FMRP targets (n = 842) and PSD genes (n = 1,453) carried a significant excess of both deletions and duplications in affected subjects (Figures 3A and 3B). Five percent (73/1,486) of affected subjects with exonic CNVs, including 52 subjects with genes not previously implicated in ASD and/or ID, carried deletions overlapping one or more FMRP targets, yielding 43 ASD candidate genes (Figure 3A; Table S10). Given that the lists of FMRP targets and PSD genes shared 279 genes, we performed conditional analyses showing that the excess of affected subjects carrying deletions overlapping PSD genes was independent of the signal in FMRP targets (OR = 2.62, 95% CI = 1.62–4.32, p = 2.24 × 10−5) and represented 4% of subjects with exonic events (59/1,486) or 3% after exclusion of pathogenic events (p = 0.007). Notably, females were overrepresented among affected subjects carrying exonic deletions overlapping FMRP targets (17 females in 73 affected subjects, 1.98-fold more than males, p = 0.022, 95% CI = 1.06–3.52).