Table 3. Comparative performance of the PMut2017 predictor on selected genes.
| Gene | Disease | #D | #N | PMut | SIFT | Polyphen | LRT | Mut. Taster | Mut. Assessor | PROVEAN |
|---|---|---|---|---|---|---|---|---|---|---|
| MECP2 | Rett syndrome | 46 | 22 | 0.86 | 0.66 | 0.85 | 0.69 | 0.64 | 0.41 | 0.53 |
| COL1A2 | Osteogenesis Imperfecta | 78 | 20 | 0.77 | 0.74 | 0.62 | 0.55 | 0.55 | 0.74 | 0.74 |
| SLC4A1 | Distal Renal Tubular Acidosis | 38 | 36 | 0.69 | 0.65 | 0.65 | 0.54 | 0.55 | 0.68 | 0.60 |
| ADAMTS13 | Upshaw-Schulman syndrome | 43 | 17 | 0.62 | 0.76 | 0.46 | 0.00 | 0.71 | 0.54 | 0.62 |
| ATM | Hereditary cancer-predisposing syndrome | 46 | 54 | 0.60 | 0.53 | 0.57 | 0.32 | 0.42 | 0.48 | 0.55 |
| ATP7B | Wilson disease | 195 | 25 | 0.48 | 0.34 | 0.49 | 0.37 | 0.43 | 0.29 | 0.52 |
| MLH1+MSH2+MSH6+PMS2 | Lynch syndrome | 159 | 78 | 0.48 | 0.32 | 0.31 | 0.23 | 0.16 | 0.43 | 0.32 |
| MYOC | Primary open angle glaucoma | 57 | 24 | 0.47 | 0.37 | 0.45 | 0.38 | 0.50 | 0.47 | 0.49 |
| TTC21B | Jeune thoracic dystrophy | 16 | 28 | 0.42 | 0.20 | 0.22 | 0.18 | 0.16 | 0.28 | 0.26 |
| SCN5A | Brugada syndrome | 154 | 46 | 0.40 | 0.32 | 0.26 | 0.43 | 0.31 | 0.34 | 0.34 |
| KCNH2+SCN5A | Congenital long QT syndrome | 270 | 54 | 0.38 | 0.32 | 0.28 | 0.36 | 0.32 | 0.30 | 0.38 |
| ABCA1 | Tangier disease | 32 | 31 | 0.37 | 0.43 | 0.31 | 0.32 | 0.47 | 0.43 | 0.47 |
| PKHD1+PKD1 | Polycystic kidney disease | 197 | 96 | 0.37 | 0.43 | 0.37 | 0.30 | 0.41 | 0.36 | 0.45 |
| FBN1 | Marfan syndrome | 385 | 20 | 0.35 | 0.31 | 0.25 | 0.21 | 0.33 | 0.32 | 0.30 |
| RYR1 | Central core disease | 147 | 25 | 0.34 | 0.27 | 0.31 | 0.00 | 0.36 | 0.28 | 0.34 |
| LDLR | Familial hypercholesterolemia | 103 | 23 | 0.32 | 0.29 | 0.08 | 0.17 | 0.09 | 0.26 | 0.25 |
| DYSF | Limb-Girdle Muscular Dystrophy | 48 | 16 | 0.31 | 0.35 | 0.27 | 0.15 | 0.21 | 0.41 | 0.39 |
| BRCA2 | Breast-ovarian cancer, familial 2 | 43 | 61 | 0.31 | 0.10 | 0.18 | 0.18 | 0.14 | 0.19 | 0.01 |
| BRCA1 | Breast-ovarian cancer, familial 1 | 27 | 36 | 0.31 | 0.24 | 0.20 | 0.38 | 0.29 | 0.30 | 0.17 |
| WFS1 | WFS1-Related Spectrum Disorders | 40 | 17 | 0.30 | 0.25 | 0.35 | 0.20 | 0.18 | 0.16 | 0.26 |
| PINK1 | Parkinson Disease | 23 | 39 | 0.25 | 0.33 | 0.48 | 0.40 | 0.41 | 0.44 | 0.30 |
| LRRK2 | Parkinson Disease | 21 | 24 | 0.19 | 0.06 | 0.14 | 0.01 | 0.13 | 0.09 | 0.14 |
| CFTR | Cystic fibrosis | 146 | 32 | 0.15 | 0.06 | 0.20 | 0.21 | 0.12 | 0.20 | 0.27 |
| PROC | Thrombophilia | 36 | 28 | 0.12 | -0.15 | -0.08 | 0.07 | 0.14 | 0.08 | -0.01 |
MCC values obtained restraining the analysis to variants on the indicated genes. Analysis for non-PMut methods performed from ANNOVAR data (42). #N Neutral mutations, #D Disease causing mutations.