQIRE VASGAARIRG
ETLGLIGFGR TGQAVAVRAK AFGFSVIFYD PYLQDGIERS LGVQRVYTLQ DLLYQSDCVS
LHCNLNEHNH HLINDFTIKQ MRQGAFLVNA ARGGLVDEKA LAQALKEGRI RGAALDVHES
EPFSFAQGPL KDAPNLICTP HTAWYSEQAS LEMREAAATE IRRAITGRIP ESLRNCVNKE
FFVTSAPWSV IDQQAIHPEL NGATYRYPPG IVGVAPGGLP AAMEGIIPGG IPVTHNLPTV
AHPSQAPSPN QPTKHGDNRE HPNEQ*

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

451 / 451

Last intron/exon boundary

1607

Theoretical NMD boundary in CDS

1106

Length of CDS

1338

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

152868

Chromosomal position

125008303

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:

10:125008303T>C_2_ENST00000309035

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:125008303T>C (GRCh38)

Gene symbol

CTBP2

Gene constraints

LOEUF: 0.52, LOF (oe): 0.38, misssense (oe): 0.88, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000309035.11

Genbank transcript ID

NM_022802 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1679-4811A>G
g.152868A>G

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	rs4962416
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	4414	25903	30317

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.326	0
	-1.084	0
(flanking)	0.019	0.005

?

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

10

Strand

-1

Original gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTACGGTGTCAGGAAACTTCCAT

Altered gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTGCGGTGTCAGGAAACTTCCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPVPSRHINI GRSQSWDAAG WYEGPWENAE SLRPLGRRSS LTYGTAEGTW FEPNHRPQDA
ALPVAAEPYL YREAVYNSVA ARKGSTPDFT FYDSRQAVMS GRSPLLPREY YSDPSGAARV
PKEPPLYRDP GVSRPVPSYG VLGSRTSWDP MQGRSPALQD AGHLYRDPGG KMIPQGRQTQ
SRAASPGRYG REQPDTRYGA EVPAYPLSQV FSDISERPID PAPARQVAPT CLVVDPSSAA
APEGSTGVAP GALNRGYGPA RESIPSKMAY ETYEADLSTF QGPGGKRTVL PEFLAFLRAE
GLAEATLGAL LQQGFDSPAV LATLEDADIK SVAPNLGQAR VLSRLANSCR TEMQLRRQDR
GGPLPRARSS SFSHRSELLH GDLASLGAAA PLQTASPRAG DPARRPSSAP SQHLLETAAT
YSAPGVGTHA PHFPSNSGYS SPTPCALTAR LSPTYPLQAG VALTNPGPSN PLHPGPRTAY
STAYTVPMEL LKRERNVAAS PLPSPHGSPQ VLRKPGAPLG PSTLPPASQS LHTPHSPYQK
VARRTGAPII VSTMLAPEPS IRPQIMNGPL HPRPLVALLD GRDCTVEMPI LKDLATVAFC
DAQSTQEIHE KVLNEAVGAM MYHTITLTRE DLEKFKALRV IVRIGSGYDN VDIKAAGELG
IAVCNIPSAA VEETADSTIC HILNLYRRNT WLYQALREGT RVQSVEQIRE VASGAARIRG
ETLGLIGFGR TGQAVAVRAK AFGFSVIFYD PYLQDGIERS LGVQRVYTLQ DLLYQSDCVS
LHCNLNEHNH HLINDFTIKQ MRQGAFLVNA ARGGLVDEKA LAQALKEGRI RGAALDVHES
EPFSFAQGPL KDAPNLICTP HTAWYSEQAS LEMREAAATE IRRAITGRIP ESLRNCVNKE
FFVTSAPWSV IDQQAIHPEL NGATYRYPPG IVGVAPGGLP AAMEGIIPGG IPVTHNLPTV
AHPSQAPSPN QPTKHGDNRE HPNEQ*

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

313 / 313

Last intron/exon boundary

3089

Theoretical NMD boundary in CDS

2726

Length of CDS

2958

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

152868

Chromosomal position

125008303

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:

10:125008303T>C_3_ENST00000411419

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:125008303T>C (GRCh38)

Gene symbol

CTBP2

Gene constraints

LOEUF: 0.14, LOF (oe): 0.04, misssense (oe): 0.61, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000411419.7

Genbank transcript ID

NM_001083914 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.59-4811A>G
g.152868A>G

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	rs4962416
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	4414	25903	30317

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.326	0
	-1.084	0
(flanking)	0.019	0.005

?

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

10

Strand

-1

Original gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTACGGTGTCAGGAAACTTCCAT

Altered gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTGCGGTGTCAGGAAACTTCCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALVDKHKVK RQRLDRICEG IRPQIMNGPL HPRPLVALLD GRDCTVEMPI LKDLATVAFC
DAQSTQEIHE KVLNEAVGAM MYHTITLTRE DLEKFKALRV IVRIGSGYDN VDIKAAGELG
IAVCNIPSAA VEETADSTIC HILNLYRRNT WLYQALREGT RVQSVEQIRE VASGAARIRG
ETLGLIGFGR TGQAVAVRAK AFGFSVIFYD PYLQDGIERS LGVQRVYTLQ DLLYQSDCVS
LHCNLNEHNH HLINDFTIKQ MRQGAFLVNA ARGGLVDEKA LAQALKEGRI RGAALDVHES
EPFSFAQGPL KDAPNLICTP HTAWYSEQAS LEMREAAATE IRRAITGRIP ESLRNCVNKE
FFVTSAPWSV IDQQAIHPEL NGATYRYPPG IVGVAPGGLP AAMEGIIPGG IPVTHNLPTV
AHPSQAPSPN QPTKHGDNRE HPNEQ*

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

410 / 410

Last intron/exon boundary

1566

Theoretical NMD boundary in CDS

1106

Length of CDS

1338

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

152868

Chromosomal position

125008303

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:

10:125008303T>C_4_ENST00000531469

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:125008303T>C (GRCh38)

Gene symbol

CTBP2

Gene constraints

LOEUF: 0.14, LOF (oe): 0.04, misssense (oe): 0.61, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000531469.5

Genbank transcript ID

NM_001321013 (by similarity), NM_001290215 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.59-4811A>G
g.152868A>G

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	rs4962416
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	4414	25903	30317

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.326	0
	-1.084	0
(flanking)	0.019	0.005

?

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

10

Strand

-1

Original gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTACGGTGTCAGGAAACTTCCAT

Altered gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTGCGGTGTCAGGAAACTTCCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALVDKHKVK RQRLDRICEG IRPQIMNGPL HPRPLVALLD GRDCTVEMPI LKDLATVAFC
DAQSTQEIHE KVLNEAVGAM MYHTITLTRE DLEKFKALRV IVRIGSGYDN VDIKAAGELG
IAVCNIPSAA VEETADSTIC HILNLYRRNT WLYQALREGT RVQSVEQIRE VASGAARIRG
ETLGLIGFGR TGQAVAVRAK AFGFSVIFYD PYLQDGIERS LGVQRVYTLQ DLLYQSDCVS
LHCNLNEHNH HLINDFTIKQ MRQGAFLVNA ARGGLVDEKA LAQALKEGRI RGAALDVHES
EPFSFAQGPL KDAPNLICTP HTAWYSEQAS LEMREAAATE IRRAITGRIP ESLRNCVNKE
FFVTSAPWSV IDQQAIHPEL NGATYRYPPG IVGVAPGGLP AAMEGIIPGG IPVTHNLPTV
AHPSQAPSPN QPTKHGDNRE HPNEQ*

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

288 / 288

Last intron/exon boundary

1444

Theoretical NMD boundary in CDS

1106

Length of CDS

1338

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

152868

Chromosomal position

125008303

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

Back to summary table

MutationT@ster 2025

Variant:

10:125008303T>C_5_ENST00000494626

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:125008303T>C (GRCh38)

Gene symbol

CTBP2

Gene constraints

LOEUF: 0.14, LOF (oe): 0.04, misssense (oe): 0.61, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000494626.6

Genbank transcript ID

NM_001290214 (by similarity), NM_001321014 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.59-4811A>G
g.152868A>G

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	rs4962416
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	4414	25903	30317

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.326	0
	-1.084	0
(flanking)	0.019	0.005

?

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

10

Strand

-1

Original gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTACGGTGTCAGGAAACTTCCAT

Altered gDNA sequence snippet

ACTGGTGTCTTGAGACTGCTGCGGTGTCAGGAAACTTCCAT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALVDKHKVK RQRLDRICEG IRPQIMNGPL HPRPLVALLD GRDCTVEMPI LKDLATVAFC
DAQSTQEIHE KVLNEAVGAM MYHTITLTRE DLEKFKALRV IVRIGSGYDN VDIKAAGELG
IAVCNIPSAA VEETADSTIC HILNLYRRNT WLYQALREGT RVQSVEQIRE VASGAARIRG
ETLGLIGFGR TGQAVAVRAK AFGFSVIFYD PYLQDGIERS LGVQRVYTLQ DLLYQSDCVS
LHCNLNEHNH HLINDFTIKQ MRQGAFLVNA ARGGLVDEKA LAQALKEGRI RGAALDVHES
EPFSFAQGPL KDAPNLICTP HTAWYSEQAS LEMREAAATE IRRAITGRIP ESLRNCVNKE
FFVTSAPWSV IDQQAIHPEL NGATYRYPPG IVGVAPGGLP AAMEGIIPGG IPVTHNLPTV
AHPSQAPSPN QPTKHGDNRE HPNEQ*

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

384 / 384

Last intron/exon boundary

1540

Theoretical NMD boundary in CDS

1106

Length of CDS

1338

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

152868

Chromosomal position

125008303

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