Extended Data Table 1.
Case-control and de novo counts of the ten Bonferroni significant genes in the main analysis.
| Gene Symbol | Case PTV | Ctrl PTV | Case mis3 | Ctrl mis3 | Case mis2 | Ctrl mis2 | De novo PTV | De novo mis3 | De novo mis2 | P value | Q value | OR (PTV) | OR (Class I) | OR (Class II) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SETD1A | 15 | 3 | 3 | 4 | 11 | 10 | 3 | 2.00E-12 | 3.62E-08 | 20.1 (5.68–108) | 10.3 (4.12–29.3) | 4.42 (1.7–11.6) | ||
| CUL1 | 8 | 1 | 2 | 0 | 7 | 16 | 3 | 2.01E-09 | 1.82E-05 | 36.1 (5.01–1570) | 44.2 (6.42–1880) | 1.76 (0.611–4.51) | ||
| XPO7 | 12 | 1 | 1 | 1 | 10 | 32 | 1 | 7.18E-09 | 4.34E-05 | 52.2 (7.84–2190) | 28.1 (6.46–253) | 1.25 (0.55–2.62) | ||
| TRIO | 18 | 16 | 0 | 0 | 24 | 102 | 2 | 6.35E-08 | 2.88E-04 | 5.02 (2.47–10.4) | 5.02 (2.47–10.4) | 0.944 (0.579–1.48) | ||
| CACNA1G | 10 | 13 | 8 | 4 | 55 | 134 | 1 | 4.57E-07 | 1.54E-03 | 3.09 (1.21–7.63) | 4.25 (2.07–8.78) | 1.68 (1.21–2.31) | ||
| SP4 | 13 | 6 | 3 | 3 | 0 | 2 | 1 | 5.08E-07 | 1.54E-03 | 9.37 (3.38–29.7) | 7.59 (3.2–19.3) | 0 (0–21.4) | ||
| GRIA3 | 5 | 0 | 3 | 2 | 10 | 24 | 1 | 1 | 5.98E-07 | 1.55E-03 | Inf (4.73-Inf) | 20.1 (4.28–188) | 1.67 (0.714–3.63) | |
| GRIN2A | 9 | 2 | 3 | 0 | 13 | 22 | 7.37E-07 | 1.67E-03 | 18.1 (3.74–172) | 24.1 (5.36–221) | 2.37 (1.1–4.92) | |||
| HERC1 | 28 | 32 | 0 | 0 | 2 | 8 | 1.26E-06 | 2.54E-03 | 3.51 (2.04–6.03) | 3.51 (2.04–6.03) | 1 (0.104–5.03) | |||
| RB1CC1 | 9 | 4 | 0 | 0 | 0 | 0 | 2 | 2.00E-06 | 3.63E-03 | 10 (2.89–43.9) | 10 (2.89–43.9) | 0 (0-Inf) |
Case-control counts displayed are the total counts for variants with minor allele count <= 5. PTV: protein-truncating variant, mis3: missense variants with MPC > 3, mis2: missense variants with MPC 2 – 3; Q value: adjusted P value after FDR adjustment; Class I: PTV and missense variants (MPC > 3); Class II: missense variants (MPC 2 – 3). Two-sided gene P values for Class I and Class II variants are calculated using the permuted Fisher’s exact test. Gene P values for de novo mutations are calculated using a one-sided Poisson rate test. The meta-analysis gene P value is calculated from the weighted Z-score method.