ClinVar Miner

Submissions for variant NM_006269.2(RP1):c.515T>G (p.Leu172Arg)

gnomAD frequency: 0.00003  dbSNP: rs180729424
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000175822 SCV000227385 uncertain significance not provided 2015-10-19 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000302193 SCV000474164 uncertain significance Retinitis pigmentosa 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Blueprint Genetics RCV000504802 SCV001239052 pathogenic Retinal dystrophy 2019-04-09 criteria provided, single submitter clinical testing
Invitae RCV000175822 SCV001533777 pathogenic not provided 2022-07-19 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 195261). This missense change has been observed in individual(s) with autosomal recessive inherited retinal dystrophy (PMID: 22334370, 28041643, 29068140, 32565670). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs180729424, gnomAD 0.05%). This sequence change replaces leucine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 172 of the RP1 protein (p.Leu172Arg).
NIHR Bioresource Rare Diseases, University of Cambridge RCV000504802 SCV000598692 likely pathogenic Retinal dystrophy 2015-01-01 no assertion criteria provided research

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