ClinVar Miner

Submissions for variant NM_024757.5(EHMT1):c.1661C>A (p.Thr554Lys)

gnomAD frequency: 0.00001  dbSNP: rs372688489
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000809861 SCV000950041 uncertain significance Kleefstra syndrome 1 2018-08-11 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals with EHMT1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with lysine at codon 554 of the EHMT1 protein (p.Thr554Lys). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and lysine. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
GeneDx RCV001759561 SCV001986960 uncertain significance not provided 2022-03-21 criteria provided, single submitter clinical testing Not observed in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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