ClinVar Miner

Submissions for variant NM_022124.6(CDH23):c.5009T>A (p.Val1670Asp)

gnomAD frequency: 0.00007  dbSNP: rs397517333
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000039193 SCV000062877 uncertain significance not specified 2010-06-18 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV001039006 SCV001202512 pathogenic not provided 2023-12-08 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 1670 of the CDH23 protein (p.Val1670Asp). This variant is present in population databases (rs397517333, gnomAD 0.04%). This missense change has been observed in individual(s) with deafness (PMID: 33316915). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 45959). Advanced 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 at Invitae 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. For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV001273551 SCV001456688 uncertain significance Usher syndrome type 1 2020-04-16 no assertion criteria provided clinical testing

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