ClinVar Miner

Submissions for variant NM_006206.6(PDGFRA):c.2366G>A (p.Gly789Asp)

gnomAD frequency: 0.00005  dbSNP: rs555553917
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000535371 SCV000630611 uncertain significance Gastrointestinal stromal tumor 2023-12-17 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 789 of the PDGFRA protein (p.Gly789Asp). This variant is present in population databases (rs555553917, gnomAD 0.006%). 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: 459056). 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.
GeneDx RCV002298646 SCV002587976 uncertain significance not provided 2022-04-28 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004023800 SCV005002059 uncertain significance Hereditary cancer-predisposing syndrome 2024-02-13 criteria provided, single submitter clinical testing The c.2366G>A (p.G789D) alteration is located in exon 17 (coding exon 16) of the PDGFRA gene. This alteration results from a G to A substitution at nucleotide position 2366, causing the glycine (G) at amino acid position 789 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Baylor Genetics RCV004568758 SCV005055198 uncertain significance Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 2023-11-03 criteria provided, single submitter clinical testing

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