Sequence-based mutation analysis
SNP's
Because the HFE-Gen has no annotated functional site, we can just adress the biochemical changes for each SNP. A change in functionality or stability can not described.
To compare the biochemical properties of the amino acid's, we used the very convenient function of wolfram alpha and the Wikipedia entry about amino acids <ref>http://en.wikipedia.org/wiki/Amino_acid</ref>.
| Mutation | Position | Database | Blosum62 | PAM1 | Pam250 | Physicochemical changes |
|---|---|---|---|---|---|---|
| S/C | 65 | HGMD/dbSNP | -1 | 5 | 3 | There is no change in size and charge, just the polarity changes . |
| I/T | 105 | HGMD/dbSNP | -1 | 11 | 6 | An OH-group is replaced by an ethyl-group which leads so a small change in size and a large change in hydrophobicity. |
| Q/H | 127 | HGMD/dbSNP | 0 | 20 | 7 | Because of the aromatic ring, the flexibility is reduced with a histidine at this position. The polarity and hydrophobicity remain the same. |
| C/Y,S | 282 | HGMD/dbSNP | -2/-1 | 3/11 | 3/7 | In both cases, the hydrophobicity is changed. Cysteine is a nonpolar whereas Serine and Tyrosine are polar amino acids. |
| R/M | 330 | HGMD | -1 | 1 | 1 | |
| A/V | 176 | HGMD | 0 | 13 | 9 | |
| R/S | 6 | HGMD | -1 | 11 | 6 | |
| T/I | 217 | dbSNP | -1 | 7 | 4 | |
| M/T | 35 | dbSNP | -1 | 6 | 5 | |
| R/M | 58 | dbSNP | -1 | 1 | 1 |
A change in polarity is just important for residues at the surface of the protein, because with a change in polarity, the hydrophobicity changes and so the water solubility decreases/increases.
SIFT
The prediction of SIFT is marked with a low confidence warning because, the sequences used for the prediction were not diverse enough.
| Mutation | Position | Prediction | Score | Cause disease |
|---|---|---|---|---|
| S/C | 65 | AFFECT PROTEIN FUNCTION | 0.00 | yes |
| I/T | 105 | AFFECT PROTEIN FUNCTION | 0.00 | yes |
| Q/H | 127 | TOLERATED | 0.16 | yes |
| C/Y,S | 282 | AFFECT PROTEIN FUNCTION | 0.00 | yes |
| R/M | 330 | TOLERATED | 0.06 | yes |
| A/V | 176 | AFFECT PROTEIN FUNCTION | 0.01 | yes |
| R/S | 6 | AFFECT PROTEIN FUNCTION | 0.01 | yes |
| T/I | 217 | TOLERATED | 1.00 | |
| M/T | 35 | TOLERATED | 1.00 | |
| R/M | 58 | AFFECT PROTEIN FUNCTION | 0.00 |
The complete prediction for each position and amino acid can be found here
We got three warning messages form SIFT for which we have no explanation at this time.
WARNING: Original amino acid H at position 31 is not allowed by the prediction. WARNING: Original amino acid S at position 45 is not allowed by the prediction. WARNING: Original amino acid Y at position 230 is not allowed by the prediction.
PolyPhen-2
| Mutation | Position | Prediction | Score | Cause disease |
|---|---|---|---|---|
| S/C | 65 | PROBABLY DAMAGING | 0.997 | yes |
| I/T | 105 | PROBABLY DAMAGING | 0.998 | yes |
| Q/H | 127 | BENIGN | 0.002 | yes |
| C/Y,S | 282 | PROBABLY DAMAGING | 1.000/0.997 | yes |
| R/M | 330 | PROBABLY DAMAGING | 0.948 | yes |
| A/V | 176 | PROBABLY DAMAGING | 0.998 | yes |
| R/S | 6 | PROBABLY DAMAGING | 0.738 | yes |
| T/I | 217 | BENIGN | 0.195 | |
| M/T | 35 | PROBABLY DAMAGING | 0.989 | |
| R/M | 58 | PROBABLY DAMAGING | 0.998 |
