ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.347A>C (p.Lys116Thr)

dbSNP: rs1705219656
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001201972 SCV001373067 uncertain significance BAP1-related tumor predisposition syndrome 2020-12-01 criteria provided, single submitter clinical testing This sequence change replaces lysine with threonine at codon 116 of the BAP1 protein (p.Lys116Thr). The lysine residue is highly conserved and there is a moderate physicochemical difference between lysine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with BAP1-related conditions. 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. 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 RCV003293992 SCV003990590 uncertain significance Hereditary cancer-predisposing syndrome 2023-03-22 criteria provided, single submitter clinical testing The p.K116T variant (also known as c.347A>C), located in coding exon 5 of the BAP1 gene, results from an A to C substitution at nucleotide position 347. The lysine at codon 116 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. 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 RCV001201972 SCV005053301 uncertain significance BAP1-related tumor predisposition syndrome 2023-11-29 criteria provided, single submitter clinical testing

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