Computational Identification of Most Deleterious Missense Mutations in Human PD-1 Gene

Table 3

Structure-based predictions of the top 4 missense variants.

Tools	R38C	D61V	R94C	D117V
MUpro	−0.187; (Decrease stability)	−0.326; (Decrease stability)	−1.307; (Decrease stability)	−0.734; (Decrease stability)
I-Mutant 2	2; (Decrease)	1; (Increase)	5; (Decrease)	5; (Decrease)
iStable 2	−0.494; (Decrease)	0.507; (Increase)	−0.90; (Decrease)	−1.24; (Decrease)
CUPSAT	−1.4; (Destabilizing)	−1.94; (Destabilizing)	0.29; (Stabilizing)	0.53; (Stabilizing)
SDM	1.32 kcal/mol; (Stabilizing)	−0.17 kcal/mol; (Destabilizing)	−0.18 kcal/mol; (Destabilizing)	1.13 kcal/mol; (Stabilizing)
mCSM	−0.43 kcal/mol; (Destabilizing)	0.14 kcal/mol; (Stabilizing)	−1.033 kcal/mol; (Destabilizing)	1.009 kcal/mol; (Stabilizing)
DUET	0.162 kcal/mol; (Stabilizing)	0.347 kcal/mol; (Stabilizing)	−0.97 kcal/mol; (Destabilizing)	1.492 kcal/mol; (Stabilizing)
MAESTROweb	0.51 kcal/mol; (Destabilizing)	1.428 kcal/mol; (Destabilizing)	0.88 kcal/mol; (Destabilizing)	−0.374 kcal/mol; (Stabilizing)
DynaMut 2	0.23 kcal/mol; (Stabilizing)	−0.7 kcal/mol; (Destabilizing)	1.51 kcal/mol; (Stabilizing)	−0.54 kcal/mol; (Destabilizing)
DeepDDG	−0.279 kcal/mol; (Destabilizing)	−0.160 kcal/mol; (Destabilizing)	−2.146 kcal/mol; (Destabilizing)	−2.833 kcal/mol; (Destabilizing)

Numbers indicate the probable mutation effect score, while bold indicates deleterious mutations.