ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.3176C>T (p.Pro1059Leu)

gnomAD frequency: 0.00001  dbSNP: rs547581739
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667571 SCV000792048 uncertain significance Usher syndrome type 2A; Retinitis pigmentosa 39 2017-06-08 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001100918 SCV001257464 uncertain significance Usher syndrome type 2A 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina RCV001003275 SCV001257465 uncertain significance Retinitis pigmentosa 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
GeneDx RCV001592848 SCV001815114 uncertain significance not provided 2020-04-21 criteria provided, single submitter clinical testing Observed in patients with Usher syndrome or retinitis pigmentosa in published literature; however, no specific patient information was provided and Licastro et al. reported no second USH2A variant in the published patient (Seyedahmadi et al., 2004; Licastro et al., 2012); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31456290, 20507924, 22952768, 15325563)
Labcorp Genetics (formerly Invitae), Labcorp RCV001592848 SCV003268204 uncertain significance not provided 2024-09-03 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1059 of the USH2A protein (p.Pro1059Leu). This variant is present in population databases (rs547581739, gnomAD 0.02%). This missense change has been observed in individual(s) with Usher syndrome and/or retinitis pigmentosa (PMID: 15325563, 22952768, 31456290). ClinVar contains an entry for this variant (Variation ID: 552332). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt USH2A protein function with a positive predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Genome-Nilou Lab RCV003451659 SCV004182367 uncertain significance Retinitis pigmentosa 39 2023-11-04 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001100918 SCV004182368 uncertain significance Usher syndrome type 2A 2023-11-04 criteria provided, single submitter clinical testing
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg RCV004817878 SCV005073337 uncertain significance Retinal dystrophy 2023-01-01 criteria provided, single submitter clinical testing
Sharon lab, Hadassah-Hebrew University Medical Center RCV001003275 SCV001161358 likely pathogenic Retinitis pigmentosa 2019-06-23 no assertion criteria provided research
Natera, Inc. RCV001100918 SCV002093938 uncertain significance Usher syndrome type 2A 2020-01-20 no assertion criteria provided clinical testing

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