Results: OGM and WGS revealed a recurrent 16p11.2 BP4-5 duplication, inherited from his healthy father, along with a de novo chromothripsis-type unbalanced t(1;18)(p22.3;q12.3), affecting several genes not currently associated with epilepsy (RIT2, PIK3C3, COL24A1, LRRC8D, DIPK1A, and DPYD), with RIT2 being a plausible candidate for the neurological phenotype due to its neuron-specific expression along with a likely reshuffling of topologically associating domains (TADs) involving SYT4, an epilepsy-candidate gene. Here, PIK3C3 is linked to epilepsy.