ClinVar Miner

Submissions for variant NM_001145661.2(GATA2):c.142T>A (p.Phe48Ile) (rs878855170)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000230807 SCV000291136 uncertain significance Lymphedema, primary, with myelodysplasia; Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency 2019-11-18 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine with isoleucine at codon 48 of the GATA2 protein (p.Phe48Ile). The phenylalanine residue is highly conserved and there is a small physicochemical difference between phenylalanine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GATA2-related conditions. ClinVar contains an entry for this variant (Variation ID: 241720). 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: "Probably Damaging"; 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001285370 SCV001471788 uncertain significance none provided 2020-02-27 criteria provided, single submitter clinical testing The GATA2 c.142T>A; p.Phe48Ile variant (rs878855170), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 241720). This variant is found on only six chromosomes (6/244980 alleles) in the Genome Aggregation Database. The phenylalanine at codon 48 is highly conserved, but computational analyses (SIFT: damaging, PolyPhen-2: benign) predict conflicting effects of this variant on protein structure/function. However, due to limited information, the clinical significance of the p.Phe48Ile variant is uncertain at this time.

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