ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.5572+1G>A

gnomAD frequency: 0.00001  dbSNP: rs775293551
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000664714 SCV000788719 likely pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2017-01-17 criteria provided, single submitter clinical testing
Invitae RCV000815036 SCV000955477 pathogenic not provided 2023-12-30 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 27 of the USH2A gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs775293551, gnomAD 0.02%). Disruption of this splice site has been observed in individual(s) with USH2A-related conditions (PMID: 25649381, 31904091; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is also known as 5776+1G>A. ClinVar contains an entry for this variant (Variation ID: 550083). Studies have shown that disruption of this splice site results in skipping of exon 28, but is expected to preserve the integrity of the reading-frame (PMID: 25649381). For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001073564 SCV001239115 likely pathogenic Retinal dystrophy 2019-06-17 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000815036 SCV002020835 pathogenic not provided 2020-12-17 criteria provided, single submitter clinical testing
GeneDx RCV000815036 SCV003837401 pathogenic not provided 2022-09-06 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 24938718, 31904091, 32037395, 31054281, 32675063, 33124170, 34416374)
Genome-Nilou Lab RCV003446294 SCV004172124 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001835904 SCV004172125 likely pathogenic Usher syndrome type 2A 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003446294 SCV004208338 pathogenic Retinitis pigmentosa 39 2024-01-23 criteria provided, single submitter clinical testing
Natera, Inc. RCV001835904 SCV002091566 pathogenic Usher syndrome type 2A 2021-05-13 no assertion criteria provided clinical testing

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