ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1570A>C (p.Thr524Pro)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002405649 SCV002708460 uncertain significance Hereditary cancer-predisposing syndrome 2022-06-09 criteria provided, single submitter clinical testing The p.T524P variant (also known as c.1570A>C), located in coding exon 13 of the BAP1 gene, results from an A to C substitution at nucleotide position 1570. The threonine at codon 524 is replaced by proline, an amino acid with highly similar properties. This amino acid position is not well 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV003100730 SCV003000401 uncertain significance BAP1-related tumor predisposition syndrome 2022-06-12 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. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with BAP1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 524 of the BAP1 protein (p.Thr524Pro).
Baylor Genetics RCV003100730 SCV005053277 uncertain significance BAP1-related tumor predisposition syndrome 2024-02-06 criteria provided, single submitter clinical testing

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