ClinVar Miner

Submissions for variant NM_005921.2(MAP3K1):c.1510G>A (p.Glu504Lys)

gnomAD frequency: 0.00008  dbSNP: rs764525244
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001198286 SCV001369166 uncertain significance 46,XY sex reversal 6 2019-09-23 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence favors the benign nature of this variant, however the evidence is insufficent to prove its benign nature. The following ACMG criteria were applied in classifying this variant: BS2.
Labcorp Genetics (formerly Invitae), Labcorp RCV001198286 SCV003277253 uncertain significance 46,XY sex reversal 6 2024-01-15 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 504 of the MAP3K1 protein (p.Glu504Lys). This variant is present in population databases (rs764525244, gnomAD 0.02%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with MAP3K1-related conditions. ClinVar contains an entry for this variant (Variation ID: 931588). 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 MAP3K1 protein function with a negative 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.

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