ClinVar Miner

Submissions for variant NM_012233.3(RAB3GAP1):c.2946A>G (p.Ter982Trp)

gnomAD frequency: 0.00021  dbSNP: rs141436429
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000502087 SCV000596658 uncertain significance not specified 2016-01-06 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000712891 SCV000843442 uncertain significance not provided 2018-04-23 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000778564 SCV000914866 uncertain significance Warburg micro syndrome 1 2018-11-26 criteria provided, single submitter clinical testing The RAB3GAP1 c.2946A>G (p.Ter982TrpextTer3) variant is a stop-lost variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. The variant is reported at a frequency of 0.000348 in the European (non-Finnish) population from the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of stop-lost variants and lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for Warburg micro syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
GeneDx RCV000712891 SCV001793856 uncertain significance not provided 2023-07-24 criteria provided, single submitter clinical testing Normal stop codon changed to a tryptophan codon, leading to the addition of 3 amino acids at the C-terminus; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV002481625 SCV002785072 uncertain significance Warburg micro syndrome 1; Martsolf syndrome 2 2022-03-03 criteria provided, single submitter clinical testing
Invitae RCV000712891 SCV003000015 uncertain significance not provided 2022-07-29 criteria provided, single submitter clinical testing This sequence change disrupts the translational stop signal of the RAB3GAP1 mRNA. It is expected to extend the length of the RAB3GAP1 protein by 3 additional amino acid residues. This variant is present in population databases (rs141436429, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with RAB3GAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 436467). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000502087 SCV005184608 uncertain significance not specified 2024-05-24 criteria provided, single submitter clinical testing Variant summary: RAB3GAP1 c.2946A>G (p.X982TrpextX3) changes the termination codon and is predicted to lead to an extended protein with additional amino acids added to the normal C-terminus. RAB3GAP1 c.2946A>G (p.X982TrpextX3) causes a frameshift which results in an extension of the protein. The variant allele was found at a frequency of 0.00019 in 251376 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in RAB3GAP1 causing RAB3GAP1-Related Disorders, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.2946A>G in individuals affected with RAB3GAP1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 436467). Based on the evidence outlined above, the variant was classified as uncertain significance.
Breakthrough Genomics, Breakthrough Genomics RCV000712891 SCV005187910 uncertain significance not provided criteria provided, single submitter not provided

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