ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.10999A>C (p.Thr3667Pro)

gnomAD frequency: 0.00006  dbSNP: rs150822759
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center RCV000490445 SCV000267554 uncertain significance Usher syndrome type 2A 2016-03-18 criteria provided, single submitter reference population
Fulgent Genetics, Fulgent Genetics RCV002503836 SCV002815273 uncertain significance Usher syndrome type 2A; Retinitis pigmentosa 39 2021-10-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002515601 SCV003297793 likely pathogenic not provided 2024-01-07 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 3667 of the USH2A protein (p.Thr3667Pro). This variant is present in population databases (rs150822759, gnomAD 0.05%). This missense change has been observed in individuals with clinical features of USH2A-related conditions (PMID: 23967202, 28041643, 31213501, 36284460). ClinVar contains an entry for this variant (Variation ID: 225512). 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%. 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.
Genome-Nilou Lab RCV003454559 SCV004182148 uncertain significance Retinitis pigmentosa 39 2023-11-04 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000490445 SCV004182149 uncertain significance Usher syndrome type 2A 2023-11-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV003454559 SCV004208127 likely pathogenic Retinitis pigmentosa 39 2024-03-18 criteria provided, single submitter clinical testing
Dept Of Ophthalmology, Nagoya University RCV003888648 SCV004707872 pathogenic Retinal dystrophy 2023-10-01 criteria provided, single submitter research
NIHR Bioresource Rare Diseases, University of Cambridge RCV000505039 SCV000598765 uncertain significance Retinitis pigmentosa 2015-01-01 no assertion criteria provided research

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