Table 3.
Gene‐set tests
| Candidate pathway | Burden p (all) | Odds ratio (all) | Standard error (all) | N SNVs (all) | N genes (all) | Burden p (LoF) | N SNVs (LoF) | Odds ratio (LoF) |
|---|---|---|---|---|---|---|---|---|
| ASD de novo nonsynonymous | 0.075 | 1.007 | 0.004 | 24,153 | 2,698 | 0.934 | 1,680 | 0.999 |
| ASD de novo loss of function | 0.637 | 0.991 | 0.019 | 1,379 | 960 | 0.602 | 1,372 | 0.990 |
| ARC/NMDAR | 0.740 | 0.987 | 0.040 | 296 | 58 | 0.383 | 23 | 1.141 |
| Calcium channels | 0.980 | 0.999 | 0.047 | 194 | 28 | 0.143 | 17 | 0.673 |
| Developmental delay | 0.048 | 1.013 | 0.006 | 10,013 | 1,284 | 0.635 | 719 | 0.986 |
| FMRP targets | 0.003 | 1.023 | 0.008 | 7,022 | 810 | 0.978 | 351 | 0.999 |
| Histones | 0.070 | 1.034 | 0.019 | 1,201 | 188 | 0.585 | 73 | 0.956 |
| Loss of function intolerant | 0.003 | 1.014 | 0.005 | 16,831 | 2,808 | 0.213 | 829 | 0.969 |
| PGC2 SZ genome‐wide significant | 0.166 | 1.023 | 0.016 | 1,614 | 295 | 0.034 | 110 | 1.165 |
| Post synaptic density (PSD) | 0.671 | 0.995 | 0.011 | 3,389 | 602 | 0.602 | 198 | 1.027 |
| Schizophrenia de novo nonsynonymous | 0.633 | 1.003 | 0.007 | 8,661 | 922 | 0.741 | 561 | 0.990 |
| Schizophrenia de novo loss of function | 0.362 | 0.970 | 0.034 | 458 | 335 | 0.343 | 457 | 0.969 |
The results of burden test (Burden p) analyses of candidate gene sets limited to SNVs with MAF < 0.001. Tests involving all nonsynonymous variants or those that are loss of function are in columns labeled, respectively, all and LoF. N SNVs is the number of variants in pathway that pass quality control with MAF < 0.001. N genes (all) is number of genes in the pathway that contain at least one nonsynonymous variant. Burden p is for the burden test of association based on minor alleles.