The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_022124.6(CDH23):c.6085C>T (p.Arg2029Trp)

CA5545996

446446 (ClinVar)

Gene: CDH23
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: e333b58d-b3ca-4e2b-b958-09402de4c847
Approved on: 2023-06-26
Published on: 2023-06-30

HGVS expressions

NM_022124.6:c.6085C>T
NM_022124.6(CDH23):c.6085C>T (p.Arg2029Trp)
NC_000010.11:g.71791167C>T
CM000672.2:g.71791167C>T
NC_000010.10:g.73550924C>T
CM000672.1:g.73550924C>T
NC_000010.9:g.73220930C>T
NG_008835.1:g.399221C>T
ENST00000224721.12:c.6085C>T
ENST00000224721.10:c.6100C>T
ENST00000622827.4:c.6085C>T
NM_022124.5:c.6085C>T
More

Pathogenic

Met criteria codes 3
PM3_Very Strong PP1 PP3
Not Met criteria codes 1
PM2

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.6085C>T variant in CDH23 is a missense variant predicted to cause substitution of arginine by tryptophan at amino acid 2029 (p.Arg2029Trp). The highest population minor allele frequency in gnomAD v2.1.1 is 0.02% (3/17816 alleles) in the East Asian population. (PM2_Supporting, BS1, and BA1 are not met). The computational predictor REVEL gives a score of 0.7, evidence that correlates with impact to CDH23 function (PP3). This variant has been detected in many individuals with hearing loss or deafness, without any reported vision loss or evidence of retinopathy. Of those individuals, over 10 were homozygous or compound heterozygous for the variant and a pathogenic or likely pathogenic and many of those were confirmed in trans (6.75 PM3_Very Strong points, PMID: 35020051, 25963016, 22899989, 17850630). The variant has been reported to segregate with hearing loss in 1 affected family member from 1 family (PP1_Supporting; PMID: 22899989, 17850630). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM3_VeryStrong, PP3, PP1. (VCEP specifications version 2; 06.26.2023).
Met criteria codes
PM3_Very Strong
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
Miyagawa 2012 PMID:22899989. 1 segregation in affected sib variants never seen on same haplotype per gnomAD co-occurrence tool, variants confirmed in trans in PMID: 17850630, likely same family based on author overlap.
PP3
REVEL 0.701
Not Met criteria codes
PM2
0.01% (3/17816) East asian alleles gnomad v2.1.1
Curation History
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