ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1249A>G (p.Arg417Gly)

gnomAD frequency: 0.00003  dbSNP: rs767064896
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000805258 SCV000945206 uncertain significance BAP1-related tumor predisposition syndrome 2024-01-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 417 of the BAP1 protein (p.Arg417Gly). This variant is present in population databases (rs767064896, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with BAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 650159). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). 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.
Sema4, Sema4 RCV002259021 SCV002537250 uncertain significance Hereditary cancer-predisposing syndrome 2022-02-19 criteria provided, single submitter curation
Ambry Genetics RCV002259021 SCV002674244 uncertain significance Hereditary cancer-predisposing syndrome 2021-07-16 criteria provided, single submitter clinical testing The p.R417G variant (also known as c.1249A>G), located in coding exon 12 of the BAP1 gene, results from an A to G substitution at nucleotide position 1249. The arginine at codon 417 is replaced by glycine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Baylor Genetics RCV000805258 SCV004214885 uncertain significance BAP1-related tumor predisposition syndrome 2023-06-27 criteria provided, single submitter clinical testing

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