Analysis using Manta and Schism for complex structural variants indicated a large, up to 2.6-kb, intronic insertion variant, likely derived from a SINV-VNTR-Alus (SVA) retrotransposable element, in the last intron of MECP2 in a male child with microcephaly, developmental delay and epileptic encephalopathy (A0131084). The gene discussed is MECP2; the disease is Global developmental delay.