Difference between revisions of "SNP effect predictions (PKU)"
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==PolyPhen== |
==PolyPhen== |
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| − | We report here the results for PolyPhen(HumDiv) and PolyPhen(HumVar), but only consider HumVar as this is the training set recommended by [http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview#prediction PolyPhen |
+ | We report here the results for PolyPhen(HumDiv) and PolyPhen(HumVar), but only consider HumVar as this is the training set recommended by [http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview#prediction PolyPhen] for our task. |
GLU76GLY |
GLU76GLY |
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G337V Neutral 1 60% |
G337V Neutral 1 60% |
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R408W Non-neutral 3 78% |
R408W Non-neutral 3 78% |
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| + | [[Category: Phenylketonuria 2012]] |
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Latest revision as of 12:03, 29 August 2012
Predictions of SNP effect
The three methods we used, agree on ARG158Gln, Arg243Gln, Leu255Ser and Arg408Trp to have damaging effect and agree on Met276Val to be functionally neutral. Glu76Gly and Ser87Arg are reported to be benign by SIFT and PolyPhen and damaging, but with low reliability, by SNAP.
For the other three SNPs, there is no agreement or clear tendency of the predictions.
SIFT
76 from E to G TOLERATED with a score of 0.18. Median sequence conservation: 3.01 Sequences represented at this position:74
87 from S to R TOLERATED with a score of 0.54. Median sequence conservation: 2.99 Sequences represented at this position:75
158 from R to Q AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 2.98 Sequences represented at this position:76
172 from Q to H AFFECT PROTEIN FUNCTION with a score of 0.03. Median sequence conservation: 3.01 Sequences represented at this position:77
243 from R to Q AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
255 from L to S AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
276 from M to V TOLERATED with a score of 0.06. Median sequence conservation: 3.01 Sequences represented at this position:77
322 from A to G AFFECT PROTEIN FUNCTION with a score of 0.01. Median sequence conservation: 3.01 Sequences represented at this position:77
337 from G to V AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
408 from R to W AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:75
PolyPhen
We report here the results for PolyPhen(HumDiv) and PolyPhen(HumVar), but only consider HumVar as this is the training set recommended by PolyPhen for our task.
GLU76GLY
HumDiv BENIGN 0.002 (sensitivity: 0.99; specificity: 0.30) HumVar BENIGN 0.007 (sensitivity: 0.97; specificity: 0.46)
SER87ARG
HumDiv BENIGN 0.091 (sensitivity: 0.93; specificity: 0.85) HumVar BENIGN 0.094 (sensitivity: 0.91; specificity: 0.68)
R158Q
HumDiv PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00)
Q172H
HumDiv POSSIBLY DAMAGING 0.705 (sensitivity: 0.86; specificity: 0.92) HumVar BENIGN 0.170 (sensitivity: 0.89; specificity: 0.72)
R243Q
HumDiv PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00)
L255S
HumDiv PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00)
M276V
HumDiv POSSIBLY DAMAGING 0.517 (sensitivity: 0.88; specificity: 0.90) HumVar BENIGN 0.081 (sensitivity: 0.92; specificity: 0.67)
A322G
HumDiv POSSIBLY DAMAGING 0.895 (sensitivity: 0.82; specificity: 0.94) HumVar POSSIBLY DAMAGING 0.707 (sensitivity: 0.78; specificity: 0.85)
G337V
HumDiv BENIGN 0.291 (sensitivity: 0.91; specificity: 0.89) HumVar POSSIBLY DAMAGING 0.597 (sensitivity: 0.81; specificity: 0.83)
R408W
HumDiv PROBABLY DAMAGING 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar PROBABLY DAMAGING 0.999 (sensitivity: 0.09; specificity: 0.99)
SNAPFUN
Including only predictions with: RI >= 0 Expected Accuracy >= 50% nsSNP Prediction Reliability Index Expected Accuracy ----- ------------ ------------------- ------------------- E76G Non-neutral 1 63% S87R Non-neutral 0 58% R158Q Non-neutral 5 87% Q172H Neutral 4 85% R243Q Non-neutral 2 70% L255S Non-neutral 1 63% M276V Neutral 1 60% A322G Neutral 1 60% G337V Neutral 1 60% R408W Non-neutral 3 78%
