To our knowledge, neither c.530A>G, p.Asn177Ser, nor c.646G>A, p.Gly216Arg, observed in family 2 has been previously reported in the literature, expanding the genotypic spectrum of PGAP2. Accordingly, the compound heterozygous presence of these variants leads to epilepsy, ID, craniofacial anomalies, and hyperphosphatasia. The gene discussed is PGAP2; the disease is epilepsy.