ClinVar Miner

Submissions for variant NM_206933.3(USH2A):c.11389+3A>T (rs753886165)

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Total submissions: 4
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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.
Invitae RCV001386131 SCV001586256 pathogenic not provided 2020-10-19 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, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs753886165, ExAC 0.01%). This variant has been observed in individual(s) with Usher syndrome (PMID: 28714225, Invitae). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 427867). Nucleotide substitutions within 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, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic.
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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