ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1534C>T (p.Arg512Cys)

gnomAD frequency: 0.00001  dbSNP: rs747938225
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV001189943 SCV001357341 uncertain significance Hereditary cancer-predisposing syndrome 2019-06-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001876219 SCV002222468 uncertain significance BAP1-related tumor predisposition syndrome 2025-01-21 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 512 of the BAP1 protein (p.Arg512Cys). This variant is present in population databases (rs747938225, gnomAD 0.007%). 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: 926989). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt BAP1 protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV001189943 SCV002706685 uncertain significance Hereditary cancer-predisposing syndrome 2022-09-07 criteria provided, single submitter clinical testing The p.R512C variant (also known as c.1534C>T), located in coding exon 13 of the BAP1 gene, results from a C to T substitution at nucleotide position 1534. The arginine at codon 512 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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