ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.1615G>A (p.Glu539Lys)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002643064 SCV002987902 uncertain significance Zellweger spectrum disorders 2022-01-20 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 539 of the PEX1 protein (p.Glu539Lys). This variant is present in population databases (rs752485627, gnomAD 0.0009%). This missense change has been observed in individual(s) with clinical features of PEX1-related conditions (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. 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 tolerated. 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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