Table 2.
Neurodevelopmental disorder genes with at least 1 LoF or missense-damaging de novo variant observed in schizophrenia. Enrichment P values were generated using a one-sided Poisson test from the analysis of all schizophrenia trios (n = 3,444). LoF = loss-of-function; DNV = de novo variant; Missdam = missense-damaging (MPC score ≥ 2). * indicate p values which survive correction for 159 neurodevelopmental disorder genes and three mutation classes (LoF, missense-damaging and LoF plus missense-damaging).
| Gene | Observed DNVs | P (uncorrected) | ||||
|---|---|---|---|---|---|---|
| Missdam | LoF | Missdam + LoF | Missdam | LoF | Missdam + LoF | |
| SLC6A1 | 3 | 0 | 3 | 5.20E-05* | 1 | 7.90E-05* |
| SCN2A | 1 | 2 | 3 | 0.15 | 0.0024 | 0.0019 |
| SMARCC2 | 0 | 2 | 2 | 1 | 0.00068 | 0.0019 |
| PUF60 | 1 | 1 | 2 | 0.056 | 0.022 | 0.003 |
| MED13L | 1 | 1 | 2 | 0.048 | 0.064 | 0.0062 |
| DEAF1 | 0 | 1 | 1 | 1 | 0.0082 | 0.011 |
| TRIO | 0 | 2 | 2 | 1 | 0.0016 | 0.014 |
| CHD8 | 0 | 2 | 2 | 1 | 0.0013 | 0.023 |
| CHD4 | 1 | 1 | 2 | 0.2 | 0.04 | 0.03 |
| KMT2C | 0 | 2 | 2 | 1 | 0.012 | 0.04 |
| PTEN | 1 | 0 | 1 | 0.029 | 1 | 0.044 |
| GNAO1 | 1 | 0 | 1 | 0.042 | 1 | 0.052 |
| TEK | 0 | 1 | 1 | 1 | 0.025 | 0.057 |
| AUTS2 | 0 | 1 | 1 | 1 | 0.03 | 0.057 |
| CSNK2A1 | 1 | 0 | 1 | 0.052 | 1 | 0.064 |
| POGZ | 0 | 1 | 1 | 1 | 0.048 | 0.066 |
| NACC1 | 1 | 0 | 1 | 0.08 | 1 | 0.085 |
| KDM5B | 0 | 1 | 1 | 1 | 0.084 | 0.092 |
| TLK2 | 1 | 0 | 1 | 0.075 | 1 | 0.1 |
| KDM6B | 0 | 1 | 1 | 1 | 0.025 | 0.13 |
| GRIN2B | 1 | 0 | 1 | 0.15 | 1 | 0.17 |
| SYNGAP1 | 0 | 1 | 1 | 1 | 0.026 | 0.21 |