Table 2.
Pathogenicity evaluation of functional CYP1A2 nsSNPs.
| Variant | PhD-SNP | SuSPect | MutPred2 | PMUT | VEST-4 |
|---|---|---|---|---|---|
| Pred (S) | Pred (S) | Pred (S) | Pred (S) | Pred (S, P-value, FDR) | |
| P36S | N (0.23) | N (16) | N (0.38) | N (0.36) | N (0.48, 0.194, 0.55) |
| P42R | P (0.53) | P (96) | P (0.69) | P (0.91) | N (0.48, 0.196, 0.55) |
| G52R | P (0.85) | P (95) | P (0.95) | P (0.91) | P (0.97, 0.003, 0.10) |
| P61L | P (0.55) | N (42) | P (0.58) | N (0.48) | N (0.69, 0.077, 0.35) |
| L65P | P (0.86) | P (92) | P (0.90) | P (0.86) | P (0.93, 0.006, 0.10) |
| G73R | P (0.86) | P (88) | P (0.91) | P (0.91) | P (0.97, 0.003, 0.10) |
| G73W | P (0.90) | P (94) | P (0.92) | P (0.91) | P (0.96, 0.003, 0.10) |
| R79C | P (0.80) | P (78) | N (0.33) | N (0.48) | N (0.17, 0.582, 0.90) |
| V85M | N (0.37) | P (53) | P (0.59) | N (0.24) | N (0.46, 0.207, 0.55) |
| L98Q | P (0.84) | P (93) | P (0.91) | P (0.91) | P (0.96, 0.003, 0.10) |
| R108Q | P (0.83) | P (86) | P (0.82) | P (0.91) | P (0.98, 0.002, 0.10) |
| R108W | P (0.89) | P (97) | P (0.90) | P (0.91) | P (0.98, 0.002, 0.10) |
| F125L | N (0.42) | N (41) | P (0.73) | N (0.30) | P (0.91, 0.008, 0.10) |
| R136C | P (0.69) | P (54) | P (0.71) | P (0.63) | P (0.76, 0.046, 0.25) |
| R137Q | P (0.82) | P (92) | P (0.75) | P (0.87) | N (0.71, 0.069, 0.35) |
| R138C | P (0.91) | P (75) | P (0.62) | P (0.78) | N (0.35, 0.291, 0.60) |
| V165G | P (0.73) | P (64) | P (0.65) | P (0.68) | N (0.53, 0.172, 0.55) |
| E168K | P (0.86) | P (75) | P (0.71) | P (0.57) | P (0.77, 0.045, 0.25) |
| F205V | P (0.87) | P (78) | P (0.77) | P (0.63) | P (0.93, 0.006, 0.10) |
| F238S | P (0.61) | N (47) | P (0.83) | N (0.28) | P (0.95, 0.004, 0.10) |
| R243C | P (0.74) | P (59) | N (0.40) | N (0.31) | N (0.40, 0.244, 0.55) |
| T324I | P (0.86) | P (54) | P (0.71) | N (0.40) | P (0.95, 0.004, 0.10) |
| T324R | P (0.92) | P (85) | P (0.83) | P (0.78) | P (0.97, 0.003, 0.10) |
| E346K | P (0.87) | P (93) | P (0.72) | P (0.90) | P (0.96, 0.003, 0.10) |
| R355Q | P (0.57) | N (44) | P (0.70) | N (0.41) | N (0.47, 0.203, 0.55) |
| R355W | P (0.82) | P (71) | P (0.77) | P (0.74) | P (0.81, 0.029, 0.20) |
| R377Q | P (0.79) | P (95) | P (0.77) | P (0.90) | P (0.94, 0.005, 0.10) |
| I386F | N (0.40) | P (57) | P (0.72) | N (0.30) | P (0.93, 0.006, 0.10) |
| H388Y | P (0.64) | P (78) | P (0.85) | P (0.85) | P (0.98, 0.002, 0.10) |
| R431W | P (0.82) | P (96) | P (0.81) | P (0.90) | P (0.89, 0.012, 0.10) |
| F432S | P (0.87) | P (95) | P (0.91) | P (0.90) | P (0.97, 0.003, 0.10) |
| K447M | N (0.47) | P (56) | P (0.64) | P (0.70) | N (0.57, 0.146, 0.55) |
| R456H | P (0.86) | P (79) | P (0.78) | P (0.89) | P (0.94, 0.005, 0.10) |
| R457P | P (0.87) | P (62) | P (0.92) | P (0.87) | N (0.70, 0.074, 0.35) |
| R457W | P (0.79) | P (80) | P (0.79) | P (0.87) | N (0.54, 0.164, 0.55) |
| E461K | P (0.91) | N (28) | P (0.80) | P (0.58) | N (0.73, 0.059, 0.30) |
| A473D | P (0.89) | P (84) | P (0.59) | P (0.91) | N (0.72, 0.064, 0.30) |
| T498N | P (0.73) | P (64) | P (0.51) | P (0.51) | N (0.48, 0.195, 0.55) |
Pred: Prediction, S: Score, P-value: Probability that a benign variant is misclassified as pathogen, FDR: False discovery rate, P: Pathogenic, N: Neutral/Benign.
The nsSNPs classified as pathogenic by all five methods are highlighted in bold.