ClinVar Miner

Submissions for variant NM_020778.5(ALPK3):c.1163A>T (p.Lys388Met)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002401774 SCV002710646 uncertain significance Cardiovascular phenotype 2021-10-29 criteria provided, single submitter clinical testing The p.K590M variant (also known as c.1769A>T), located in coding exon 5 of the ALPK3 gene, results from an A to T substitution at nucleotide position 1769. The lysine at codon 590 is replaced by methionine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV005097741 SCV005800129 uncertain significance not provided 2024-02-25 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with methionine, which is neutral and non-polar, at codon 590 of the ALPK3 protein (p.Lys590Met). This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with ALPK3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1779729). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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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