Table 1.
Gene sets enriched for rare coding variants conferring risk for schizophrenia at FDR < 1%. The effect sizes and corresponding P-values from enrichment tests of each variant type (case-control SNVs, DNM, and case-control CNVs) are shown for each gene set, along with the Fisher’s combined P-value (Pmeta) and the FDR-corrected Q-value (Qmeta). We only show the most significant gene set if there are multiple ones from the same data set or biological process (see Supplementary Table 1 for all 1,766 gene sets). Ngenes: number of genes in the gene set; Est: effect size estimate and its lower and upper bound assuming a 95% CI; DNM: de novo mutation.
| Name | Ngenes | EstSNV | 95% CI of EstSNV | PSNV | EstDNM | 95% CI of EstDNM | PDNM | EstCNV | 95% CI of EstCNV | PCNV | Pmeta | Qmeta |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ExAC LoF intolerant genes (pLI > 0.9) |
3488 | 1.24 | 1.16-1.31 | < 5.0 x 10-7 | 1.36 | 1.1-1.68 | 0.0067 | 1.21 | 1.15-1.28 | 0.00026 | < 3.60 x 10-10 | 4.30 x 10-7 |
| Dominant, diagnostic DDG2P genes, in which LoF variants result in developmental disorders with brain abnormalities | 156 | 1.42 | 1.07-1.88 | 0.011 | 4.18 | 2.21-8.03 | 0.00073 | 1.92 | 1.54-2.39 | 0.0016 | 2.30 x 10-6 | 0.00067 |
| Sanders et al. autism risk genes (FDR < 10%) | 66 | 1.28 | 0.97-1.69 | 0.0095 | 3.96 | 1.65-9.94 | 0.019 | 2.21 | 1.75-2.79 | 0.00033 | 9.50 x 10-6 | 0.0017 |
| Darnell et al. targets of FMRP | 790 | 1.24 | 1.13-1.36 | 8.5 x 10-6 | 1.31 | 0.83-2.09 | 0.17 | 1.32 | 1.2-1.47 | 0.0032 | 9.30 x 10-7 | 0.00038 |
| Cotney et al. CHD8-targeted promoters (hNSC and human brain tissue) | 2920 | 1.09 | 1.02-1.16 | 0.0008 | 1.77 | 1.36-2.31 | 0.00025 | 1.11 | 1.05-1.18 | 0.027 | 1.10 x 10-6 | 0.00038 |
| G2CDB: mouse cortex post-synaptic density consensus | 1527 | 1.20 | 1.11-1.3 | 2.5 x 10-6 | 1.57 | 1.06-2.33 | 0.028 | 1.04 | 0.96-1.11 | 0.32 | 3.90 x 10-6 | 0.00097 |
| Weynvanhentenryck et al. CLIP targets of RBFOX | 967 | 1.21 | 1.11-1.33 | 4.8 x 10-5 | 1.84 | 1.21-2.8 | 0.0085 | 1.07 | 0.98-1.17 | 0.2 | 1.30 x 10-5 | 0.002 |
| NMDAR network (defined in Purcell et al.) | 61 | 1.66 | 1.09-2.54 | 0.0061 | 5.60 | 2.06-16.09 | 0.017 | 2.46 | 1.78-3.4 | 0.0028 | 3.70 x 10-5 | 0.0044 |
| GOBP: chromatin modification (GO:0016568) | 519 | 1.29 | 1.13-1.49 | 0.00018 | 2.26 | 1.32-3.94 | 0.0099 | 1.12 | 0.99-1.28 | 0.18 | 4.20 x 10-5 | 0.0046 |