ClinVar Miner

Submissions for variant NM_006206.6(PDGFRA):c.2935C>T (p.Arg979Cys)

gnomAD frequency: 0.00006  dbSNP: rs587778597
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000228242 SCV000289195 uncertain significance Gastrointestinal stromal tumor 2024-02-01 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 979 of the PDGFRA protein (p.Arg979Cys). This variant is present in population databases (rs587778597, gnomAD 0.01%). This missense change has been observed in individual(s) with breast cancer (PMID: 24969172). ClinVar contains an entry for this variant (Variation ID: 135019). 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 RCV002433614 SCV002747798 uncertain significance Hereditary cancer-predisposing syndrome 2019-11-25 criteria provided, single submitter clinical testing The p.R979C variant (also known as c.2935C>T), located in coding exon 21 of the PDGFRA gene, results from a C to T substitution at nucleotide position 2935. The arginine at codon 979 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration was identified in one individual from a BRCA1/2-negative familial breast cancer kindred who underwent whole exome sequencing (Wen H et al. BMC Cancer 2014 Jun;14:470). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
ITMI RCV000121788 SCV000085986 not provided not specified 2013-09-19 no assertion provided reference population

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