ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.7631T>C (p.Met2544Thr)

gnomAD frequency: 0.00002  dbSNP: rs1371610729
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001236431 SCV001409154 uncertain significance Chédiak-Higashi syndrome 2021-08-31 criteria provided, single submitter clinical testing This sequence change replaces methionine with threonine at codon 2544 of the LYST protein (p.Met2544Thr). The methionine residue is moderately conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with LYST-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
CeGaT Center for Human Genetics Tuebingen RCV001311682 SCV001501959 uncertain significance not provided 2020-10-01 criteria provided, single submitter clinical testing

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