Table 2.
Statistical analysis of missense variants with documented biological function testing.
| SIFT | PolyPhen-2 | Concordant Prediction | |
|---|---|---|---|
| True positive (N) | 36 | 36 | 36 |
| True negative (N) | 7 | 8 | 7 |
| False positive (N) | 3 | 2 | 2 |
| False negative (N) | 6 | 6 | 6 |
| Total (N) | 52 | 52 | 51 |
| Sensitivity (%) | 85.7 | 85.7 | 85.7 |
| Specificity (%) | 70.0 | 80.0 | 77.8 |
| Positive predictive value (%) | 92.3 | 94.7 | 94.7 |
| Negative predictive value (%) | 53.8 | 57.1 | 53.8 |
| Accuracy (%) | 82.7 | 84.6 | 84.3 |
| MCC | 0.5 | 0.6 | 0.6 |
N: Number of variants. MCC: Matthews correlation coefficient