Difference between revisions of "Sequence-based mutation analysis"
From Bioinformatikpedia
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!Database |
!Database |
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!Blosum62 |
!Blosum62 |
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| + | !PAM1 |
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!Pam250 |
!Pam250 |
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!Physicochemical changes |
!Physicochemical changes |
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| − | | S/C || 65 || HGMD/dbSNP || -1 || 3 |
+ | | S/C || 65 || HGMD/dbSNP || -1 || 5 || 3 |
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| − | | I/T || 105 || HGMD/dbSNP || -1 || 6 |
+ | | I/T || 105 || HGMD/dbSNP || -1 || 11 || 6 |
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| − | | Q/H || 127 || HGMD/dbSNP || 0 || 7 |
+ | | Q/H || 127 || HGMD/dbSNP || 0 || 20 || 7 |
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| − | | C/Y,S || 282 || HGMD/dbSNP || -2/-1 || 3/7 |
+ | | C/Y,S || 282 || HGMD/dbSNP || -2/-1 || 3/11 || 3/7 |
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| − | | R/M || 330 || HGMD || -1 || 1 |
+ | | R/M || 330 || HGMD || -1 || 1 || 1 |
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| − | | A/V || 176 || HGMD || 0 || 9 |
+ | | A/V || 176 || HGMD || 0 || 13 || 9 |
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| − | | R/S || 6 || HGMD || -1 || 6 |
+ | | R/S || 6 || HGMD || -1 || 11 || 6 |
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| − | | T/I || 217 || dbSNP || -1 || 4 |
+ | | T/I || 217 || dbSNP || -1 || 7 || 4 |
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| − | | M/T || 35 || dbSNP || -1 || 5 |
+ | | M/T || 35 || dbSNP || -1 || 6 || 5 |
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| − | | R/M || 58 || dbSNP || -1 || 1 |
+ | | R/M || 58 || dbSNP || -1 || 1 || 1 |
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Revision as of 11:42, 26 June 2011
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.
| Mutation | Position | Database | Blosum62 | PAM1 | Pam250 | Physicochemical changes |
|---|---|---|---|---|---|---|
| S/C | 65 | HGMD/dbSNP | -1 | 5 | 3 | |
| I/T | 105 | HGMD/dbSNP | -1 | 11 | 6 | |
| Q/H | 127 | HGMD/dbSNP | 0 | 20 | 7 | |
| C/Y,S | 282 | HGMD/dbSNP | -2/-1 | 3/11 | 3/7 | |
| 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 |
SIFT
| Mutation | Position | Prediction | Cause disease |
|---|---|---|---|
| S/C | 65 | AFFECT PROTEIN FUNCTION | yes |
| I/T | 105 | AFFECT PROTEIN FUNCTION | yes |
| Q/H | 127 | TOLERATED | yes |
| C/Y,S | 282 | AFFECT PROTEIN FUNCTION | yes |
| R/M | 330 | TOLERATED | yes |
| A/V | 176 | AFFECT PROTEIN FUNCTION | yes |
| R/S | 6 | AFFECT PROTEIN FUNCTION | yes |
| T/I | 217 | TOLERATED | |
| M/T | 35 | TOLERATED | |
| R/M | 58 | AFFECT PROTEIN FUNCTION |
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 | Cause disease |
|---|---|---|---|
| S/C | 65 | yes | |
| I/T | 105 | yes | |
| Q/H | 127 | yes | |
| C/Y,S | 282 | yes | |
| R/M | 330 | yes | |
| A/V | 176 | yes | |
| R/S | 6 | yes | |
| T/I | 217 | ||
| M/T | 35 | ||
| R/M | 58 |
