ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.2183G>C (p.Arg728Pro)

dbSNP: rs773230722
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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 RCV000774721 SCV000908660 uncertain significance Hereditary cancer-predisposing syndrome 2019-06-26 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001144880 SCV001305498 uncertain significance BAP1-related tumor predisposition syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV001144880 SCV001563651 uncertain significance BAP1-related tumor predisposition syndrome 2021-07-19 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with BAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 629894). This variant is present in population databases (rs773230722, ExAC 0.02%). This sequence change replaces arginine with proline at codon 728 of the BAP1 protein (p.Arg728Pro). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and proline.

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