ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1715C>T (p.Pro572Leu)

dbSNP: rs1553644798
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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 RCV000582491 SCV000687949 uncertain significance Hereditary cancer-predisposing syndrome 2021-12-05 criteria provided, single submitter clinical testing This missense variant replaces proline with leucine at codon 572 of the BAP1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in a heterozygous individual affected with an unspecified cancer (PMID: 28873162). 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.
Invitae RCV000649807 SCV000771641 uncertain significance BAP1-related tumor predisposition syndrome 2022-09-17 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 572 of the BAP1 protein (p.Pro572Leu). 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: 490807). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BAP1 protein function. 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 RCV000582491 SCV002712311 uncertain significance Hereditary cancer-predisposing syndrome 2021-03-25 criteria provided, single submitter clinical testing The p.P572L variant (also known as c.1715C>T), located in coding exon 13 of the BAP1 gene, results from a C to T substitution at nucleotide position 1715. The proline at codon 572 is replaced by leucine, an amino acid with similar properties. This amino acid position is 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.

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