ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.5858-1G>A

dbSNP: rs397518023
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
SingHealth Duke-NUS Institute of Precision Medicine RCV003445127 SCV005881600 likely pathogenic Retinitis pigmentosa 39 2025-02-05 criteria provided, single submitter clinical testing Variant is predicted to cause nonsense-mediated decay in a gene where LOF is a known cause of pathogenicity (PVS1). Variant is not found in gnomAD genomes and homozygous allele count in gnomAD exomes is less than 0 (PM2).
Baylor Genetics RCV003445127 SCV004208380 pathogenic Retinitis pigmentosa 39 2023-12-18 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001826596 SCV004172110 likely pathogenic Usher syndrome type 2A 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003445127 SCV004172109 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000821430 SCV002020834 pathogenic not provided 2020-01-30 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000821430 SCV000962185 pathogenic not provided 2025-01-06 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 29 of the USH2A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). This variant is present in population databases (rs397518023, gnomAD 0.006%). Disruption of this splice site has been observed in individual(s) with autosomal recessive USH2A-related conditions (PMID: 25649381, 30948794; internal data). 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: 48545). 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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000041871 SCV000065567 pathogenic Rare genetic deafness 2012-01-18 criteria provided, single submitter clinical testing The 5858-1G>A variant in USH2A has not been reported in the literature nor previ ously identified by our laboratory. However, the 5858-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the inv ariant region of the splice consensus sequence. In summary, this variant meets o ur criteria to be classified as pathogenic.
Natera, Inc. RCV001826596 SCV002091557 pathogenic Usher syndrome type 2A 2020-04-04 no assertion criteria provided clinical testing
Counsyl RCV000665613 SCV000789763 likely pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2017-02-16 no assertion criteria provided clinical testing This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com.

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