rs28931594

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5

The ENST00000382848.5(GJB2):​c.148G>T​(p.Asp50Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D50N) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 33)

Consequence

GJB2
ENST00000382848.5 missense

Scores

12
6
1

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 6.04
Variant links:
Genes affected
GJB2 (HGNC:4284): (gap junction protein beta 2) This gene encodes a member of the gap junction protein family. The gap junctions were first characterized by electron microscopy as regionally specialized structures on plasma membranes of contacting adherent cells. These structures were shown to consist of cell-to-cell channels that facilitate the transfer of ions and small molecules between cells. The gap junction proteins, also known as connexins, purified from fractions of enriched gap junctions from different tissues differ. According to sequence similarities at the nucleotide and amino acid levels, the gap junction proteins are divided into two categories, alpha and beta. Mutations in this gene are responsible for as much as 50% of pre-lingual, recessive deafness. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PM1
In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 5 uncertain in ENST00000382848.5
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr13-20189434-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 17020.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.991
PP5
Variant 13-20189434-C-A is Pathogenic according to our data. Variant chr13-20189434-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 17028.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GJB2NM_004004.6 linkuse as main transcriptc.148G>T p.Asp50Tyr missense_variant 2/2 ENST00000382848.5 NP_003995.2
GJB2XM_011535049.3 linkuse as main transcriptc.148G>T p.Asp50Tyr missense_variant 2/2 XP_011533351.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GJB2ENST00000382848.5 linkuse as main transcriptc.148G>T p.Asp50Tyr missense_variant 2/21 NM_004004.6 ENSP00000372299 P1
GJB2ENST00000382844.2 linkuse as main transcriptc.148G>T p.Asp50Tyr missense_variant 1/1 ENSP00000372295 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Autosomal dominant keratitis-ichthyosis-hearing loss syndrome Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 01, 2004- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.61
BayesDel_addAF
Pathogenic
0.54
D
BayesDel_noAF
Pathogenic
0.54
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Pathogenic
0.92
D;D;D
Eigen
Pathogenic
0.68
Eigen_PC
Uncertain
0.57
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.96
.;.;D
M_CAP
Pathogenic
0.59
D
MetaRNN
Pathogenic
0.99
D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
2.9
M;M;M
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.63
T
PROVEAN
Pathogenic
-6.5
D;D;.
REVEL
Pathogenic
0.92
Sift
Uncertain
0.0010
D;D;.
Sift4G
Pathogenic
0.0010
D;D;.
Polyphen
1.0
D;D;D
Vest4
0.73
MutPred
0.91
Gain of loop (P = 0.2045);Gain of loop (P = 0.2045);Gain of loop (P = 0.2045);
MVP
0.97
MPC
0.30
ClinPred
1.0
D
GERP RS
5.2
Varity_R
0.94
gMVP
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs28931594; hg19: chr13-20763573; API