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 computed assertion could be determined for this classification!


Variant: NM_004086.3(COCH):c.259G>T (p.Gly87Trp)

CA389344541

1297642 (ClinVar)

Gene: COCH (HGNC:1690)
Condition: nonsyndromic genetic deafness (MONDO:0019497)
Inheritance Mode: Autosomal dominant inheritance
UUID: 1600fb4a-a1af-4849-852c-f40e7bafeca6
Approved on: 2026-09-16
Published on: 2026-09-28

HGVS expressions

NM_004086.3(COCH):c.259G>T (p.Gly87Trp)
NM_004086.3:c.259G>T
NC_000014.9:g.30878830G>T
CM000676.2:g.30878830G>T
NC_000014.8:g.31348036G>T
CM000676.1:g.31348036G>T
NC_000014.7:g.30417787G>T
NG_008211.2:g.9296G>T
ENST00000216361.9:c.454G>T
ENST00000396618.9:c.259G>T
ENST00000555117.2:c.259G>T
ENST00000643575.1:c.259G>T
ENST00000643697.1:n.504G>T
ENST00000644874.2:c.259G>T
ENST00000216361.8:c.259G>T
ENST00000396618.7:c.259G>T
ENST00000460581.6:c.-78G>T
ENST00000475087.5:c.259G>T
ENST00000553772.5:c.239+1102G>T
ENST00000553833.5:n.413G>T
ENST00000555881.5:c.83-1622G>T
ENST00000556908.5:c.211G>T
ENST00000557065.1:c.156-593G>T
NM_001135058.1:c.259G>T
NM_004086.2:c.259G>T
NR_038356.1:n.1618-2278C>A
NM_001347720.1:c.454G>T
NM_001135058.2:c.259G>T
NM_001347720.2:c.454G>T
More

Likely Pathogenic

Met criteria codes 4
PP1_Strong PP4 PP3 PM2_Supporting
Not Met criteria codes 2
BS3 PS4

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 2.0

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The variant NM_004086.3:c.259G>T in COCH is a missense variant predicted to cause substitution of Glycine to Tryptophan at amino acid 87 (p.Gly87Trp). The highest population minor allele frequency in gnomAD v4.1.1 is 0.00008474% (1/1180026 -European [non-Finnish], PM2_Supporting met). The in silico predictor REVEL yields a score of 0.911, which is above the threshold of 0.7 (PP3 met). This variant was identified in a Dutch family (PMID:16835921), in which it segregated with progressive, late-onset HL and concomitant vestibular dysfunction in 16 affected family members (PP1_Strong met). Given the highly specific phenotype of progressive hearing loss with vestibular dysfunction, the HL-VCEP decided to apply PP4 evidence criteria. Functional studies showed no alteration in protein secretion or aggregate formation; however, protein cleavage was not evaluated. Therefore, BS3_Supporting was not applied. In summary, based on the current evidence (PP1_Strong, PP4, PP3 & PM2_Supporting), the variant NM_004086.3(COCH):c.259G>T (p.Gly87Trp) is classified as Likely-Pathogenic for autosomal dominant non-syndromic SNHL based on the ACMG/AMP criteria applied, as specified by the ClinGen HL-VCEP (ClinGen Hearing Loss VCEP specifications version 2; 09/16/2026).
Met criteria codes
PP1_Strong
This variant was identified in a Dutch family (PMID:16835921), in which it segregated with progressive, late-onset HL and concomitant vestibular dysfunction in 16 affected family members.
PP4
Given the highly specific phenotype of progressive hearing loss with vestibular dysfunction, the HL-VCEP decided to apply PP4 evidence criteria.
PP3
The in silico predictor REVEL yields a score of 0.911, which is above the threshold of 0.7
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.1 is 0.00008474% (1/1180026 -European [non-Finnish]).
Not Met criteria codes
BS3
Functional studies showed no alteration in protein secretion or aggregate formation; however, protein cleavage was not evaluated. Therefore, BS3_P was not applied.
PS4
This variant was identified in only one Dutch family (PMID:16835921).
Curation History
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