ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.1478A>G (p.Tyr493Cys)

gnomAD frequency: 0.00001  dbSNP: rs756570931
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
DBGen Ocular Genomics RCV001591881 SCV001816017 likely pathogenic Retinitis pigmentosa 39 2021-06-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001882712 SCV002167019 likely pathogenic not provided 2023-10-04 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 493 of the USH2A protein (p.Tyr493Cys). This variant is present in population databases (rs756570931, gnomAD 0.002%). This missense change has been observed in individuals with clinical features of retinitis pigmentosa (PMID: 28894305, 32037395; Invitae). ClinVar contains an entry for this variant (Variation ID: 1213938). 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 USH2A 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.
Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel RCV003324566 SCV004030337 likely pathogenic Retinitis pigmentosa 2023-07-24 criteria provided, single submitter research Clinical significance based on ACMG v2.0
Genome-Nilou Lab RCV001591881 SCV004182874 likely pathogenic Retinitis pigmentosa 39 2023-11-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV001591881 SCV004208278 likely pathogenic Retinitis pigmentosa 39 2024-03-17 criteria provided, single submitter clinical testing

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