ClinVar Miner

Submissions for variant NM_006206.6(PDGFRA):c.1616T>C (p.Ile539Thr)

dbSNP: rs1553904366
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000531966 SCV000630565 uncertain significance Gastrointestinal stromal tumor 2017-02-15 criteria provided, single submitter clinical testing This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a PDGFRA-related disease. 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 disruptive, but these predictions have not been confirmed by published functional studies. In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. This sequence change replaces isoleucine with threonine at codon 539 of the PDGFRA protein (p.Ile539Thr). The isoleucine residue is highly conserved and there is a moderate physicochemical difference between isoleucine and threonine.
Ambry Genetics RCV003302792 SCV003999036 uncertain significance Hereditary cancer-predisposing syndrome 2023-04-28 criteria provided, single submitter clinical testing The p.I539T variant (also known as c.1616T>C), located in coding exon 10 of the PDGFRA gene, results from a T to C substitution at nucleotide position 1616. The isoleucine at codon 539 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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