AP3D1 variants cause Hermansky–Pudlak syndrome 10; a patient with this syndrome shared several features with patients with AGAP1 variants, including global developmental delay, epilepsy, dystonia, hypotonia, poor feeding, diminished cortical volumes and poor myelination detected by neuroimaging, and microcephaly (Ammann et al., 2016). This evidence concerns the gene AGAP1 and microcephaly.