ClinVar Miner

Submissions for variant NM_006206.6(PDGFRA):c.115G>A (p.Val39Met)

gnomAD frequency: 0.00001  dbSNP: rs1553902356
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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 RCV000633757 SCV000755030 uncertain significance Gastrointestinal stromal tumor 2019-06-01 criteria provided, single submitter clinical testing This sequence change replaces valine with methionine at codon 39 of the PDGFRA protein (p.Val39Met). The valine residue is moderately conserved and there is a small physicochemical difference between valine and methionine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PDGFRA-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Ambry Genetics RCV002358776 SCV002621913 uncertain significance Hereditary cancer-predisposing syndrome 2024-11-22 criteria provided, single submitter clinical testing The p.V39M variant (also known as c.115G>A), located in coding exon 2 of the PDGFRA gene, results from a G to A substitution at nucleotide position 115. The valine at codon 39 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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