ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.11389+3A>T

gnomAD frequency: 0.00001  dbSNP: rs753886165
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV001074399 SCV001239979 pathogenic Retinal dystrophy 2019-08-07 criteria provided, single submitter clinical testing
Ocular Genomics Institute, Massachusetts Eye and Ear RCV001376314 SCV001573416 pathogenic Retinitis pigmentosa 39 2021-04-08 criteria provided, single submitter research The USH2A c.11389+3A>T 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: PM2, PP3, PP1, PVS1. Based on this evidence we have classified this variant as Pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV001386131 SCV001586256 pathogenic not provided 2022-07-19 criteria provided, single submitter clinical testing This sequence change falls in intron 58 of the USH2A gene. It does not directly change the encoded amino acid sequence of the USH2A protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs753886165, gnomAD 0.006%). This variant has been observed in individual(s) with Usher syndrome (PMID: 28714225; 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: 427867). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001386131 SCV002027980 pathogenic not provided 2025-02-06 criteria provided, single submitter clinical testing RNA studies demonstrate a damaging effect resulting in protein truncation and the skipping of exon 58 (PMID: 28714225); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 31045651, 31047384, 32093671, 33608557, 36110214, 34519870, 34906470, 32467589, 28714225, 35052368, 34148116, 35870892, 36819107, Li2022[paper], 38790200)
Genome-Nilou Lab RCV001376314 SCV004173939 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV001376314 SCV004208271 pathogenic Retinitis pigmentosa 39 2023-11-16 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005018824 SCV005645310 pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2024-02-10 criteria provided, single submitter clinical testing
Rui Chen Lab, Baylor College of Medicine RCV000515699 SCV000579424 pathogenic Usher syndrome type 2A 2017-05-09 no assertion criteria provided research

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