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 S3 CYP2D6 single nucleotide polymorphism (SNP) frequencies

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

M33388	mRNA position	SNP	mRNA feature	Effect	dbSNP	Hausa (20)	Yoruba (20)	Ibo (20)	Luo (29)	Maasai (13)	Shona (15)	Venda (9)	TZ Bantu (10)	Total (136)
1444	-175	G > A	5' UTR		rs1080993	0.05	0.12	0.31	0.22	0.05	0.11	0.06	0.30	0.17
1469	-150	C > T	5' UTR		nrs	0.09	0.03	0	0	0	0	0	0	0.01
1534	-85	T > C	5' UTR		nrs	0.04	0	0	0	0	0.03	0	0	0.01
1577	-42	wt > insG	5' UTR		rs28371695	0.19	0.35	0.13	0.21	0.05	0.20	0.13	0.10	0.19
1696	77	G > A	Exon 1	R26H (*43)	rs28371696	0.04	0	0.03	0	0	0.03	0	0.05	0.02
1701	82	C > T	Exon 1	R28C (*22)	nrs	0	0	0	0	0	0	0	0.05	< 0.01
1719	100	C > T	Exon 1	P34S (*10)	rs1065852	0.15	0.12	0.10	0.09	0.05	0	0.19	0.10	0.10
1833	214	G > C	Intron		rs1080995	0.50	0.41	0.27	0.36	0.45	0.57	0.17	0.43	0.38
1840	221	C > A	Intron		rs1080996	0.50	0.41	0.27	0.38	0.45	0.64	0.30	0.43	0.40
1842	223	C > G	Intron		rs1080997	0.50	0.41	0.27	0.36	0.45	0.56	0.20	0.38	0.38
1846	227	T > C	Intron		rs1080998	0.50	0.41	0.27	0.36	0.45	0.50	0.25	0.50	0.38
1851	232	G > C	Intron		rs1080999	0.50	0.41	0.30	0.36	0.50	0.70	0.25	0.75	0.42
1852	233	A > C	Intron		rs1080999	0.50	0.41	0.27	0.38	0.45	0.67	0.25	0.50	0.40
1864	245	A > G	Intron		rs1081000	0.50	0.41	0.27	0.31	0.45	0.70	0.25	0.67	0.39
1929	310	G > T	Intron		rs28371699	0	0.27	0.07	0.25	0.31	0.25	0	nd	0.18
2273	654	C > T	Intron		Novel	nd	0	0	0.07	nd	0.08	0.07	0.07	0.07
2365	746	C > G	Intron		nrs	nd	nd	nd	0.36	nd	0.40	0.31	0.50	0.40
2462	843	T > G	Intron		rs28371702	0.14	0.40	0.20	0.33	0.38	0.33	0.13	0.20	0.29
2625	1006	C > T	Exon 2	R101R	Novel	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.05	0.01
2642	1023	C > T	Exon 2	T107I (*17)	rs28371706	0.20	0.20	0.22	0.22	0.17	0.20	0.19	0.15	0.20
2658	1039	C > T	Exon 2	F112F	rs1081003	0.00	0.13	0.13	0.04	0.00	0.00	0.13	0.05	0.06
2686	1067	T > G	Intron		Novel	0.13	0.13	0.19	0.04	0.08	0.07	0.19	0.10	0.11
3227	1608	G > A	Exon 3	V119M (*70)	Novel	0	0	0	0.02	0	0	0	0	< 0.01
3240	1621	G > T	Exon 3	R123L	Novel	0	0	0	0	0	0	0	0.05	< 0.01
3278	1659	G > A	Exon 3	V136M (*29)	rs1058164	0.11	0.10	0.28	0.24	0.04	0.17	0.06	0.25	0.17
3280	1661	G > C	Exon 3	V136V	rs28371708	0.29	0.43	0.35	0.32	0.46	0.37	0.33	0.30	0.35
3335	1716	G > A	Exon 3	E155K (*45)	rs28371710	0.08	0	0	0.09	0.04	0	0.17	0	0.05
3465	1846	G > A	Intron	Splicing defect (*4)	nrs	0.03	0.08	0.08	0.04	0.04	0.00	0.00	0.05	0.04
3483	1863_1864	ins (TTTCGC CCC)X2	Exon 4	174_175ins(FRP)X2	nrs	0	0	0	0.04	0.08	0	0	0	0.02
3485	1866	C > T	Exon 4	N175N	nrs	0	0	0	0.02	0.00	0	0	0	< 0.01
3488	1869	T > C	Exon 4	G176G	nrs	0	0.03	0	0.00	0.00	0	0	0	< 0.01
3617	1998	T > C	Exon 4	F219F	novel	nd	nd	0	0.00	nd	0.03	0	0.05	0.02
4194	2575	C > A	Exon 5	P267P	nrs	nd	nd	nd	0.05	nd	0.03	0.22	0	0.07
4221	2602	G > T	Exon 5	L276L	novel	nd	nd	nd	0.05	nd	0	0.06	0	0.02
4280	2661	G > A	Intron		nrs	nd	nd	nd	0.05	nd	0.03	0.11	0.05	0.06
4379	2760	T > A	Intron		Novel	nd	nd	nd	0.00	nd	0.10	0.06	0	0.04
4469	2850	C > T	Exon 6	R296C (*2)	nrs	nd	nd	nd	0.55	nd	0.63	0.44	0.65	0.58
4607	2988	G > A	Intron		nrs	nd	nd	nd	0.00	nd	0.03	0	0	0.01
4802	3183	G > A	Exon 7	V338M (*29)	nrs	0.13	0.10	0.29	0.20	0.04	0.17	0.06	0.13	0.16
4873	3254	T > C	Exon 7	H361H	rs2743457	0.09	0.00	0.00	0.07	0.08	0	0.13	0	0.04
4880	3259_3260	wt > insTG	Exon 7	375 fs (*42)	nrs	0	0	0	0	0	0.03	0	0	< 0.01
5003	3384	A > C	Intron		nrs	0.30	0.45	0.34	0.28	0.42	0.37	0.25	0.38	0.65
5016	3397	C > A	Intron		novel	0	0	0	0	0	0	0.06	0	< 0.01
5180	3561	G > C	Intron		novel	0	0	0	0.02	0	0	0.06	0.06	0.01
5201	3582	A > G	Intron		nrs	0.08	0.11	0.11	0.09	0.04	0.00	0.13	0.00	0.08
5203	3584	G > A	Intron		nrs	0.54	0.34	0.26	0.43	0.46	0.47	0.44	0.44	0.41
5326	3707	G > A	Intron		nrs	0	0	0.03	0	0	0.03	0	0	0.01
5349	3721	wt > delGT	Intron		nrs	0	0.03	0	0	0	0	0	0	< 0.01
5409	3790	C > T	Intron	Splice site	nrs	0.53	0.34	0.26	0.44	0.54	0.47	0.44	0.44	0.42
5472	3853	G > A	Exon 8	E410K (*27)	nrs	0	0	0	0.06	0.04	0	0	0.06	0.02
5652	4033	C > T	Intron	Splice site	Novel	0	0	0	0.02	0	0	0.06	0.06	0.01
5676	4057	G > A	Exon 9	G445E	Novel	0	0	0	0.04	0	0	0	0	0.01
5799	4180	G > C	Exon 9	S486T	rs1135850	0.68	0.55	0.66	0.72	0.63	0.63	0.75	0.67	0.66
6013	4394	wt > delAG	3' UTR		Novel	0	0	0	0	0	0.10	0.06	0	0.02
6020	4401	C > T	3' UTR		nrs	0.09	0.10	0.11	0.07	0.04	0	0.25	0.06	0.08
6100	4481	G > A	3' UTR		nrs	0.12	0.08	0.03	0.11	0.21	0.23	0.07	0.19	0.12
6275	4656	wt > delACA	3' UTR		nrs	0.44	0.09	0.03	0.23	0.31	0.08	0.33	0.33	0.20
6341	4722	T > G	3' UTR		nrs	0.63	0.57	0.73	0.57	nd	nd	nd	0.25	0.58

mRNA position = relative to A of ATG start codon; wt = wild type; del = deletion; ins = insertion; UTR = untranslated region; s = stop codon; (*) = described alleles carrying that particular mutation; fs = frame shift; aa = amino acid; 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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