In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs)

Sudandiradoss, C.; Sethumadhavan, Rao

doi:10.1007/s11568-009-9027-3

The HUGO Journal

Official Journal of the Human Genome Organisation

Table 3 Summary of nsSNPs that were predicted to have functional significance by PolyPhen algorithm

From: In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs)

Gene name	SNP ID	Nucleotide change	Amino acid change	PSIC	References
KCNQ1	rs45606931	A → G	362 K → R	1.516	Predicted in this work
	rs45594640	C → T	583 R → C	1.858	Tranebjaerg et al. (1999)
	rs45478697	C → T	341 A → V	1.656	Tranebjaerg et al. (1999)
	rs2522018	A → C	64 P → H	1.785	Predicted in this work
	rs179489	C → G	168 G → R	1.856	Splawski et al. (1998)
KCNH2	rs45607339	C → T	784 R → W	2.654	Splawski et al. (2000) and Yang et al. (2002)
	rs41314366	A → G	859 T → M	2.050	Predicted in this work
	rs41313764	A → G	1018 P → S	1.800	Predicted in this work
	rs41313761	A → G	1020 P → L	1.879	Splawski et al. (2000)
	rs41313074	A → G	1016 P → L	2.250	Splawski et al. (2000)
	rs41307319	A → C	137 M → I	1.539	Predicted in this work
	rs41307280	A → G	1016 P → S	1.800	Splawski et al. (2000)
	rs41307271	A → G	1026 P → L	2.250	Splawski et al. (2000)
	rs36210422	C → T	176 R → W	1.914	Splawski et al. (2000) and Laitinen et al. (2000)
	rs36210421	G → T	1047 R → L	1.575	Predicted in this work
	rs28928905	A → G	490 A → T	1.542	Splawski et al. (2000) and Yoshida et al. (2001)
	rs28928904	G → T	593 I → R	1.928	Benson et al. (1996) and Splawski et al. (2000)
	rs11538710	A → T	506 I → N	2.435	Predicted in this work
	rs9333649	A → G	572 G → S	1.824	Splawski et al. (2000) and Larsen et al. (2000)
	rs1805123	A → C	897 K → T	1.722	Splawski et al. (2000) and Yang et al. (2002) and Laitinen et al. (2000)
	rs731506	G → T	41 V → G	1.939	Predicted in this work
SCN5A	rs45620037	C → T	220 T → I	1.912	Benson et al. (2003)
	rs45600438	C → T	568 R → C	2.359	Predicted in this work
	rs45589741	C → T	1249 F → L	2.001	Predicted in this work
	rs45563942	C → T	1835 I → T	1.793	Predicted in this work
	rs45546039	A → G	222 R → Q	1.595	Predicted in this work
	rs45514691	C → T	1582 R → C	2.495	Predicted in this work
	rs45489199	C → G	2005 P → A	1.645	Predicted in this work
	rs45475899	A → G	833 G → R	2.172	Predicted in this work
	rs45465995	C → T	1896 R → W	2.399	Predicted in this work
	rs41313681	A → G	656 P → L	2.201	Predicted in this work
	rs41313031	A → G	1307 L → F	1.500	Predicted in this work
	rs41311135	A → G	975 R → W	1.768	Predicted in this work
	rs41311127	A → G	1292 F → S	1.763	Predicted in this work
	rs41311061	A → G	438 M → T	2.224	Predicted in this work
	rs41276525	A → G	216 → L	1.998	Predicted in this work
	rs28937318	A → G	367 R → H	1.820	Smits et al. (2002)
	rs28937316	A → G	1643 R → H	1.820	Splawski et al. (2000)
	rs7626962	G → T	1102 S → Y	1.604	Predicted in this work
	rs6791924	A → G	34 R → C	2.008	Yang et al. (2002)
KCNE1	rs45457092	C → G	52 G → A	1.824	Predicted in this work
	rs28933384	C → T	7 T → I	2.050	Schulze-Bahr et al. (1997)
	rs17857111	C → T	32 R → H	1.704	The MGC Project Team (2004), Splawski et al. (2000)
KCNE2	rs45600841	C → T	60 F → L	1.775	Millat et al. (2006)
KCNE2	rs35759083	A → G	8 T → I	1.711	Abbott et al. (1999) and Millat et al. (2006)

nsSNPs scores found to have functional significance by both SIFT and PolyPhen are shown in bold

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