Table 1. Additional genes discovered in intellectual disability.
Genes achieving the genome-wide significance (P < 6.4 × 10−7) are shown when considering only missense de novo mutations with PrimateAI-3D scores ≥0.821. Counts of protein-truncating and missense DNMs are provided. P values for gene enrichment are shown when the statistical test was run only with missense mutations with PrimateAI-3D score ≥0.821 and when it was repeated for all missense mutations.
| Missense | P value | ||||
|---|---|---|---|---|---|
|
| |||||
| HGNC symbol | Protein-truncating variants | PrimateAI-3D score ≥0.821 | All missense | PrimateAI-3D score ≥0.821 | All missense |
|
| |||||
| AP1G1 | 2 | 4 | 5 | 4.1×10−7 | 5.9×l0−5 |
| ATP2B2 | 1 | 9 | 11 | 2 1×10−7 | 1.4×10−3 |
| CELF2 | 2 | 4 | 4 | i.2×10−7 | 6.7×10−5 |
| MAP4K4 | 2 | 6 | 7 | 3.9×10−7 | 5.0×10−4 |
| MED13 | 3 | 6 | 9 | 6.6×10−8 | 3.5×l0−5 |
| MFN2 | 0 | 6 | 8 | 3.4×10−7 | 1.0×10−5 |
| NR4A2 | 2 | 4 | 5 | 3.7×10−7 | 3.3×10−5 |
| PIP5K1C | 0 | 8 | 9 | 2.8×10−8 | 4.9×l0−4 |
| RAB5C | 2 | 4 | 5 | 8.6×10−8 | 1.5×10−5 |
| SPOP | 1 | 4 | 6 | 4.1×10−7 | 1.7×10−6 |
| SPTBN2 | 1 | 10 | 16 | 3.9×10−7 | 4.5×10−3 |
| XP01 | 1 | 7 | 7 | 5.0×10−7 | 7.2×10−4 |
| EIF4A2 | 2 | 4 | 4 | 1.7×10−7 | 2.1×10−4 |
| LMBRD2 | 0 | 3 | 4 | 6.0×10−7 | 1.3×10−4 |
| MARK2 | 4 | 3 | 5 | 2.3×10−7 | 3.8×10−5 |
| N0TCH1 | 4 | 6 | 17 | 4.1×10−7 | 1.3×10−6 |