10-124994582-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP5BS2
The NM_022802.3(CTBP2):c.2287G>A(p.Val763Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
CTBP2
NM_022802.3 missense
NM_022802.3 missense
Scores
2
13
4
Clinical Significance
Conservation
PhyloP100: 3.87
Genes affected
CTBP2 (HGNC:2495): (C-terminal binding protein 2) This gene produces alternative transcripts encoding two distinct proteins. One protein is a transcriptional repressor, while the other isoform is a major component of specialized synapses known as synaptic ribbons. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases. A portion of the 3' untranslated region was used to map this gene to chromosome 21q21.3; however, it was noted that similar loci elsewhere in the genome are likely. Blast analysis shows that this gene is present on chromosome 10. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP5
Variant 10-124994582-C-T is Pathogenic according to our data. Variant chr10-124994582-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 1696848.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAdExome4 at 29 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTBP2 | ENST00000309035.11 | c.2287G>A | p.Val763Met | missense_variant | Exon 5 of 9 | 1 | NM_022802.3 | ENSP00000311825.6 | ||
CTBP2 | ENST00000337195.10 | c.667G>A | p.Val223Met | missense_variant | Exon 7 of 11 | 1 | ENSP00000338615.5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251324Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135810
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GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461688Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727154
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Pulmonary artery atresia Pathogenic:1
-
Henan Key Laboratory of Chronic Disease Management, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;.;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;.;.;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.;M;M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Uncertain
Sift
Benign
T;D;D;T;T;T
Sift4G
Uncertain
D;D;D;D;D;D
Polyphen
P;D;.;P;P;P
Vest4
MutPred
0.51
.;.;Loss of catalytic residue at V291 (P = 0.0532);.;.;.;
MVP
MPC
2.0
ClinPred
D
GERP RS
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gMVP
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at