Screening and Evaluation of Deleterious SNPs in APOE Gene of Alzheimer’s Disease

Table 1

I-Mutant, SIFT and PolyPhen results of APOE.

				SIFT		PolyPhen
SNP ADs	Alleles	Amino acid change	DDG	Tolerance index	Predicted impact	PSIC score	Predicted impact
rs121918399	C/T	R43C	0.66	0.07	Potentially intolerant	1.534	Possibly damaging
rs121918398	A/G	R292H	−2.06	0.06	Potentially intolerant	1.979	Possibly damaging
rs121918397	G/A	R163H	0.05	0.16	Borderline	1.961	Probably damaging
rs121918395	C/T	R246C	−0.48	0.06	Potentially intolerant	2.386	Possibly damaging
rs121918394	A/C	K164Q	−1.28	0.08	Potentially intolerant	1.550	Possibly damaging
rs121918393	C/A	R154S	−0.51	0.10	Potentially intolerant	1.962	Possibly damaging
rs121918392	G/A	E21K	1.17	0.18	Borderline	1.373	Borderline
rs41382345	A/T	E139V	−1.32	0.00	Intolerant	2.246	Probably damaging
rs28931579	A/C	S314R	−0.09	0.12	Borderline	1.343	Borderline
rs28931578	G/A	R152Q	−0.43	0.01	Intolerant	1.772	Possibly damaging
rs28931577	G/A	A117T	0.65	0.06	Intolerant	1.451	Borderline
rs28931576	A/G	T60A	0.57	0.15	Borderline	0.669	Benign
rs11542041	C/A	R132S	−2.75	0.00	Intolerant	2.204	Probably damaging
rs11542040	C/A	P102T	−1.20	0.00	Intolerant	2.396	Probably damaging
rs11542035	G/A	R137H	0.83	0.13	Borderline	0.080	Benign
rs11542034	A/G	E150G	−1.24	0.00	Intolerant	2.284	Probably damaging
rs11542032	G/A	E189K	−0.89	0.01	Intolerant	1.607	Possibly damaging
rs11542030	A/G	Q205R	0.48	0.11	Borderline	0.794	Benign
rs11542029	C/T	R50C	−0.82	0.00	Intolerant	2.654	Probably damaging
rs11542027	C/T	S215F	0.84	0.01	Intolerant	1.437	Borderline
rs11083750	C/A	P102Q	−1.15	NA	NA	2.396	probably damaging
	C/G	P102R	−1.18	NA	NA	2.621	probably damaging
rs769455	C/T	R163C	0.08	0.00	Intolerant	1.502	Possibly damaging
rs769452	T/C	L46P	−0.11	0.12	Borderline	1.334	Borderline
rs429358	T/C	C130R	−0.07	1.00	Tolerant	0.231	Benign
rs7412	C/T	R176C	−1.19	0.02	Intolerant	2.654	Probably damaging

Note: nsSNPs which were found to be deleterious by I-Mutant and SIFT as well as PolyPhen are highlighted as bold.