Difference between revisions of "ASPA Sequence Based Mutation Analysis"

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{| class="wikitable" border="1" style="text-align:center; border-spacing:0;"
  
{| class="wikitable" border="1" style="text-align:center; border-spacing:0;"
−
! Pos. || Mutation || Blosum Score || Worst? || PAM250 Score || Worst? || PAM1 Score || Worst? || PSSP Mutated || Wildtype || MSA Mutated || Wildtype || Polyphen Prediction || Score || Sift Prediction || Score || Median Conservation || SNAP Prediction || Reliability || Exp. Accuracy
 +
! Mutation || Pos. || Blosum Score || Worst? || PAM250 Score || Worst? || PAM1 Score || Worst? || PSSP Mutated || Wildtype || MSA Mutated || Wildtype || Polyphen Prediction || Score || Sift Prediction || Score || Median Conservation || SNAP Prediction || Reliability || Exp. Accuracy
 
|-
  
|-
−
| Tyr->Cys || 0 || -2 || no || -0.5 || no || 3 || no || -2 || 15 || 0.0% || 73.7% || damaging || 1.0 || affect || 0.00 || 3.02 || Non-neutral || 5 || 87%
 +
| Tyr->Cys || 231 || -2 || no || -0.5 || no || 3 || no || -2 || 15 || 0.0% || 73.7% || damaging || 1.0 || affect || 0.00 || 3.02 || Non-neutral || 5 || 87%
 
|-
  
|-
−
| Ala->Glu || 0 || -1 || no || 0 || no || 17 || no || -4 || 3 || 0.0% || 68.8% || damaging || 1.0 || affect || 0.02 || 3.14 || Non-neutral || 3 || 78%
 +
| Ala->Glu || 305 || -1 || no || 0 || no || 17 || no || -4 || 3 || 0.0% || 68.8% || damaging || 1.0 || affect || 0.02 || 3.14 || Non-neutral || 3 || 78%
 
|-
  
|-
−
| Arg->His || 0 || 0 || no || 0.6 || no || 8 || no || -1 || 8 || 0.0% || 100.0% || damaging || 1.0 || affect || 0.01 || 3.02 || Non-neutral || 6 || 93%
 +
| Arg->His || 71 || 0 || no || 0.6 || no || 8 || no || -1 || 8 || 0.0% || 100.0% || damaging || 1.0 || affect || 0.01 || 3.02 || Non-neutral || 6 || 93%
 
|-
  
|-
−
| Glu->Gly || 0 || -2 || no || -0.8 || no || 7 || no || -5 || 8 || 0.0% || 100.0% || damaging || 1.0 || affect || 0.00 || 3.02 || Non-neutral || 7 || 96%
 +
| Glu->Gly || 24 || -2 || no || -0.8 || no || 7 || no || -5 || 8 || 0.0% || 100.0% || damaging || 1.0 || affect || 0.00 || 3.02 || Non-neutral || 7 || 96%
 
|-
  
|-
−
| Cys->Arg || 0 || -3 || yes || -2.2 || yes || 1 || no || -3 || 3 || 0.0% || 100.0% || damaging || 0.999 || affect || 0.01 || 3.07 || Non-neutral || 6 || 93%
 +
| Cys->Arg || 152 || -3 || yes || -2.2 || yes || 1 || no || -3 || 3 || 0.0% || 100.0% || damaging || 0.999 || affect || 0.01 || 3.07 || Non-neutral || 6 || 93%
 
|-
  
|-
−
| Met->Thr || 0 || -1 || no || -0.6 || no || 6 || no || 14 || 2 || 0.0% || 57.9% || benign || 0.0 || tolerated || 0.16 || 3.02 || Non-neutral || 0 || 58%
 +
| Met->Thr || 82 || -1 || no || -0.6 || no || 6 || no || 14 || 2 || 0.0% || 57.9% || benign || 0.0 || tolerated || 0.16 || 3.02 || Non-neutral || 0 || 58%
 
|-
  
|-
−
| Thr->Ile || 0 || -1 || no || -0.6 || no || 7 || no || 1 || 16 || 0.0% || 73.7% || damaging || 1.0 || affect || 0.04 || 3.07 || Non-neutral || 2 || 70%
 +
| Thr->Ile || 166 || -1 || no || -0.6 || no || 7 || no || 1 || 16 || 0.0% || 73.7% || damaging || 1.0 || affect || 0.04 || 3.07 || Non-neutral || 2 || 70%
 
|-
  
|-
−
| Pro->His || 0 || -2 || no || -1.1 || no || 3 || no || 0 || 4 || 5.3% || 94.7% || damaging || 1.0 || affect || 0.00 || 3.07 || Non-neutral || 6 || 93%
 +
| Pro->His || 183 || -2 || no || -1.1 || no || 3 || no || 0 || 4 || 5.3% || 94.7% || damaging || 1.0 || affect || 0.00 || 3.07 || Non-neutral || 6 || 93%
 
|-
  
|-
−
| Met->Arg || 0 || -1 || no || -1.7 || no || 4 || no || -1 || 3 || 0.0% || 94.7% || damaging || 0.991 || affect || 0.03 || 3.04 || Non-neutral || 5 || 87%
 +
| Met->Arg || 195 || -1 || no || -1.7 || no || 4 || no || -1 || 3 || 0.0% || 94.7% || damaging || 0.991 || affect || 0.03 || 3.04 || Non-neutral || 5 || 87%
 
|-
  
|-
−
| Lys->Glu || 0 || 1 || no || 1.2 || no || 4 || no || 0 || 0 || 0.0% || 73.7% || benign || 0.014 || tolerated || 0.83 || 3.02 || Neutral || 3 || 78%
 +
| Lys->Glu || 213 || 1 || no || 1.2 || no || 4 || no || 0 || 0 || 0.0% || 73.7% || benign || 0.014 || tolerated || 0.83 || 3.02 || Neutral || 3 || 78%
 
|}
  
|}

Revision as of 23:49, 4 July 2011

Mutations

CM994594

Mutation: Tyr to Cys at position 231; we got it from dbSNP.


CM940124

Mutation: Ala to Glu at position 305; we got it from dbSNP.


RS104894553

Mutation: Arg to His at position 71; we got it from HGMD.


RS104894551

Mutation: Glu to Gly at position 24; we got it from HGMD.


RS104894548

Mutation: Cys to Arg at position 152; we got it from HGMD.


RS80099330

Mutation: Met to Thr at position 82; we got it from HGMD.


CM063847

Mutation: Thr to Ile at position 166; we got it from dbSNP.


CM990193

Mutation: Pro to His at position 183; we got it from dbSNP.


CM990195

Mutation: Met to Arg at position 195; we got it from dbSNP.


CM055097

Mutation: Lys to Glu at position 213; we got it from dbSNP.



PSSM

x y 

          A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V   A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
  24 E   -4 -3 -3 -1 -7  0  8 -5 -3 -6 -6 -2 -5 -6 -4 -3 -4 -6 -5 -6    0   0   0   0   0   1  99   0   0   0   0   0   0   0   0   0   0   0   0   0  2.24 1.67
  71 R   -4  8 -3 -2 -6 -2 -3 -5 -1 -5 -4 -1  1 -5 -5 -3 -4 -5 -4 -5    0  88   0   3   0   0   0   0   1   0   0   0   5   0   0   0   0   0   0   0  1.96 1.46
  82 M    1 -2  1  2 -1  0 -1  1  0 -1 -2 -1  2 -3  1 -1  2 -3 -2 -1   10   2   6  10   1   4   4  12   3   4   4   3   5   1   6   5  14   0   2   5  0.15 1.53
 152 C   -2 -3 -1  1  3 -2 -2 -3 -2  3 -1 -4  2 -2 -2 -3 -2 -5 -1  5    2   2   3   8   6   2   2   2   1  16   3   1   4   1   3   2   2   0   2  39  0.64 2.02
 166 T    2 -2 -1 -1 -2 -2 -1 -1 -1 -3 -2 -4 -2  3 -2  2  3  1  3 -1   15   2   2   3   1   1   5   5   1   1   4   1   1  12   2  15  16   2  10   3  0.34 2.09
 183 P    0 -1  0 -1  1  0 -1  1  0 -4 -1 -1  0 -1  4  0 -1  4  0 -2    9   3   4   4   3   4   3  12   3   0   6   4   3   3  17   6   3   6   3   3  0.26 1.80
 195 M    1 -1 -4 -1  2 -1 -1  1  1  1  0 -4  3  1 -5 -1  2 -5  0  1   12   3   0   3   5   3   3   9   4   9   7   0   9   5   0   4  11   0   4   8  0.21 1.85
 213 K   -1  1  0  2  1  0  0 -1  1 -1 -1  0  1  0  1 -1  0 -5  0 -1    6   7   4  10   3   5   5   4   3   4   8   7   3   4   8   5   6   0   3   5  0.07 2.08
 231 Y    0  0 -4 -4 -2 -2 -2 -3 -4 -1  0  2  1  2 -4 -1 -2  6  4 -1   10   6   0   1   1   1   3   2   0   3   8  14   4   8   1   4   2  13  15   5  0.52 1.95
 305 A    3 -4 -5 -5  2 -4 -4 -4 -5  1  2 -4 -2  0 -4 -2 -3 -5 -3  5   24   0   0   0   4   0   0   0   0   7  17   0   0   3   0   3   0   0   0  41  0.71 1.09


Multiple Sequence Alignment

We calculated our MSA using T-Coffee

alt text


Table of Results

Mutation Pos. Blosum Score Worst? PAM250 Score Worst? PAM1 Score Worst? PSSP Mutated Wildtype MSA Mutated Wildtype Polyphen Prediction Score Sift Prediction Score Median Conservation SNAP Prediction Reliability Exp. Accuracy
Tyr->Cys 231 -2 no -0.5 no 3 no -2 15 0.0% 73.7% damaging 1.0 affect 0.00 3.02 Non-neutral 5 87%
Ala->Glu 305 -1 no 0 no 17 no -4 3 0.0% 68.8% damaging 1.0 affect 0.02 3.14 Non-neutral 3 78%
Arg->His 71 0 no 0.6 no 8 no -1 8 0.0% 100.0% damaging 1.0 affect 0.01 3.02 Non-neutral 6 93%
Glu->Gly 24 -2 no -0.8 no 7 no -5 8 0.0% 100.0% damaging 1.0 affect 0.00 3.02 Non-neutral 7 96%
Cys->Arg 152 -3 yes -2.2 yes 1 no -3 3 0.0% 100.0% damaging 0.999 affect 0.01 3.07 Non-neutral 6 93%
Met->Thr 82 -1 no -0.6 no 6 no 14 2 0.0% 57.9% benign 0.0 tolerated 0.16 3.02 Non-neutral 0 58%
Thr->Ile 166 -1 no -0.6 no 7 no 1 16 0.0% 73.7% damaging 1.0 affect 0.04 3.07 Non-neutral 2 70%
Pro->His 183 -2 no -1.1 no 3 no 0 4 5.3% 94.7% damaging 1.0 affect 0.00 3.07 Non-neutral 6 93%
Met->Arg 195 -1 no -1.7 no 4 no -1 3 0.0% 94.7% damaging 0.991 affect 0.03 3.04 Non-neutral 5 87%
Lys->Glu 213 1 no 1.2 no 4 no 0 0 0.0% 73.7% benign 0.014 tolerated 0.83 3.02 Neutral 3 78%
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