ClinVar Miner

Submissions for variant NM_022124.6(CDH23):c.5584G>A (p.Glu1862Lys)

gnomAD frequency: 0.00001  dbSNP: rs773004408
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV002248985 SCV002516248 likely pathogenic Usher syndrome type 1D 2022-05-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV003475309 SCV004210652 likely pathogenic Pituitary adenoma 5, multiple types 2023-07-14 criteria provided, single submitter clinical testing
Invitae RCV003774706 SCV004655199 likely pathogenic not provided 2023-07-13 criteria provided, single submitter clinical testing This missense change has been observed in individual(s) with CDH23-related conditions (PMID: 33095980, 33576794, 35020051). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1862 of the CDH23 protein (p.Glu1862Lys). This variant is present in population databases (rs773004408, gnomAD 0.003%). ClinVar contains an entry for this variant (Variation ID: 1685258). 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. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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