ClinVar Miner

Submissions for variant NM_012233.3(RAB3GAP1):c.559C>T (p.Arg187Ter)

gnomAD frequency: 0.00001  dbSNP: rs764260054
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001858612 SCV002247231 pathogenic not provided 2021-11-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg187*) in the RAB3GAP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RAB3GAP1 are known to be pathogenic (PMID: 23420520). This variant is present in population databases (rs764260054, gnomAD 0.007%). This premature translational stop signal has been observed in individual(s) with clinical features of Warburg micro syndrome (PMID: 28454995, 29878067). ClinVar contains an entry for this variant (Variation ID: 800891). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001858612 SCV003805282 pathogenic not provided 2022-08-15 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28454995, 29878067)
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000985081 SCV004805023 pathogenic Warburg micro syndrome 1 2024-03-17 criteria provided, single submitter research
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000985081 SCV001133041 likely pathogenic Warburg micro syndrome 1 2019-09-26 no assertion criteria provided clinical testing

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