PGAP2 encodes a protein involved in the fatty acid remodeling steps of GPI-anchor maturation, where it may catalyze the second step by reacylating lyso-GPI intermediates at sn-2 of inositol phosphate with saturated fatty acid chains 1. This remodeling process is critical for proper integration of GPI-anchored proteins into lipid rafts and their surface expression 1. The protein functions in the Golgi membrane during GPI-anchor processing 2. Biallelic pathogenic variants in PGAP2 cause hyperphosphatasia with impaired intellectual development syndrome 3 (HPMRS3), an autosomal recessive disorder characterized by severe intellectual disability, developmental delay, epilepsy, microcephaly, and elevated alkaline phosphatase 34. Recent case reports have expanded the phenotypic spectrum to include digital anomalies such as brachydactyly, camptodactyly, and syndactyly, as well as macrocephaly in some patients 5. The clinical presentation often includes drug-resistant epilepsy and developmental encephalopathy 4. PGAP2 deficiency disrupts proper GPI-anchored protein processing, leading to their secretion rather than membrane anchoring, which can be exploited for biotechnological applications in cell line selection 2. The disorder belongs to the inherited GPI deficiencies (IGDs) group of diseases 6.