In summary, by filtering and comparison to genes that are (1) evolutionary constrained in the brain, (2) implicated in autism and epilepsy, (3) spanned by ExAC deletions, or (4) affected by neuropsychiatric associated de novo mutations, we observed a significant enrichment of deletions in genes potentially involved in neuropsychiatric diseases, namely GRIN2A, GABRB3, SHANK1, ITPR1, CNTN1, SCN1A, PCDHB4, IQGAP2, SACS, KCNQ1 and CAPN1. Interaction network analysis identified a hub connecting many of the epilepsy candidate genes identified in this and previous studies. Here, SHANK1 is linked to autism.