ClinVar Miner

Submissions for variant NM_000322.5(PRPH2):c.582-1G>A

dbSNP: rs1800118693
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001212443 SCV001384026 pathogenic PRPH2-related disorder 2023-11-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 1 of the PRPH2 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 PRPH2 are known to be pathogenic (PMID: 8111389, 8485575, 8485576, 8675410, 16916875, 17504850, 22863181, 25675413, 26061163, 27365499, 29555955, 33546218). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with autosomal dominant retinal disease (PMID: 25698705, 26024099). ClinVar contains an entry for this variant (Variation ID: 942452). 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.
NEI Ophthalmic Genomics Laboratory, National Institutes of Health RCV001250354 SCV001424682 likely pathogenic Stargardt disease 2020-01-07 criteria provided, single submitter clinical testing The variant NM_000322.4:c.582-1G>A in the PRPH2 gene has been previously studied(PMID 25698705). We found this variant in 1 patient(s) in a PRPH2 cohort study (Reeves et al. 2020). This variant is listed in dbSNP and/or HGMD (CS153504). It is absent in gnomAD browser. It is not enriched in the PRPH2 disease cohort. We invoked ACMG criteria [PVS1, PM2] and classified NM_000322.4:c.582-1G>A in the PRPH2 gene as a Likely Pathogenic mutation.
Leiden Open Variation Database RCV001530353 SCV001745151 pathogenic not provided 2021-04-06 no assertion criteria provided curation Curator: Global Variome, with Curator vacancy. Submitter to LOVD: Manon Peeters.

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