Involved in the fatty acid remodeling steps of GPI-anchor maturation where the unsaturated acyl chain at sn-2 of inositol phosphate is replaced by a saturated stearoyl chain (PubMed:17021251, PubMed:24439110). May catalyze the first step of the fatty acid remodeling, by removing the unsaturated acyl chain at sn-2 of inositol phosphate, generating a lyso-GPI intermediate (Probable). The fatty acid remodeling steps is critical for the integration of GPI-APs into lipid rafts (By similarity). {ECO:0000250|UniProtKB:A2V7M9, ECO:0000269|PubMed:17021251, ECO:0000269|PubMed:24439110, ECO:0000305|PubMed:24439110}. This is the function of Ensembl gene identifier ENSG00000161395 (PGAP3, post-GPI attachment to proteins phospholipase 3).