Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria

Table 1

List of nsSNPs predicted to be deleterious by SIFT, PolyPhen, PANTHER, and I-Mutant 2.0 in the coding region of HGD gene.

rs IDs	Allele frequency and change	AA position	SIFT		PolyPhen		PANTHER		I-Mutant 2.0		Reference
			Tolerance index	Predicted impact	PSIC score	Predicted impact	subPSEC score	Predicted impact	DDG	Predicted impact
rs138356501	A(0.000)/T(1.000)	Y37F	0.15	Tolerant	0.534	Benign	−1.92527	Tolerated	0.01	Increase stability
rs138846036	A(0.012)/C(0.988)	A48S	0.12	Tolerant	0.497	Benign	−2.05903	Tolerated	−0.59	Decrease stability
rs141965690	A(0.000)/T(1.000)	E74V	0.29	Tolerant	0.524	Benign	−2.29059	Tolerated	0.33	Increase stability
rs2255543	A(0.262)/T(0.738)	Q80H	0.45	Tolerant	0.258	Benign	−1.49933	Tolerated	−1.17	Decrease Stability	[35]
rs35702995	A(0.996)/C(0.004)	E87A	0.50	Tolerant	0.881	Benign	−2.18204	Tolerated	−1.85	Decrease Stability
rs143267384	A(0.000)/T(1.000)	E101V	0.06	Tolerant	1.817	Probably damaging	−2.67878	Tolerated	0.82	Increase stability
rs28941783	A(0.000)/G(1.000)	G161R	0.00	Intolerant	2.711	Probably damaging	−5.98264	Deleterious	−2.23	Decrease Stability	[36]
rs140543217	A(0.000)/G(1.000)	L163F	0.00	Intolerant	1.105	Benign	−3.70687	Deleterious	−1.12	Decrease stability
rs28942100	C/T; (No frequency)	P230S	0.00	Intolerant	2.986	Probably damaging	−5.30874	Deleterious	−1.72	Decrease Stability	[35, 36]
rs120074174	A(0.000)/G(1.000)	G270R	0.00	Intolerant	2.790	Probably damaging	−5.85971	Deleterious	−0.40	Decrease Stability	[36]
rs148641817	G(1.000)/T(0.000)	A293E	0.09	Tolerant	1.128	Benign	−1.96145	Tolerated	0.84	Increase stability
rs120074170	G/T; (No frequency)	V300G	0.00	Intolerant	2.975	Probably damaging	−4.393	Deleterious	−5.21	Decrease Stability	[35, 36]
rs143556739	A(0.001)/G(0.999)	R307C	0.01	Intolerant	1.535	Probably damaging	−3.80886	Deleterious	−1.59	Decrease stability
rs143396290	C(1.000)/T(0.000)	D326N	0.02	Intolerant	0.503	Benign	−2.1555	Tolerated	0.37	Increase stability
rs120074171	G/T; (No frequency)	R330S	0.00	Intolerant	2.830	Probably damaging	−3.2862	Deleterious	−3.53	Decrease Stability	[37]
rs139501220	A(0.000)/C(1.000)	M339I	0.00	Intolerant	2.858	Probably damaging	−3.23432	Deleterious	−2.26	Decrease stability
rs120074173	A(1.000)/G(0.000)	M368V	0.00	Intolerant	2.373	Probably damaging	−2.45276	Tolerated	−0.35	Decrease Stability	[37]
rs149326001	G(1.000)/T(0.000)	T369N	0.00	Intolerant	1.535	Probably damaging	−2.88444	Tolerated	−0.60	Decrease stability
rs120074172	A/G; (No frequency)	H371R	0.00	Intolerant	3.419	Probably damaging	−3.08256	Deleterious	−0.95	Decrease Stability	[37]
rs150145204	C(0.001)/G(0.999)	D376E	0.84	Tolerant	0.089	Benign	−1.09282	Tolerated	0.14	Increase stability
rs141753513	C(1.000)/G(0.000)	E379Q	0.01	Intolerant	1.096	Benign	−2.62114	Tolerated	−0.38	Decrease stability
rs138558042	A(0.000)/G(1.000)	P373L	0.00	Intolerant	2.074	Probably damaging	−2.72749	Tolerated	−0.66	Decrease stability

Highly deleterious by SIFT, Panther, PolyPhen and I-Mutant were indicated as bold.