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Table 2 Ranking computational phenotype predictors for their abilities to distinguish pathogenic PAX2 missense variants from putatively benign gnomAD variants

From: Phenotypic spectrum and genetics of PAX2-related disorder in the Chinese cohort

Predictor All pathogenic versus gnomAD RCS versus non-RCS
P-value AUC 95% CI P-value AUC 95% CI
FoldX (complex) 0 0.752 0.641, 0.864 0.035 0.661 0.463, 0.858
FoldX (monomer) 0.035 0.611 0.496, 0.725 0.0132 0.6645 0.429, 0.792
REVEL 0 0.819 0.734, 0.903 0.02 0.723 0.556, 0.89
Polyphen2 0 0.805 0.689, 0.921 0.152 0.638 0.461, 0.815
VEST4 0 0.779 0.68, 0.879 0.025 0.716 0.548, 0.884
GERP 0 0.735 0.63, 0.84 0.174 0.631 0.454, 0.807
CADD 0 0.716 0.621, 0.811 0.114 0.652 0.475, 0.829
MutationTaster 0.005 0.646 0.556, 0.736 0.315 0.597 0.414, 0.779
MetaSVM 0.26 0.559 0.481, 0.637 0.544 0.442 0.257, 0.627
phyloP30way 0.61 0.527 0.43, 0.624 0.802 0.524 0.339, 0.709
LRT 0 0.281 0.194, 0.368 0.574 0.446 0.261, 0.631
PROVEAN 0 0.222 0.133, 0.312 0.117 0.349 0.169, 0.53
SIFT 0 0.15 0.066, 0.235 0.124 0.352 0.178, 0.527
FATHMM 0 0.146 0.065, 0.227 0.011 0.257 0.095, 0.419