ClinVar Miner

Submissions for variant NM_012233.3(RAB3GAP1):c.2007C>A (p.His669Gln)

gnomAD frequency: 0.00006  dbSNP: rs587780426
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000118093 SCV000152425 uncertain significance not provided 2013-11-20 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000267107 SCV000416399 uncertain significance Warburg micro syndrome 1 2018-01-13 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.
GeneDx RCV000118093 SCV001823709 uncertain significance not provided 2021-12-23 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000118093 SCV003510870 uncertain significance not provided 2022-11-15 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt RAB3GAP1 protein function. ClinVar contains an entry for this variant (Variation ID: 130066). This variant has not been reported in the literature in individuals affected with RAB3GAP1-related conditions. This variant is present in population databases (rs587780426, gnomAD 0.01%). This sequence change replaces histidine, which is basic and polar, with glutamine, which is neutral and polar, at codon 669 of the RAB3GAP1 protein (p.His669Gln).

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