ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.11155C>T (p.Arg3719Cys)

gnomAD frequency: 0.00001  dbSNP: rs758951363
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001302831 SCV001492055 likely pathogenic not provided 2023-12-29 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 3719 of the USH2A protein (p.Arg3719Cys). This variant is present in population databases (rs758951363, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with USH2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1005883). 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) performed at Invitae indicates that this missense variant is expected to disrupt USH2A protein function with a positive predictive value of 95%. This variant disrupts the p.Arg3719 amino acid residue in USH2A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 25133613, 28157192, 29641573, 30190494, 30280194). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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.
Natera, Inc. RCV001836270 SCV002088338 uncertain significance Usher syndrome type 2A 2021-01-27 no assertion criteria provided clinical testing

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