The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_004004.6(GJB2):c.110T>C (p.Val37Ala)

CA6904317

449490 (ClinVar)

Gene: GJB2
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 1d8c5ad9-8453-4ae4-8c22-1b4c7b044189
Approved on: 2024-04-22
Published on: 2024-07-02

HGVS expressions

NM_004004.6:c.110T>C
NM_004004.6(GJB2):c.110T>C
NM_004004.6(GJB2):c.110T>C (p.Val37Ala)
NC_000013.11:g.20189472A>G
CM000675.2:g.20189472A>G
NC_000013.10:g.20763611A>G
CM000675.1:g.20763611A>G
NC_000013.9:g.19661611A>G
NG_008358.1:g.8504T>C
ENST00000382844.2:c.110T>C
ENST00000382848.5:c.110T>C
ENST00000382844.1:c.110T>C
ENST00000382848.4:c.110T>C
NM_004004.5:c.110T>C

Likely Pathogenic

Met criteria codes 3
PM5_Strong PM3 PP3
Not Met criteria codes 2
PM2 PS3

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.1101T>C variant in GJB2 is a missense variant predicted to cause substitution of valine by alanine at amino acid 37 (p.Val37Ala). The highest population filtering allele frequency in gnomAD v4 is 0.03% (25/74924 alleles) in the African American population (PM2_Supporting, BA1, and BS1 not met). This variant has been identified in 11 heterozygous individuals who did not harbor a second variant in GJB2 (PMID 21287563, PMID 17666888, PMID 15365987,GeneDx Internal Data, Invitae Internal Data), but has also been detected in 1 patient with hearing loss in trans with a pathogenic variant (1 point, PM3; Partners LMM internal data SCV000967620.2, GeneDx Internal Data, Invitae Internal Data). The REVEL computational prediction analysis tool produced a score of 0.675, which rounded up to 0.7 is above the threshold necessary to apply PP3 (PP3). Two different pathogenic missense variants (p.Val37Ile and p.Val37Phe) have been previously identified at this codon of GJB2 which may indicate that this residue is critical to the function of the protein (PM5_Strong, p.Val37Ile ClinVar Variation ID 17023, PMID 31160754; p.Val37Phe ClinVar Variation ID:179256 PMID: 37108562). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive nonsyndromic hearing loss based on the ACMG/AMP criteria applied as specified by the ClinGen Hearing Loss VCEP: PM3, PM5_Strong, PP3. (Hearing Loss VCEP specifications version 2; 4/22/2024)
Met criteria codes
PM5_Strong
Two different pathogenic missense variants (p.Val37Ile and p.Val37Phe) have been previously identified at this codon of GJB2 which may indicate that this residue is critical to the function of the protein (PM5_Strong, p.Val37Ile ClinVar Variation ID 17023, PMID 31160754; p.Val37Phe ClinVar Variation ID:179256 PMID: 37108562)).
PM3
This variant has been identified in 11 heterozygous individuals who did not harbor a second variant in GJB2 (PMID 21287563, PMID 17666888, PMID 15365987,GeneDx Internal Data, Invitae Internal Data), but has also been detected in 1 patient with hearing loss in trans with a pathogenic variant (1 point, PM3; Partners LMM internal data SCV000967620.2, GeneDx Internal Data, Invitae Internal Data).
PP3
The REVEL score is 0.675, which is lower than our pathogenic cutoff of 0.7. However, the HL VCEP experts have voted to round up and apply PP3.
Not Met criteria codes
PM2
The highest population filtering allele frequency in gnomAD v4 is 0.03% (25/74924 alleles) in the African American population (PM2_Supporting, BA1, and BS1 not met).
PS3
Bioinformatic analysis was used to predict the effect of the p.Val37Ala variant on GJB2 and molecular modeling determined that there may be a loss of protein structure. However, because no in vitro or in vivo experiments were done, this was not counted towards PS3.
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