ClinVar

Description

The PIK3CA c.1035T>A (p.Asn345Lys) variant was identified at an allelic fraction consistent with somatic origin. This variant has been reported in at least three individuals affected with PROS disorders (Parker VER et al., PMID: 30270358, Tian W et al., PMID: 35122151; McNulty SN et al., PMID: 31585106). The PIK3CA c.1035T>A (p.Asn345Lys) variant has been reported in numerous cases in the cancer database COSMIC (COSMIC Genomic Mutation ID COSV55873276 ) and it has been reported in the ClinVar database as pathogenic by two submitters (ClinVar ID: 376050). This variant is absent from the general population (gnomAD V.3.1.2), indicating it is not a common variant. The PIK3CA c.1035T>A (p.Asn345Lys) variant is considered to be a strong oncogenic variant (Gymnopoulos M et al., PMID: 17376864) and resides in the C2 catalytic subunit of PIK3CA that is defined as a critical functional domain (Madsen R et al., PMID: 30197175; Keppler-Noreuil KM et al., PMID: 25557259). Functional in vitro studies show that this variant leads to autonomous phosphorylation of AKT and activation of the downstream AKT-mTOR signaling, indicating that this variant impacts protein function (Gymnopoulos M et al., PMID: 17376864). The PIK3CA gene is defined by the ClinGen Brain Malformations expert panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (Lai A et al. PMID: 35997716). Based on an internally-developed protocol informed by the ACMG/AMP guidelines (Richards S et al., PMID: 25741868) and gene-specific practices from the ClinGen Criteria Specification Registry PIK3CA c.1035T>A (p.Asn345Lys) variant is classified as pathogenic.