ClinVar Miner

Submissions for variant NM_001301365.1(LYST):c.3203A>G (p.Gln1068Arg)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768017 SCV000898809 uncertain significance Chédiak-Higashi syndrome 2018-11-13 criteria provided, single submitter clinical testing LYST NM_000081.3 exon 6 p.Gln1068Arg (c.3203A>G): This variant has not been reported in the literature but is present in 0.01% (4/34532) of Latino alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/1-235969233-T-C). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Invitae RCV000768017 SCV001221647 uncertain significance Chédiak-Higashi syndrome 2019-05-07 criteria provided, single submitter clinical testing This sequence change replaces glutamine with arginine at codon 1068 of the LYST protein (p.Gln1068Arg). The glutamine residue is weakly conserved and there is a small physicochemical difference between glutamine and arginine. This variant is present in population databases (rs779951954, ExAC 0.009%). This variant has not been reported in the literature in individuals with LYST-related disease. 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. 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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