ClinVar Miner

Submissions for variant NM_012233.3(RAB3GAP1):c.1588C>T (p.Arg530Cys)

gnomAD frequency: 0.00008  dbSNP: rs541272906
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001134800 SCV001294557 uncertain significance Warburg micro syndrome 1 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.
Invitae RCV001856724 SCV002120421 uncertain significance not provided 2022-02-24 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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. ClinVar contains an entry for this variant (Variation ID: 894357). This variant has not been reported in the literature in individuals affected with RAB3GAP1-related conditions. This variant is present in population databases (rs541272906, gnomAD 0.09%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 530 of the RAB3GAP1 protein (p.Arg530Cys).
Ambry Genetics RCV002556880 SCV003745057 uncertain significance Inborn genetic diseases 2021-01-13 criteria provided, single submitter clinical testing The c.1588C>T (p.R530C) alteration is located in exon 17 (coding exon 17) of the RAB3GAP1 gene. This alteration results from a C to T substitution at nucleotide position 1588, causing the arginine (R) at amino acid position 530 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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