Although 54 genes were previously implicated in ASD, the DAPPLE analysis singled out an additional 97 CNV or SNV high-confidence candidate genes (Figure 5B; Table S16). We found that compared to the 54 ASD-implicated genes, the newly selected 97 CNV or SNV genes had a comparably high pHI (median pHI = 0.58, Figure 6A). This is consistent with the observation that ASD subjects have more deletions with haploinsufficient genes than do controls (Figure 6B). Furthermore, similar to genes with known disease-causing mutations (Figure 6C), those genes have high functional-indispensability scores and a comparable high degree of centrality (i.e., high number of direct neighbors) and number of networks in which they are involved (Figures 6D and 6E). Compared to the genome average, they are also among the top 75% of more-conserved genes (on the basis of Genomic Evolutionary Rate Profiling scores and PhyloP) and are highly expressed in the brain. Interestingly, 39 of the 97 genes are either FMRP-related or PSD genes (of the initial 151 genes identified by DAPPLE, 51 are FMRP interactors and 24 are PSD genes). Thus, despite little overlap in genes, the strong interconnectedness between the resulting networks identifies pathways through which the effects of distinct mutations might converge.