ClinVar Miner

Submissions for variant NM_006218.4(PIK3CA):c.1049A>G (p.Asp350Gly)

dbSNP: rs1553821144
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000622911 SCV000741908 uncertain significance Inborn genetic diseases 2016-10-21 criteria provided, single submitter clinical testing
GeneDx RCV003318606 SCV004022737 pathogenic not provided 2023-01-31 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Clinical Genomics Laboratory, Washington University in St. Louis RCV005251158 SCV005902178 pathogenic PIK3CA related overgrowth syndrome 2024-12-11 criteria provided, single submitter clinical testing A PIK3CA c.1049A>G (p.Asp350Gly) variant was identified at an allelic fraction consistent with somatic origin. This variant has been reported in multiple individuals with PIK3CA-Related Overgrowth Spectrum (PROS) disorders (Goss JA et al., PMID: 31909475; Zhang B et al., PMID: 37658401; Parker VER et al., PMID: 30270358; Gripp KW et al., PMID: 27191687). This variant has been reported in the ClinVar database as pathogenic in a germline state by a single submitter (ClinVar Variation ID: 521363) and it has also been reported in numerous cases in the cancer database COSMIC (Genomic Mutation ID: COSV55877939). This variant is absent from the general population (gnomAD v4.1.0), indicating it is not a common variant. The PIK3CA c.1049A>G (p.Asp350Gly) variant resides within the C2 domain of PIK3CA that is defined as a critical functional domain (Lai et al, PMID: 35997716). The PIK3CA gene is defined by the ClinGen Brain Malformations Variant Curation Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease (Lai et al, PMID: 35997716). Another variant in the same codon, c.1048G>A (p.Asp350Asn), has been reported and is considered pathogenic (ClinVar Variation ID: 418658). Based on available information and an internally developed protocol informed by the ACMG/AMP guidelines for variant interpretation and gene-specific practices from the ClinGen Criteria Specification Registry (Leon-Quintero FZ et al., PMID: 39434542), the PIK3CA c.1049A>G (p.Asp350Gly) variant is classified as pathogenic.

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