Table 1.

MCC used to evaluate the performance of the seven tools

Genes	SIFT	PolyPhen2	VEST4	REVEL	ReVe	ClinPred	CAPICE
G6PD	0.41	0.42	0.59	0.61	0.56	0.52	0.33
ALAS2	–	0.41	–	0.63	0.61	0.73	0.58
RS1	0.38	0.43	0.69	0.59	0.69	0.69	0.43
MTM1	0.60	0.67	0.71	0.58	0.56	0.66	0.55
OTC	0.38	0.38	0.61	0.46	0.46	0.65	0.51
PHEX	0.42	0.55	0.62	0.58	0.48	0.62	0.41
F8	0.38	0.61	0.75	0.82	0.77	0.74	0.63
IL2RG	0.52	0.59	0.74	0.78	0.61	0.78	0.58
L1CAM	0.42	0.49	0.73	0.65	0.64	0.58	0.51
CLCN5	0.55	0.65	0.59	0.42	0.56	0.58	0.53
IDS	0.62	0.72	0.68	0.64	0.70	0.79	0.67
GLA	0.26	0.29	0.57	0.53	0.51	0.52	0.31
ABCD1	0.60	0.63	0.72	0.68	0.69	0.75	0.53
F9	0.25	0.30	0.39	0.57	0.59	0.50	0.41
GJB1	0.31	0.35	0.49	0.67	0.53	0.53	0.34
AVPR2	0.56	0.59	0.77	0.62	0.75	0.73	0.65
PDHA1	0.62	0.53	0.70	0.60	0.55	0.80	0.57
BTK	0.69	0.52	0.80	0.80	0.76	0.72	0.58
OCRL	0.54	0.76	0.78	0.76	0.68	0.62	0.71
NDP	–	0.57	–	0.64	0.59	0.75	0.48
HPRT1	0.44	0.24	0.73	0.62	0.65	0.79	0.48

*As suggested by their respective authors, the pathogenicity thresholds used for SIFT, PolyPhen2, VEST4, REVEL, ReVe, ClinPred and CAPICE were 0.05, 0.85, 0.5, 0.5, 0.7, 0.5 and 0.02, respectively.

†The highest MCC value for each gene is highlighted in bold.

‡The SIFT and VEST4 prediction scores for ALAS2 and NDP variants in the transcript of interest were unavailable.

MCC, Matthews correlation coefficient.