Extended Data Table 2. de novo overlap.

Test of overlap between genes mapping to schizophrenia-associated loci in the present study and genes affected by nonsynonymous (NS) de novo mutations. Enrichment was calculated using the dnenrich permutation framework as described³⁴. Genes within the GWS loci were weighted by 1/N, where N is the number of coding genes within each associated locus. The observed test statistic (stat) is the sum of weights of genes impacted by de novo mutations. The expected test statistics are calculated by averaging over 50,000 permuted de novo mutation sets. Genes within schizophrenia-associated loci affected by de novo mutations are listed (multiple hits listed in parentheses). Cohorts: SCZ = schizophrenia, ID = intellectual disability, ASD = autism spectrum disorder. All mutations analysed annotated according to a unified system (see supplementary tables 1 and 2 of ref³⁴). Genes with LoF de novo mutations are underlined and in italics.

Disease group	NS (N)	P	0 NS in PGC2 loci	Observed (stat)	Expected (stat)	Genes
SCZ	702	0.0061	25	10.97	5.27	CACNACI(x2) CCDC39 CDCH(x2) CRCL CUL3 DPEP2 DPYD(x2) EP300 ESAM GRIN2A LRP1 NCAN PDCDCC PTPRF RIMSC SBNOC SGSM2 SLC7A6 STAGC TMEM2C9 ZDHHC5 ZNF536
ID	141	0.00002	11	6.87	1.05	GRIAC GRIN2A(x2) LRPC NEKC NGEF SATB2 SREBF2 STAGC TCFH(x2)
ASD	789	0.035	19	9.99	5.93	APH1A CNOTC CSMDC CUL3 CYPC7AC CYP26BC EPHX2 LRPC MAPK3 MEF2C MPP6 MYOC5A NISCH PBRMC PRKDC RIMS1 TSNAREC WDR55 ZNF80HA
Controls	434	0.15	16	4.88	3.28	ANKRDHH CCCorf87 CCDC39 CDK2APC CHRMH DPEP2 EP300 LRPC LRRCH8 MAN2AC MYOCA OSBPL3 RAIC SF3BC SREBF2 TLE3