ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.11875_11876del (p.Gln3959fs)

dbSNP: rs779791079
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000179599 SCV000231869 pathogenic not provided 2014-10-08 criteria provided, single submitter clinical testing
Counsyl RCV000671027 SCV000795965 pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2017-11-26 criteria provided, single submitter clinical testing
GeneDx RCV000179599 SCV001168547 pathogenic not provided 2018-08-30 criteria provided, single submitter clinical testing The c.11875_11876delCA variant in the USH2A gene has been reported previously in association with Usher syndrome (Dreyer et al., 2008). The c.11875_11876delCA variant causes a frameshift starting with codon Glutamine 3959, changes this amino acid to an Asparagine residue, and creates a premature Stop codon at position 53 of the new reading frame, denoted p.Gln3959AsnfsX53. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.11875_11876delCA variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.11875_11876delCA as a pathogenic variant.
Blueprint Genetics RCV001073824 SCV001239388 pathogenic Retinal dystrophy 2018-05-22 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000179599 SCV001418176 pathogenic not provided 2024-01-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln3959Asnfs*53) in the USH2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). This variant is present in population databases (rs779791079, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with clinical features of retinal dystrophy (PMID: 28041643). ClinVar contains an entry for this variant (Variation ID: 198318). For these reasons, this variant has been classified as Pathogenic.
Ocular Genomics Institute, Massachusetts Eye and Ear RCV001376411 SCV001573539 pathogenic Retinitis pigmentosa 39 2021-04-08 criteria provided, single submitter research The USH2A c.11875_11876del variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PP3. Based on this evidence we have classified this variant as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000671027 SCV002792884 likely pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2022-03-30 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001376411 SCV004182061 likely pathogenic Retinitis pigmentosa 39 2023-11-04 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001826918 SCV004182062 likely pathogenic Usher syndrome type 2A 2023-11-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV001376411 SCV004208129 pathogenic Retinitis pigmentosa 39 2024-03-04 criteria provided, single submitter clinical testing
NIHR Bioresource Rare Diseases, University of Cambridge RCV000505154 SCV000598771 pathogenic Retinitis pigmentosa 2015-01-01 no assertion criteria provided research
Natera, Inc. RCV001826918 SCV002088319 pathogenic Usher syndrome type 2A 2020-09-01 no assertion criteria provided clinical testing

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