The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_004004.6(GJB2):c.584T>C (p.Met195Thr)

CA387460849

438620 (ClinVar)

Gene: GJB2
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 288595d2-108b-486b-affa-9200bf31dcc8
Approved on: 2024-05-15
Published on: 2024-07-02

HGVS expressions

NM_004004.6:c.584T>C
NM_004004.6(GJB2):c.584T>C (p.Met195Thr)
NC_000013.11:g.20188998A>G
CM000675.2:g.20188998A>G
NC_000013.10:g.20763137A>G
CM000675.1:g.20763137A>G
NC_000013.9:g.19661137A>G
NG_008358.1:g.8978T>C
ENST00000382844.2:c.584T>C
ENST00000382848.5:c.584T>C
ENST00000382844.1:c.584T>C
ENST00000382848.4:c.584T>C
NM_004004.5:c.584T>C
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PS3_Moderate PP3 PM5 PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.584T>C is a missense variant predicted to cause a substitution of methionine by threonine at amino acid 195 (p.Met195Thr). The highest population minor allele frequency in gnomAD v4.1.0 is 0.0022% (4/60018, CI 95%) in the Admixed American population (PM2_Supporting). The c.584T>C variant has been detected in trans with c.35delG in one individual with moderate-severe hearing loss (PMID: 19235794). The computational predictor REVEL gives a score of 0.968 which is above the threshold of 0.7, evidence that correlates with impact to GJB2 function (PP3). Another missense variant c.583G>C (p.Met195Val; ClinVar Variation ID: 22537) in the same codon has been classified as pathogenic for hearing loss by the ClinGen Hearing Loss VCEP (PM5). Analysis in Hela cells demonstrated that the CX26-p.Met195Thr protein formed a gap junction but with significantly decreased dye transfer. Additionally, electrophysiological characterization of the mutant in Xenopus oocytes resulted in a completely non-functional channel (PS3_Moderate; PMID: 23967136). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive non-syndromic hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP (PM2_Supporting, PP3, PM3, PM5, PS3_Moderate; Version 2; 5/15/24).
Met criteria codes
PM2_Supporting
The highest minor allele frequency in gnomAD v.4: 0,0022% (4/60018, CI 95%) in the Admixed American population.
PS3_Moderate
Analysis in Hela cell line demonstrated that the CX26-p.Met195Thr protein formed a gap junction but with significant decreased dye transfer. Besides, electrophysiological characterization of the mutant in Xenopus oocyte resulted in completely non-functional channel.
PP3
Revel score: 0.968
PM5
Another missense variant c.583G>C p.Met195Val (ClinVar Variation ID: 22537) in the same codon has been classified as pathogenic for hearing loss by the ClinGen Hearing Loss VCEP
PM3
This variant has been detected in trans with c.35delG variant in 1 individual with moderate-severe hearing loss (case data checked with the author of the paper: PMID: 19235794).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.