Table 6.
Genes Enriched with DNMs in the DEE Cohorts
| Gene |
De Novo LoF Variants |
De Novo Functional Variants |
||||||
|---|---|---|---|---|---|---|---|---|
| Observed | Expected | p Value | c.p Value | Observed | Expected | p Value | c.p Value | |
| CDKL5 | 3 | 0 | 8.57E−9 | 0.0003∗ | 5 | 0 | 8.90E−10 | 3.49E−5∗ |
| DNM1 | 0 | 0 | 1 | 1 | 6 | 0 | 1.03E−11 | 4.04E−7∗ |
| GABRB3 | 0 | 0 | 1 | 1 | 4 | 0 | 7.58E−9 | 0.0003∗ |
| GNAO1 | 0 | 0 | 1 | 1 | 4 | 0 | 4.47E−9 | 0.0002∗ |
| IQSEC2 | 3 | 0 | 6.76E−9 | 0.00026∗ | 3 | 0 | 1.14E−5 | 0.45 |
| KCNQ2 | 0 | 0 | 1 | 1 | 4 | 0 | 1.69E−7 | 0.007∗ |
| KCNT1 | 0 | 0 | 1 | 1 | 4 | 0.1 | 9.12E−7 | 0.036∗ |
| SCN1A | 7 | 0 | 1.84E−17 | 7.2E−13∗ | 14 | 0.1 | 6.37E−27 | 2.5E−22∗ |
| SCN2A | 0 | 0 | 1 | 1 | 7 | 0.1 | 3.81E−12 | 1.49E−7∗ |
| SCN8A | 1 | 0 | 0.007 | 1 | 7 | 0.1 | 3.08E−12 | 1.21E−7∗ |
| SLC35A2 | 2 | 0 | 4.74E−7 | 0.018∗ | 3 | 0 | 4.89E−7 | 0.019∗ |
| STXBP1 | 1 | 0 | 0.006 | 1 | 6 | 0 | 1.27E−12 | 4.98E−8∗ |
c.p value is the corrected p value = p value × 2 × 19,618 (significant < 0.05, indicated by an asterisk). LoF variants are nonsense, frameshift, and CSS de novo variants. Functional variants are LoF and missense variants.