ClinVar Miner

Submissions for variant NM_006206.6(PDGFRA):c.3083T>A (p.Val1028Asp)

dbSNP: rs765476521
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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 RCV000704829 SCV000833799 uncertain significance Gastrointestinal stromal tumor 2024-01-03 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 1028 of the PDGFRA protein (p.Val1028Asp). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with PDGFRA-related conditions. ClinVar contains an entry for this variant (Variation ID: 581103). 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) performed at Invitae indicates that this missense variant is not expected to disrupt PDGFRA protein function with a negative predictive value of 80%. 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 RCV002319565 SCV002608882 uncertain significance Hereditary cancer-predisposing syndrome 2024-08-26 criteria provided, single submitter clinical testing The p.V1028D variant (also known as c.3083T>A), located in coding exon 21 of the PDGFRA gene, results from a T to A substitution at nucleotide position 3083. The valine at codon 1028 is replaced by aspartic acid, an amino acid with highly dissimilar properties. This amino acid position is not 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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