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.8083G>A (p.Asp2695Asn)

CA5546544

422345 (ClinVar)

Gene: CDH23
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 51c7fb5b-8d92-4c34-998f-609fa5ed21b3

HGVS expressions

NM_022124.6:c.8083G>A
NM_022124.6(CDH23):c.8083G>A (p.Asp2695Asn)
NC_000010.11:g.71806186G>A
CM000672.2:g.71806186G>A
NC_000010.10:g.73565943G>A
CM000672.1:g.73565943G>A
NC_000010.9:g.73235949G>A
NG_008835.1:g.414240G>A
ENST00000224721.12:c.8083G>A
ENST00000642965.1:c.2016G>A
ENST00000647092.1:c.1680G>A
ENST00000224721.10:c.8098G>A
ENST00000398788.4:c.1363G>A
ENST00000475158.1:n.1619G>A
ENST00000619887.4:c.1363G>A
ENST00000622827.4:c.8083G>A
NM_001171933.1:c.1363G>A
NM_001171934.1:c.1363G>A
NM_022124.5:c.8083G>A

Uncertain Significance

Met criteria codes 4
PM2_Supporting PP4 PP3 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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.8083G>A variant in CDH23 is a missense variant predicted to cause substitution of aspartic acid by asparagine at amino acid 2695 (p.Asp2695Asn). The highest population minor allele frequency in gnomAD v2.1.1 is 0.005% (4/74190) in European (non-Finnish) population, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.007]) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.789, which is above the threshold of 0.7, evidence that correlates with impact to CDH23 function (PP3). This variant has been detected in a total of three individuals with phenotypes consistent with CDH23-related disorders. One individual with hearing loss was compound heterozygous for the variant and a pathogenic variant, however phase was unknown (c.6085C>T p.Arg2029Trp , 0.5 PM3 points, PMID: 35020051). The second individual was a one-year-old female with hearing loss who harbored the c.6866A>G p.Asn2289Ser variant of uncertain significance in trans (0.25 PM3 points, ARUP internal data SCV000602953.1). The third individual had hearing loss and retinopathy, which is highly specific for Usher syndrome,, and harbored the c.7225-1G>A variant of uncertain significance in trans (0.25 PM3 points, PP4, PMID: 30081015). This individual also had seizures, developmental delay, and ADHD and a de novo ANKRD11 variant thought to cause these additional features. In summary, this variant has been classified as uncertain significance based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_Supporting, PP3, PP4, PM3. (VCEP specifications version 2; 06.26.2023).
Met criteria codes
PM2_Supporting
UPDATE 04.25.2023: PM2_Supporting downgrade, MAF of 0.005% (4/74190) in European (non-Finnish), below the AR cutoff of 0.007% gnomAD v2.1.1. PREVIOUS: The variant is present in 0.005% (4/74190) of European (non-Finnish) chromosomes in gnomAD v2.1.1 and in 0.0046% (3/64546) of European (non-Finnish) chromosomes in gnomAD v3.
PP4
PMID: 30081015 (and likely same individual as GeneDx internal data, scored under individual 2 under PM3). Variant in trans with c.7225-1G>A in an individual with hearing loss and RP. Also had Seizure, DD, ADHD and a de novo ANKRD11 variant thought to cause these additional features .
PP3
The REVEL Score is 0.789 and the residue is conserved across all vertebrates present in the UCSC MSA. No splicing impact is predicted by the splicing predictors (including MaxEntScan) in Alamut.
PM3
TOTAL: 1 POINT FROM 3 PROBANDS: [1] Variant found in 1y/o Caucasian female with moderate bilateral sensorineural hearing loss and mild bilateral hydronephrosis that resolved spontaneously. The c.6866A>G (p.Asn2289Ser) variant was also found in the patient and parental testing confirmed that the two CDH23 variants are in trans. Lastly the patient was also found to have the variant c.837+1delG in the WHRN gene (ARUP Labs internal data). 0.25pts [2] This variant was also seen in a proband that had hearing loss, speech delay, ear pits, and minor dysmorphic features in a custom panel of 34 genes. The variant was found to be in trans with the c.7225-1G>A variant in CDH23. The c.7225-1G>A variant has only been reported in ClinVar in this proband and it is absent in gnomAD v2.1.1 and v3 (GeneDX internal data ). In-frame exon, <10% of protein). Another variant at same consensus splice site, 7225-2A>G reported HOM in an individual with USH1 (PMID: 25468891), so PM2_Supporting, PVS1_Moderate, PM3_Supporting, PP4, VUS. This evidence was scored 0.25 points for PM3. UPDATE 6.27.2023 - Likely the same individual reported in PMID: 30081015 [3] UPDATE 6.27.2023: Variant reported in PMID: 35020051 table S2 in an individual with nonsyndromic hearing loss at age 41, wears hearing aids, no RP. Reported with c.6085C>T p.Arg2029Trp, which is Path by the VCEP for nonsyndromic deafness; however, cis/trans was not confirmed 0.5pts.
Approved on: 2023-06-26
Published on: 2023-10-05
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.