ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1498G>A (p.Gly500Ser)

gnomAD frequency: 0.00001  dbSNP: rs1378012462
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000801140 SCV000940905 uncertain significance BAP1-related tumor predisposition syndrome 2024-01-26 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 500 of the BAP1 protein (p.Gly500Ser). 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: 646782). 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 expected to disrupt BAP1 protein function with a positive 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 RCV002388479 SCV002700523 uncertain significance Hereditary cancer-predisposing syndrome 2022-08-30 criteria provided, single submitter clinical testing The p.G500S variant (also known as c.1498G>A), located in coding exon 13 of the BAP1 gene, results from a G to A substitution at nucleotide position 1498. The glycine at codon 500 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. 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.
Baylor Genetics RCV000801140 SCV004214899 uncertain significance BAP1-related tumor predisposition syndrome 2023-05-24 criteria provided, single submitter clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.