Table 2.
P values (Wilcoxon rank-sum test) for de novo mutations in ASD, EPI, ID, and SCZ studies. ASD-FMRP analyses are based on de novo mutations in ASD cases that hit FMRP targets. The best performing individual annotation is also reported (for missense variants only).
| Disease | n | Variant type | Score | P value |
|---|---|---|---|---|
| ASD | 2,027 | Missense and Nonsense | Eigen | 6.0E-03 |
| Eigen-PC | 1.6E-02 | |||
| CADD-score v1.0 | 8.4E-02 | |||
| CADD-score v1.1 | 3.2E-01 | |||
| 1,753 | Missense only | Eigen | 9.0E-02 | |
| Eigen-PC | 1.5E-01 | |||
| CADD-score v1.0 | 7.4E-01 | |||
| CADD-score v1.1 | 5.8E-01 | |||
| PolyPhenDiv | 5.4E-02 | |||
|
| ||||
| ASD-FMRP | 132 | Missense and Nonsense | Eigen | 4.2E-05 |
| Eigen-PC | 9.4E-06 | |||
| CADD-score v1.0 | 5.5E-03 | |||
| CADD-score v1.1 | 4.7E-03 | |||
| 113 | Missense only | Eigen | 3.2E-04 | |
| Eigen-PC | 9.4E-05 | |||
| CADD-score v1.0 | 4.2E-02 | |||
| CADD-score v1.1 | 1.7E-02 | |||
| MA | 1.0E-04 | |||
|
| ||||
| EPI | 210 | Missense and Nonsense | Eigen | 3.1E-03 |
| Eigen-PC | 5.0E-03 | |||
| CADD-score v1.0 | 4.0E-02 | |||
| CADD-score v1.1 | 2.0E-01 | |||
| 184 | Missense only | Eigen | 6.0E-03 | |
| Eigen-PC | 1.3E-02 | |||
| CADD-score v1.0 | 8.1E-02 | |||
| CADD-score v1.1 | 1.7E-01 | |||
| PolyPhenVar | 3.0E-03 | |||
|
| ||||
| ID | 114 | Missense and Nonsense | Eigen | 1.7E-06 |
| Eigen-PC | 1.1E-06 | |||
| CADD-score v1.0 | 3.7E-06 | |||
| CADD-score v1.1 | 9.5E-03 | |||
| 99 | Missense only | Eigen | 6.7E-05 | |
| Eigen-PC | 6.0E-05 | |||
| CADD-score v1.0 | 3.5E-05 | |||
| CADD-score v1.1 | 3.3E-02 | |||
| MA | 1.0E-04 | |||
|
| ||||
| SCZ | 636 | Missense and Nonsense | Eigen | 9.9E-01 |
| Eigen-PC | 9.8E-01 | |||
| CADD-score v1.0 | 1.5E-01 | |||
| CADD-score v1.1 | 1.8E-01 | |||
| 573 | Missense only | Eigen | 6.3E-01 | |
| Eigen-PC | 5.8E-01 | |||
| CADD-score v1.0 | 9.8E-01 | |||
| CADD-score v1.1 | 2.8E-02 | |||
| PhastPri | 9.5E-02 | |||