ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.125C>T (p.Pro42Leu)

dbSNP: rs1705241156
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV001182375 SCV001347810 uncertain significance Hereditary cancer-predisposing syndrome 2021-07-15 criteria provided, single submitter clinical testing This missense variant replaces proline with leucine at codon 42 of the BAP1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001876057 SCV002176536 uncertain significance BAP1-related tumor predisposition syndrome 2024-03-19 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 42 of the BAP1 protein (p.Pro42Leu). This variant is not present in population databases (gnomAD no frequency). 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: 922343). 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 disruptive. 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 RCV001182375 SCV003913057 uncertain significance Hereditary cancer-predisposing syndrome 2023-02-28 criteria provided, single submitter clinical testing The p.P42L variant (also known as c.125C>T), located in coding exon 4 of the BAP1 gene, results from a C to T substitution at nucleotide position 125. The proline at codon 42 is replaced by leucine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Baylor Genetics RCV001876057 SCV004213235 uncertain significance BAP1-related tumor predisposition syndrome 2023-08-06 criteria provided, single submitter clinical testing

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