ObjectiveAutoinflammation and PLCγ2‐associated antibody deficiency and immune dysregulation (APLAID) syndrome is an autoinflammatory disease caused by gain‐of‐function variants in PLCG2. This study investigates the pathogenic mechanism of a novel variant of PLCG2 in a patient with APLAID syndrome.MethodsWhole exome sequencing and Sanger sequencing were used to identify the pathogenic variant in the patient. Single‐cell RNA sequencing, immunoblotting, luciferase assay, IP‐one ELISA, calcium flux assay, quantitative PCR, and immunoprecipitation were used to define inflammatory signatures and evaluate the effects of the PLCG2 variant on protein functionality and immune signaling.ResultsWe identified a novel de novo variant, PLCG2 p.D993Y, in a patient with colitis, pansinusitis, skin rash, edema, recurrent respiratory infections, B cell deficiencies, and hypogammaglobulinemia. The single‐cell transcriptome revealed exacerbated inflammatory responses in the patient's PBMCs. Expression of the D993Y variant in HEK293T, COS‐7, and PLCG2 knock‐out THP‐1 cell lines showed heightened PLCγ2 phosphorylation, elevated IP3 production and intracellular Ca2+ release, and activation of the MAPK, NFκB, and NFAT signaling pathways compared to control‐transfected cells. In vitro experiments indicated that the D993Y variant altered amino acid properties, disrupting the interaction between the catalytic and auto‐inhibitory domains of PLCγ2, resulting in PLCγ2 auto‐activation.ConclusionsOur findings demonstrated that the PLCG2 D993Y variant is a gain‐of‐function mutation via impairing its auto‐inhibition, activating multiple inflammatory signaling pathways, thus leading to APLAID syndrome. This study further broadens the molecular underpinnings and phenotypic spectrum of PLCγ2‐related disorders.