ClinVar Miner

Submissions for variant NM_006206.6(PDGFRA):c.2306A>T (p.Lys769Met)

gnomAD frequency: 0.00032  dbSNP: rs373061721
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000467651 SCV000546626 likely benign Gastrointestinal stromal tumor 2024-01-27 criteria provided, single submitter clinical testing
Ambry Genetics RCV001015024 SCV001175808 uncertain significance Hereditary cancer-predisposing syndrome 2019-02-14 criteria provided, single submitter clinical testing The p.K769M variant (also known as c.2306A>T), located in coding exon 15 of the PDGFRA gene, results from an A to T substitution at nucleotide position 2306. The lysine at codon 769 is replaced by methionine, an amino acid with similar properties. 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV003736579 SCV004565216 uncertain significance not provided 2023-09-28 criteria provided, single submitter clinical testing The PDGFRA c.2306A>T; p.Lys769Met variant (rs373061721), to our knowledge, is not reported in the medical literature in association with gastrointestinal stromal tumors but is reported in ClinVar (Variation ID: 135014). This variant is found in the African/African-American population with an allele frequency of 0.09% (23/24962 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.548). Due to limited information, the clinical significance of this variant is uncertain at this time.
GeneDx RCV003736579 SCV005401558 uncertain significance not provided 2024-05-17 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 28422736, 24728327, 37095444)
ITMI RCV000121783 SCV000085981 not provided not specified 2013-09-19 no assertion provided reference population
PreventionGenetics, part of Exact Sciences RCV003422002 SCV004118304 uncertain significance PDGFRA-related disorder 2024-09-22 no assertion criteria provided clinical testing The PDGFRA c.2306A>T variant is predicted to result in the amino acid substitution p.Lys769Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.092% of alleles in individuals of African descent in gnomAD and has conflicting interpretations of likely benign and uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/135014/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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