ClinVar Miner

Submissions for variant NM_206933.3(USH2A):c.1227G>A (p.Trp409Ter) (rs397517979)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000438959 SCV000515864 pathogenic not provided 2015-03-18 criteria provided, single submitter clinical testing The W409X nonsense variant in the USH2A gene has been reported previously in association withUsher syndrome type II and isolated retinitis pigmentosa (Weston et al., 2000; Neveling et al., 2012). Thisvariant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The W409X variant was not observed in approximately 6,500 individuals ofEuropean and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not acommon benign variant in these populations. We interpret the W409X variant as pathogenic.
Broad Institute Rare Disease Group, Broad Institute RCV000589870 SCV000693909 pathogenic Retinitis pigmentosa 39 2017-06-25 criteria provided, single submitter research Very rare in reference population databases, in gnomAD, 2/275918 chromosomes (PM2). Nonsense variant in known disease gene where loss of function results in disease (PVS1). Found in trans with previously reported likely pathogenic missense variant (p.Arg2894Lys) (PM3). Previously reported in three cases, two apparently unrelated Dutch families, one homozygous and the other a compound heterozygote with c.1256G>T (p.C419F) (in PMID:10729113) and compound heterozygous with c.12575G>A (p.R4192H) (PMID: 22334370).
Counsyl RCV000667167 SCV000791574 pathogenic Usher syndrome, type 2A; Retinitis pigmentosa 39 2017-05-12 criteria provided, single submitter clinical testing
Invitae RCV000438959 SCV001203571 pathogenic not provided 2019-12-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Trp409*) in the USH2A gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with USH2A-related conditions (PMID: 10729113, 22334370). ClinVar contains an entry for this variant (Variation ID: 379205). Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). For these reasons, this variant has been classified as Pathogenic.

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