In Silico Screening and Molecular Dynamics Simulation of Disease-Associated nsSNP in TYRP1 Gene and Its Structural Consequences in OCA3

Table 1

nsSNPs analyzed by four computational methods PolyPhen 2.0, SIFT, I-Mutant 3.0, and PANTHER in TYRP1 gene.

SNP ID	Mutation	PolyPhen 2.0		SIFT		I-MUTANT 3.0		PANTHER
		PSIC	Prediction	Score	Prediction	DDG	Stability	subPSEC	Prediction
rs202189890	S270R	0.996	Damaging	0.18	Tolerated	−0.43	Neutral	−2.23829	Tolerated
rs202126779	T253M	0.996	Damaging	0.08	Tolerated	−0.32	Decrease	−3.02723	Deleterious
rs201899938	S8F	0.963	Damaging	0.7	Tolerated	0.20	Neutral	−2.19231	Tolerated
rs201789348	E139K	0.301	Benign	0.24	Tolerated	−0.97	Decrease	−3.62832	Deleterious
rs201605146	S470N	0.134	Benign	0.36	Tolerated	−0.48	Neutral	−2.11901	Tolerated
rs201457510	G63S	1.000	Damaging	0.00	Deleterious	−1.17	Neutral	−4.06048	Deleterious
rs201345670	M266T	0.772	Damaging	0.00	Deleterious	−1.63	Decrease	−3.93879	Deleterious
rs201293896	R146W	0.975	Damaging	0.02	Deleterious	−0.36	Decrease	−5.75453	Deleterious
rs200882524	L487F	0.998	Damaging	0.23	Tolerated	−0.98	Decrease	−4.01429	Deleterious
rs200754545	W249G	1.000	Damaging	0.00	Deleterious	−2.43	Decrease	−7.90178	Deleterious
rs200607153	A486T	0.029	Benign	0.05	Deleterious	−0.56	Decrease	−2.56844	Tolerated
rs199989943	R73W	0.999	Damaging	0.02	Deleterious	−0.24	Neutral	−5.69984	Deleterious
rs199823942	T366M	0.014	Benign	0.01	Deleterious	−0.43	Decrease	−4.14092	Tolerated
rs193035382	C303G	1.000	Damaging	0.00	Deleterious	−1.49	Decrease	−3.02248	Deleterious
rs188236569	Y522C	1.000	Damaging	0.01	Deleterious	−0.79	Decrease	−4.39247	Deleterious
rs187959351	G300E	1.000	Damaging	0.86	Tolerated	−0.39	Decrease	−3.66042	Deleterious
rs184910238	A380S	1.000	Damaging	0.05	Deleterious	−0.66	Decrease	−2.88075	Tolerated
rs183546444	P476T	0.000	Benign	1.00	Tolerated	−1.13	Decrease	−2.05148	Tolerated
rs182508840	T275A	0.064	Benign	0.10	Tolerated	−1.58	Decrease	−2.92255	Tolerated
rs181755026	E524A	0.001	Benign	0.22	Tolerated	−0.45	Decrease	−2.15096	Tolerated
rs151091299	S305R	0.992	Damaging	0.01	Deleterious	−0.22	Neutral	−3.02846	Deleterious
rs150899857	R505H	0.753	Damaging	0.07	Tolerated	−1.32	Decrease	−3.32609	Deleterious
rs149856598	G309E	0.566	Damaging	0.00	Deleterious	−0.80	Decrease	−3.82367	Deleterious
rs149324507	V189L	1.000	Damaging	0.00	Deleterious	−0.79	Decrease	−3.93115	Deleterious
rs148777155	S498P	0.761	Damaging	0.19	Tolerated	−0.27	Neutral	−4.76166	Deleterious
rs148248971	A409V	0.972	Damaging	0.01	Deleterious	−0.02	Decrease	−3.75227	Deleterious
rs147212712	L7P	0.924	Damaging	0.01	Deleterious	−1.44	Decrease	NA	NA
rs146962444	D123V	0.628	Damaging	0.03	Deleterious	−0.34	Neutral	−3.42156	Deleterious
rs146838872	V33A	0.000	Benign	0.45	Tolerated	−0.86	Decrease	−2.4943	Tolerated
rs146467307	V373I	0.013	Benign	0.54	Tolerated	−0.61	Decrease	−2.69258	Tolerated
rs146027807	R153C	1.000	Damaging	0.05	Tolerated	−0.90	Decrease	−5.95016	Deleterious
rs144438412	A67T	0.001	Benign	0.36	Tolerated	−0.69	Decrease	−2.56649	Tolerated
rs144206983	S207I	0.968	Damaging	0.24	Tolerated	0.43	Increase	NA	NA
rs143705229	A31G	0.159	Benign	0.02	Deleterious	−1.39	Decrease	−4.24808	Deleterious
rs143610120	N132I	1.000	Damaging	0.00	Deleterious	0.82	Increase	−6.81596	Deleterious
rs143106698	F383L	0.999	Damaging	0.04	Deleterious	−0.99	Decrease	−3.52387	Deleterious
rs143004036	N96Y	0.987	Damaging	0.00	Deleterious	−0.20	Neutral	−4.96986	Deleterious
rs142019860	Q520K	0.067	Benign	0.05	Tolerated	−0.16	Decrease	−2.41741	Tolerated
rs141949653	N435H	1.000	Damaging	0.00	Deleterious	−0.72	Decrease	−4.94266	Deleterious
rs141834891	R23W	0.02	Benign	0.22	Tolerated	0.13	Neutral	−2.04234	Tolerated
rs141196295	R114C	0.019	Benign	0.00	Deleterious	−0.68	Neutral	−4.80738	Deleterious
rs140233627	S506G	0.004	Benign	0.40	Tolerated	−0.96	Decrease	−2.00879	Tolerated
rs139946740	G309R	0.754	Damaging	0.00	Deleterious	−0.56	Decrease	−5.11275	Deleterious
rs139670838	R55H	0.771	Damaging	0.13	Tolerated	−1.12	Decrease	−3.93481	Deleterious
rs138272660	R471W	0.986	Damaging	0.00	Deleterious	−0.23	Neutral	−5.61942	Deleterious
rs138038972	R125K	0.000	Benign	0.21	Tolerated	−1.00	Neutral	−2.33412	Tolerated
rs121912778	R374G	1.000	Damaging	0.06	Tolerated	−1.48	Decrease	−3.98421	Deleterious
rs113146199	D343V	1.000	Damaging	0.00	Deleterious	0.14	Decrease	−4.03201	Deleterious
rs78071458	G174L	0.993	Damaging	0.00	Deleterious	−0.29	Decrease	−4.71688	Deleterious
rs61758405	A24T	0.219	Benign	0.02	Deleterious	−0.52	Decrease	−3.03529	Deleterious
rs61752939	T262M	1.000	Damaging	0.00	Deleterious	−0.34	Decrease	−5.00198	Deleterious
rs61752937	R93H	0.998	Damaging	0.04	Deleterious	−1.60	Decrease	−3.09393	Deleterious
rs61752864	A70T	0.859	Damaging	0.09	Tolerated	−0.66	Decrease	−2.58273	Tolerated
rs41306053	D308N	0.000	Benign	0.70	Tolerated	−1.12	Decrease	−2.04757	Tolerated
rs41305647	Q518H	0.000	Benign	0.23	Tolerated	−0.43	Decrease	−2.67099	Tolerated
rs41305645	Q530R	0.029	Benign	0.43	Tolerated	−0.07	Neutral	−2.1177	Tolerated
rs41303653	G485A	0.000	Benign	1.00	Tolerated	−0.63	Neutral	−3.35217	Deleterious
rs41303651	R505C	0.861	Damaging	0.01	Deleterious	−0.89	Neutral	−2.64052	Tolerated
rs35197549	V319G	0.997	Damaging	0.01	Deleterious	−1.86	Decrease	−3.20938	Deleterious
rs16929374	R326H	1.000	Damaging	0.00	Deleterious	−1.21	Decrease	−4.86382	Deleterious
rs3202399	E413K	0.976	Damaging	0.18	Tolerated	−1.07	Decrease	−2.76125	Tolerated
VAR_068176	R93C	0.999	Damaging	0.01	Deleterious	−1.24	Decrease	−4.10005	Deleterious
VAR_026828	R356Q	1.000	Damaging	0.00	Deleterious	−1.49	Decrease	−5.86235	Deleterious

SNPs highlighted in bold are predicted to be deleterious.