Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects

Matimba, Alice; Del-Favero, Jurgen; Van Broeckhoven, Christine; Masimirembwa, Collen

doi:10.1186/1479-7364-3-2-169

Human Genomics

Table S2 CYP2C19 single nucleotide polymorphism (SNP) frequencies

From: Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects

NC_000010.9	mRNA position	SNP	mRNA feature	Effect	dbSNP	Hausa (20)	Yoruba (20)	Ibo (20)	Luo (30)	Maasai (13)	Shona (15)	Venda (9)	TZ Bantu (10)	Total (137)
96653591	-97	T > C	5' UTR		rs4986894	0.13	0.18	0.33	0.07	0.08	0.2	0.11	0.15	0.15
96653743	55	A > C	Exon 1	I19L (*15)	rs17882687	0	0	0	0.05	0	0	0	0.05	0.02
96653787	99	T > C	Exon 1	P33P	rs17885098	0.05	0.08	0.15	0.18	0.15	0.17	0.17	0.30	0.15
96653871	183	T > C	Intron		rs17882201	0	0	0	0	0	0	0.06	0	< 0.01
96653876	188	G > A	Intron		rs17881883	0	0	0.03	0	0	0.07	0.11	0.05	0.02
96653919	231	A > C	Intron		Novel	0	0	0	0.01	0	0	0	0	< 0.01
96665810	12122	A > G	Intron		rs7916649	0.5	0.37	0.29	0.58	0.50	0.25	0.28	0.33	0.41
96665994	12306	G > A	Intron		rs17878649	0	0	0.03	0.08	0.04	0.10	0.06	0.10	0.05
96666148	12460	G > C	Exon 2	E92D	rs17878459	0	0	0	0	0	0.03	0	0	< 0.01
96666295	12607	wt > insC	Intron		Novel	0	0	0	0.03	0.04	0	0	0	0.01
96666325	12637	C > T	Intron		Novel	0.03	0.1	0	0	0.04	0	0.06	0	0.03
96666350	12662	A > G	Intron	Splice site	rs12769205	0.16	0.2	0.33	0.09	0.12	0.27	0.22	0.2	0.18
96666378	12690	G > A	Exon 3	V113I	Novel	0	0	0	0	0	0	0.06	0	< 0.01
96666472	12784	G > A	Exon 3	R144H (*9)	rs17884712	0	0	0	0	0	0	0.06	0	< 0.01
96671557	17869	G > T	Exon 4	R186P (*22)	Novel	0	0	0	0	0	0	0	0.06	< 0.01
96671636	17948	G > A	Exon 4	W212X (*3)	rs4986893	0	0	0	0	0.04	0	0	0	< 0.01
96671895	18207	G > A	Intron		Novel	0	0	0	0.02	0	0	0	0.06	< 0.01
96671917	18229	T > A	Intron		rs17884938	0.06	0.03	0.05	0.07	0.00	0.10	0	0	0.05
96671942	18254	T > C	Intron		Novel	0.03	0.03	0	0	0	0	0	0	0.01
96672506	18818	T > C	Intron	Pre-miRNA (has-mir-139)	Novel	0	0.03	0	0	0	0	0	0	< 0.01
96672599	18911	A > G	Intron		rs7088784	0.05	0.08	0.15	0.14	0.15	0.17	0.17	0.25	0.13
96672764	19076	T > C	Intron	Splice site	Novel	0	0	0	0	0	0.03	0	0	< 0.01
96672842	19154	G > A	Exon 5	P227P (*2)	rs4244285	0.13	0.15	0.33	0.07	0.08	0.23	0.17	0.15	0.15
96673020	19332	G > A	Intron	Pre-miRNA (has-mir-448)	Novel	0	0	0	0	0.08	0	0	0	< 0.01
96711141	57453	G > C	Intron		Novel	0	0	0.04	0.03	0	0.03	0	0	0.02
96711200	57512	A > G	Intron		Novel	0.03	0.05	0.08	0.03	0.04	0	0	0.05	0.04
96711255	57567	A > T	Intron		Novel	0	0	0.04	0.03	0	0.07	0.11	0.10	0.04
96711263	57575	T > C	Intron		Novel	0	0	0.04	0.03	0	0.03	0	0	0.02
96711325	57637	wt > delG	Intron		Novel	0.03	0.05	0.08	0.07	0.08	0.10	0.00	0.10	0.06
96711366	57678	T > G	Intron		rs28399511	0	0	0	0	0.04	0	0	0	< 0.01
96711428	57740	G > C	Intron		rs4417205	0.14	0.15	0.21	0.09	0.13	0.23	0.22	0.20	0.15
96711677	57989	G > C	Intron		Novel	0	0	0	0.02	0	0.1	0	0	0.02
96733848	80160	C > T	Exon 7	V330V	rs3758580	0.12	0.18	0.25	0.07	0.08	0.17	0.17	0.15	0.13
96733849	80161	G > A	Exon 7	V331I	rs3758581	0.03	0.03	0	0	0.04	0	0	0	0.01
96734317	80629	T > A	Intron		Novel	0.03	0.05	0	0	0.05	0	0	0	0.01
96740794	87106	T > C	Intron		rs4917623	0.38	0.13	0.21	0.31	0.23	0.03	0.06	0.15	0.22
96740978	87290	T > C	Exon 8	R410C (*13)	rs17879685	0	0	0.04	0.03	0	0.03	0	0	0.02
96741001	87313	A > C	Exon 8	G417G	rs17886522	0.03	0.05	0.08	0.07	0.04	0.10	0	0	0.06
96741110	87422	A > G	Intron		Novel	0.03	0	0	0	0.08	0	0	0	0.02
96741163	87475	G > C	Intron		rs17880188	0.08	0.13	0	0.07	0.04	0.11	0.06	0	0.07
96741210	87522	C > T	Intron		rs17885567	0.05	0.08	0.21	0.10	0.08	0.13	0.11	0.10	0.1
96743266	89578	T > A	Intron		rs12779363	0	0	0.06	0.04	0	0.03	0	0	0.01
96743597	89909	C > T	Intron		rs12268020	0.22	0.31	0.17	0.09	0.17	0.20	0.17	0.20	0.19
96741001	90011	A > G	Intron	Splice site	rs4451645	0.13	0.14	0	0.07	0.04	0.13	0.11	0	0.08
96743897	90209	A > C	Exon 9	X491C; 26 extra aa (*12)	nrs	0	0	0	0.04	0	0.03	0	0	0.01
96743989	90301	C > T	3' UTR		Novel	0.01	0	0	0	0	0	0	0	< 0.01
96743990	90302	C > T	3' UTR		Novel	0	0	0	0.04	0	0.03	0	0	0.01
96744221	90533	C > T	3' UTR		Novel	0	0	0.05	0.04	0	0.04	0	0	0.02

mRNA position = relative to A of ATG start codon; wt = wild type; del = deletion; ins = insertion; UTR = untranslated region; pre-miRNA = introduction of a pre-miRNA sequence; X = stop codon; aa = amino acid; (*) = described alleles carrying that particular mutation; nrs = rs number not yet assigned; nd = not determined. Number of individual samples studied per population is indicated in bold in parenthesis.

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ISSN: 1479-7364

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