Table 3:
Genes recurrently hit by PTV DNMs
| Gene symbol | Coding bases (canonical) | pLI | PTV DNM Poisson p-value | PTV DNM | Missense DNM | PTV transmitted | PTV non-transmitted | Damaging Missense transmitted | Damaging Missense non-transmitted |
|---|---|---|---|---|---|---|---|---|---|
| SETD1A | 5124 | 1 | 7.77E-06 | 3 | 0 | 0 | 0 | 1 | 4 |
| GALNT9 | 714 | 0.56 | 1.27E-05 | 2 | 0 | 0 | 0 | 2 | 0 |
| TAF13 | 375 | 0.08 | 2.43E-05 | 2 | 0 | 0 | 0 | 0 | 0 |
| HENMT1 | 1182 | 0 | 3.61E-05 | 2 | 0 | 1 | 0 | 0 | 0 |
| SV2B | 2052 | 0.34 | 1.50E-04 | 2 | 0 | 1 | 0 | 1 | 2 |
| NRXN3 | 3186 | 1 | 2.12E-04 | 2 | 0 | 0 | 0 | 6 | 6 |
| SMARCC2 | 3645 | 1 | 6.03E-04 | 2 | 0 | 0 | 0 | 0 | 1 |
| RB1CC1 | 4785 | 1 | 8.32E-04 | 2 | 0 | 0 | 0 | 3 | 3 |
| HIVEP3 | 7221 | 0.84 | 1.04E-03 | 2 | 0 | 0 | 0 | 2 | 4 |
| MKI67 | 9771 | 0 | 1.55E-03 | 2 | 1 | 0 | 3 | 4 | 3 |
| CHD8 | 7746 | 1 | 3.04E-03 | 2 | 1 | 0 | 0 | 1 | 3 |
| TRIO | 9294 | 1 | 3.11E-03 | 2 | 0 | 4 | 0 | 11 | 2 |
| DNAH9 | 13461 | 0 | 5.07E-03 | 2 | 0 | 6 | 1 | 8 | 7 |
| KIAA1109 | 15018 | 0.72 | 7.70E-03 | 2 | 1 | 1 | 0 | 14 | 12 |
| KMT2C | 14736 | 1 | 8.13E-03 | 2 | 2 | 0 | 0 | 6 | 7 |
| TTN | 107976 | 0 | 1.83E-01 | 2 | 3 | 14 | 8 | 59 | 58 |
Single gene p-values (all one-sided and unadjusted) are from a Poisson rate test of PTV counts against the DNM model (Online methods).