TABLE 10

Correlation analysis between prediction score for deleterious nsSNPs and number of functional nsSNPs by either SIFT or PolyPhen algorithm confirmed by in vivo/in vitro experiments

Data are analyzed by Pearson's χ2 test.

Algorithm
Category
nsSNPs Predicted as Deleterious
nsSNPs with Phenotypical Effect Conformed by in Vivo/in Vitro Studies
nsSNPs with Phenotypical Effect Conformed by Site-Directed Mutagenesis
Number
Number
%a
 Number
% b
SIFT prediction 0 185 116 62.70 74 40.00
0.01-0.05 123 54 43.90 35 28.46
Sum 308 170 55.20 109 35.39
P value 0.001 0.038
PolyPhen prediction Probably damaging 238 135 56.72 88 36.97
Possibly damaging 100 36 36.00 24 24.00
Sum 338 171 50.59 112 33.14
P value
0.001
0.000

  • ↵ a % = 100 × (number of nsSNPs with phenotypical effect conformed by in vivo/in vitro studies/number of nsSNPs predicted as deleterious).

  • ↵ b % = 100 × (number of nsSNPs with phenotypical effect conformed by site-directed mutagenesis/number of nsSNPs predicted as deleterious).