ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.1588A>C (p.Lys530Gln)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001203161 SCV001374311 uncertain significance Chédiak-Higashi syndrome 2022-07-05 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 530 of the LYST protein (p.Lys530Gln). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LYST-related conditions. ClinVar contains an entry for this variant (Variation ID: 934716). 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.
Ambry Genetics RCV002561118 SCV003546762 uncertain significance Inborn genetic diseases 2021-03-03 criteria provided, single submitter clinical testing The c.1588A>C (p.K530Q) alteration is located in exon 5 (coding exon 3) of the LYST gene. This alteration results from a A to C substitution at nucleotide position 1588, causing the lysine (K) at amino acid position 530 to be replaced by a glutamine (Q). The p.K530Q alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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