ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1873G>A (p.Glu625Lys)

dbSNP: rs1482404545
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000564884 SCV000672821 uncertain significance Hereditary cancer-predisposing syndrome 2023-04-06 criteria provided, single submitter clinical testing The p.E625K variant (also known as c.1873G>A), located in coding exon 14 of the BAP1 gene, results from a G to A substitution at nucleotide position 1873. The glutamic acid at codon 625 is replaced by lysine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. 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.
Color Diagnostics, LLC DBA Color Health RCV000564884 SCV000687972 uncertain significance Hereditary cancer-predisposing syndrome 2019-02-28 criteria provided, single submitter clinical testing
Invitae RCV000692761 SCV000820603 uncertain significance BAP1-related tumor predisposition syndrome 2023-08-25 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. 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. ClinVar contains an entry for this variant (Variation ID: 485294). This variant has not been reported in the literature in individuals affected with BAP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 625 of the BAP1 protein (p.Glu625Lys).
Baylor Genetics RCV000692761 SCV004213200 uncertain significance BAP1-related tumor predisposition syndrome 2023-10-09 criteria provided, single submitter clinical testing

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