ClinVar Miner

Submissions for variant NM_032638.5(GATA2):c.371C>T (p.Thr124Met)

gnomAD frequency: 0.00001  dbSNP: rs569301892
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001067794 SCV001232874 uncertain significance Deafness-lymphedema-leukemia syndrome; Monocytopenia with susceptibility to infections 2023-07-17 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GATA2 protein function. ClinVar contains an entry for this variant (Variation ID: 861292). This variant has not been reported in the literature in individuals affected with GATA2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 124 of the GATA2 protein (p.Thr124Met).
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV002292380 SCV002584937 uncertain significance Myelodysplastic syndrome 2022-08-10 criteria provided, single submitter clinical testing The GATA2 c.371C>T (p.Thr124Met) missense change has a maximum subpopulation frequency of 0.0065% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and to our knowledge functional studies have not been performed. To our knowledge, this variant has not been reported in individuals presenting with GATA2-associated clinical phenotypes. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.
Fulgent Genetics, Fulgent Genetics RCV005029659 SCV005659424 uncertain significance Acute myeloid leukemia; Deafness-lymphedema-leukemia syndrome; Monocytopenia with susceptibility to infections; Myelodysplastic syndrome 2024-05-14 criteria provided, single submitter clinical testing

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