First Comprehensive In Silico Analysis of the Functional and Structural Consequences of SNPs in Human GalNAc-T1 Gene

Table 2

Characterization of SNPs by using PolyPhen-2, PANTHER, and Fathmm based classification systems.

Amino acid change	PolyPhen-2			PANTHER		Fathmm
A1#A2	Score	Prediction	Specificity/sensitivity	subPSEC Score	Prediction	Score	Prediction
A5T	0.411	Benign	0.90/0.89	−2.96529	Tolerated	0.59	Tolerated
L20V	0.000	Benign	0.00/1.00	−2.65438	Tolerated	0.69	Tolerated
L25V	0.960	Probably damaging	0.95/0.78	−3.45127	Deleterious	0.35	Tolerated
D46G	0.004	Benign	0.59/0.97	−3.34504	Deleterious	0.51	Tolerated
P54L	0.001	Benign	0.15/0.99	−4.27568	Deleterious	0.56	Tolerated
D71E	0.000	Benign	0.00/1.00	−3.40972	Deleterious	0.68	Tolerated
D71H	0.132	Benign	0.86/0.93	−5.24027	Deleterious	0.49	Tolerated
S143P	0.999	Probably damaging	0.99/0.14	−7.4941	Deleterious	0.15	Tolerated
V216M	0.411	Benign	0.90/0.89	−5.56762	Deleterious	0.26	Tolerated
G258V	1.000	Probably damaging	1.00/0.00	−4.40932	Deleterious	0.35	Tolerated
N379H	0.000	Benign	0.00/1.00	−3.41433	Deleterious	−0.35	Tolerated
I384V	0.000	Benign	0.00/1.00	−3.81526	Deleterious	−0.31	Tolerated
G401D	0.000	Benign	0.00/1.00	−3.23851	Deleterious	1.56	Tolerated
Y414D	1.000	Probably damaging	1.00/0.00	−9.17274	Deleterious	−1.82	Damaging
N440H	0.048	Benign	0.83/0.94	−4.06922	Deleterious	−1.17	Tolerated
P510T	0.009	Benign	0.77/0.96	−3.46487	Deleterious	−1.09	Tolerated
N541S	0.000	Benign	0.00/1.00	−2.80107	Tolerated	−1.03	Tolerated
V553I	0.000	Benign	0.00/1.00	−2.409	Tolerated	−0.98	Tolerated

PolyPhen-2: probably damaging (probabilistic score > 0.85), possibly damaging (probabilistic score > 0.15), and benign (remaining).
PANTHER: deleterious or intolerant (subPSEC score ≤ −3), less deleterious (subPSEC score ≥ −3).