ClinVar Miner

Submissions for variant NM_022124.6(CDH23):c.9616C>T (p.Arg3206Cys)

gnomAD frequency: 0.00004  dbSNP: rs778711089
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV004529534 SCV000363939 uncertain significance CDH23-related disorder 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000376823 SCV000363940 uncertain significance Usher syndrome type 1D 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000261912 SCV000363941 uncertain significance Autosomal recessive nonsyndromic hearing loss 12 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV001582928 SCV001820076 uncertain significance not provided 2024-09-11 criteria provided, single submitter clinical testing Reported in an individual with nonsyndromic hearing loss who harbored an additional variant in the CDH23 gene, although segregation data was not provided to confirm the phase of these two variants (PMID: 27068579); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27068579, 15537665)
Fulgent Genetics, Fulgent Genetics RCV002487338 SCV002781371 uncertain significance Autosomal recessive nonsyndromic hearing loss 12; Usher syndrome type 1D; Pituitary adenoma 5, multiple types 2021-07-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001582928 SCV003441525 uncertain significance not provided 2024-11-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 3206 of the CDH23 protein (p.Arg3206Cys). This variant is present in population databases (rs778711089, gnomAD 0.04%). This missense change has been observed in individual(s) with clinical features of CDH23-related conditions (PMID: 27068579). ClinVar contains an entry for this variant (Variation ID: 300474). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CDH23 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Natera, Inc. RCV001828309 SCV002095271 uncertain significance Usher syndrome type 1 2020-01-31 no assertion criteria provided clinical testing

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