Table 5. In silico analysis of the effect of 16 PITX2 benign variants.
| No | Missense variants | SIFT Score | PolyPhen-2 Score | MutPred Score | MutationTaster Score | Provean Score | PANTHER-PSEP Score | PMUT Score | FATHMM Score | nsSNPAnalyzer Score | Align GV-GD Score | REVEL Score |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | P41S | 0.25 (√) | 0.002 (√) | 0.201 (√) | 74 (×) | 0.325 (√) | PD (×) | 0.16 (√) | -2.80 (×) | 0.38 (√) | C65 (×) | 0.237 (√) |
| 2 | Q75P | 0.33 (√) | 0.000 (√) | 0.371 (√) | 76 (×) | -0.065 (√) | PD (×) | 0.14 (√) | -2.77 (×) | 0.27 (√) | C65 (×) | 0.503 (×) |
| 3 | V81M | 0.11 (√) | 0.459 (×) | 0.063 (√) | 21 (√) | -0.023 (√) | PB (√) | 0.08 (√) | -2.74 (×) | 0.14 (√) | C15 (×) | 0.501 (×) |
| 4 | A188T | 0.68 (√) | 0.027 (√) | 0.329 (√) | 58 (×) | -1.018 (√) | PD (×) | 0.04 (√) | -2.86 (×) | 0.57 (√) | C55 (×) | 0.151 (√) |
| 5 | M207V | 0.62 (√) | 0.069 (√) | 0.386 (√) | 21 (×) | -1.461 (√) | PD (×) | 0.15 (√) | -2.61 (×) | 0.47 (√) | C15 (×) | 0.185 (√) |
| 6 | R203C | 0 (×) | 0.968 (×) | 0.150 (√) | 81 (×) | -0.455 (√) | PB (√) | 0.03 (√) | -2.51 (×) | 0.12 (√) | C65 (×) | 0.146 (√) |
| 7 | Q193T | 0.38 (√) | 0.270 (√) | 0.196 (√) | 84 (×) | 0.630 (√) | PD (×) | 0.02 (√) | -.2.60 (×) | 0.00 (×) | C35 (×) | 0.152 (√) |
| 8 | Y131D | 0 (×) | 0.812 (×) | 0.121 (√) | 35 (×) | -0.010 (√) | PD (×) | 0.03 (√) | -1.64 (√) | 0.01 (×) | C65 (×) | 0.251 (√) |
| 9 | G166D | 0 (×) | 0.557 (×) | 0.283 (√) | 76 (×) | -0.357 (√) | PB (√) | 0.31 (√) | -2.58 (×) | 0.01 (×) | C65 (×) | 0.224 (√) |
| 10 | H151Y | 0 (×) | 0.512 (×) | 0.045 (√) | 75 (×) | -2.400 (√) | PD (×) | 0.03 (√) | -2.62 (×) | 0.01 (×) | C65 (×) | 0.169 (√) |
| 11 | I138F | 0 (×) | 0.671 (×) | 0.056 (√) | 57 (×) | -0.390 (√) | PB (√) | 0.2 (√) | -2.69 (×) | 0.04 (×) | C0 (√) | 0.145 (√) |
| 12 | G205S | 0.68 (√) | 0.017 (√) | 0.193 (√) | 87 (×) | -0.372 (√) | PB (√) | 0.15 (√) | -2.62 (×) | 0.78 (√) | C55 (×) | 0.147 (√) |
| 13 | G186R | 0 (×) | 1.000 (×) | 0.212 (√) | 48 (×) | -1.092 (√) | PD (×) | 0.08 (√) | -2.86 (×) | 0.00 (×) | C65 (×) | 0.103 (√) |
| 14 | H57Q | 0 (×) | 0.736 (×) | 0.056 (√) | 63 (×) | -3.010 (×) | PB (√) | 0.03 (√) | -2.55 (×) | 0.00 (×) | C15 (×) | 0.112 (√) |
| 15 | A246D | 0 (×) | 1.000 (×) | 0.440 (√) | 44 (×) | -0.769 (√) | PD (×) | 0.18 (√) | -2.65 (×) | 0.01 (×) | C65 (×) | 0.181 (√) |
| 16 | G148W | 0 (×) | 0.844 (×) | 0.195 (√) | 65 (×) | -0.242 (√) | PB (√) | 0.31 (√) | -2.74 (×) | 0.04 (×) | C65 (×) | 0.109 (√) |
PB; probably benign, PD; probably damaging
√ correspond to functional characterization; ×, do not correspond to functional characterization.