ClinVar Miner

Submissions for variant NM_001145661.2(GATA2):c.371C>A (p.Thr124Lys) (rs569301892)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000459028 SCV000541501 uncertain significance Lymphedema, primary, with myelodysplasia; Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency 2019-08-28 criteria provided, single submitter clinical testing This sequence change replaces threonine with lysine at codon 124 of the GATA2 protein (p.Thr124Lys). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and lysine. While this variant is present in population databases (rs569301892), the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in an individual with a GATA2-related disease, but has been reported in a healthy individual undergoing genome sequencing (PMID: 24728327). ClinVar contains an entry for this variant (Variation ID: 134464). 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. In summary, this variant is a rare missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.
ITMI RCV000121146 SCV000085314 not provided not specified 2013-09-19 no assertion provided reference population

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