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

BMC Medical Genomics

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

Predictor	All pathogenic versus gnomAD			RCS versus non-RCS
Predictor	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

ISSN: 1755-8794