ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro)

gnomAD frequency: 0.00002  dbSNP: rs752377040
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667292 SCV000791722 uncertain significance Usher syndrome type 2A; Retinitis pigmentosa 39 2017-05-22 criteria provided, single submitter clinical testing
Baylor Genetics RCV001004140 SCV001162873 pathogenic Usher syndrome type 2A criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001059699 SCV001224336 pathogenic not provided 2024-01-24 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 5060 of the USH2A protein (p.Ser5060Pro). This variant is present in population databases (rs752377040, gnomAD 0.06%). This missense change has been observed in individual(s) with retinitis pigmentosa and/or Usher syndrome (PMID: 25649381, 29625443, 29899460, 31904091; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 552090). 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 not expected to disrupt USH2A protein function with a negative predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001075374 SCV001240995 uncertain significance Retinal dystrophy 2018-06-12 criteria provided, single submitter clinical testing
Baylor Genetics RCV003465473 SCV004208148 likely pathogenic Retinitis pigmentosa 39 2024-03-28 criteria provided, single submitter clinical testing
Dept Of Ophthalmology, Nagoya University RCV001075374 SCV004707187 uncertain significance Retinal dystrophy 2023-10-01 criteria provided, single submitter research

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