ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.3092A>G (p.Lys1031Arg)

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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 RCV002050829 SCV002109977 uncertain significance Chédiak-Higashi syndrome 2020-11-16 criteria provided, single submitter clinical testing This sequence change replaces lysine with arginine at codon 1031 of the LYST protein (p.Lys1031Arg). The lysine residue is weakly conserved and there is a small physicochemical difference between lysine and arginine. This variant is present in population databases (rs746751530, ExAC 0.02%). This variant has not been reported in the literature in individuals with LYST-related conditions. 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, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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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