Table 4. Prediction scores from SIFT, PROVEAN, Polyphen-2, PANTHER, SNPs3D, Mutation Assessor and MutPred tools of the nsSNPs selected as the most damaging in MC1R gene.
| SNP ID | Mutation | SIFT score | PROVEANsc ore | PolyPhen-2 PSIC score | PANTHER | SNPs3D SMV score | Mutation assessor | MutPred | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| subPSEC | Pdeleterious | FIS score | Functional Impactor | g score | Molecular Mechanism Disrupted (P) | ||||||
| rs201787533 | L48P | 0 | -6.202 | 1 | -4.77696 | 0.85532 | -2.64 | 3.250 | medium | 0.717 | Loss of catalytic residue at L48 (P = 0.0274) |
| rs372590533 | R67W | 0 | -5.538 | 1 | -5.53364 | 0.92647 | -1.19 | 3.880 | high | 0.535 | Loss of solvent accessibility (P = 0.0087) |
| rs377122753 | H70Y | 0 | -5.526 | 0.996 | -3.71378 | 0.67123 | -1.61 | 3.785 | high | 0.746 | |
| rs377297107 | P72L | 0 | -9.182 | 0.997 | -6.50925 | 0.97095 | -1.07 | 3.055 | medium | 0.767 | |
| rs34474212 | S83P | 0.001 | -3.287 | 0.999 | -3.35336 | 0.58743 | -1.06 | 3.800 | high | 0.759 | |
| rs149922657 | R151H | 0 | -4.533 | 1 | -4.31313 | 0.78804 | -0.59 | 2.580 | medium | 0.542 | Loss of solvent accessibility (P = 0.0299) |
| rs376670171 | S172I | 0 | -3.222 | 0.996 | -4.19542 | 0.76771 | -0.71 | 4.190 | high | 0.759 | Loss of glycosylation at S172 (P = 0.0252) |
| rs377499038 | L206P | 0 | -6.564 | 1 | -6.45286 | 0.96932 | -2.64 | 3.910 | high | 0.824 | Loss of stability (P = 0.0428) * |
| rs200051702 | T242I | 0 | -5.619 | 0.999 | -3.53343 | 0.63028 | -1.61 | 3.620 | high | 0.815 | |
| rs371214731 | G255R | 0 | -4.036 | 0.992 | -3.60908 | 0.64773 | -0.78 | 3.175 | medium | 0.824 | |
| rs200215218 | P256S | 0 | -7.311 | 1 | -5.89441 | 0.94757 | -1.96 | 4.255 | high | 0.844 | |
| rs368281517 | C273Y | 0 | -9.733 | 1 | -6.92057 | 0.98056 | -0.59 | 3.530 | high | 0.854 | Gain of methylation at K278 (P = 0.0482) * |
| rs369542041 | C289R | 0 | -8.928 | 0.981 | -3.52876 | 0.62919 | -1.37 | 3.380 | medium | 0.885 | |
| rs368507952 | R306H | 0.001 | -3.680 | 0.999 | -5.97409 | 0.95139 | -1.75 | 3.835 | high | 0.799 | |
(*)The molecular mechanism disrupted show the actionable hypothesis when the probability of deleterious mutation (g score) are bigger than 0.5 and the probability of impacted structural or functional properties (p score) are < 0.05.