ABCMdb

PMID: 17404718

King CR, Xiao M, Yu J, Minton MR, Addleman NJ, Van Booven DJ, Kwok PY, McLeod HL, Marsh S
Identification of NR1I2 genetic variation using resequencing.
Eur J Clin Pharmacol. 2007 Jun;63(6):547-54. Epub 2007 Apr 3., [PubMed]

Sentences

No. Mutations Sentence Comment

96 ABCB1 p.Pro66Ser ABCB1 p.Pro66Ser ABCB1 p.Pro66Ser ABCB1 p.Pro66Ser Table 2 Validated NR1I2 allele frequencies NR1I2 -2098 C>T NR1I2 -566 A>C NR1I2 -205[GAGAAG] NRI12 IVS2+55 A>G NR1I2 IVS2+78 A>G NR1I2 IVS6-17 C>T NR1I2 +1792 A>G European African European African European African European African European African European African European African n 89 94 82 94 77 82 75 92 89 94 92 92 95 89 Wt 31 80 28 74 27 42 39 88 40 55 65 31 64 45 Het 48 14 43 20 40 27 30 4 30 34 25 49 29 36 Var 10 0 11 0 10 13 6 0 19 5 2 12 2 8 p c-0.62 c-0.07 a-0.60 a-0.11 [+] 0.61 [+] 0.68 a-0.72 a-0.02 a-0.62 a-0.23 c-0.84 c-0.60 a-0.83 a-0.29 q t-0.38 t-0.93 c-0.40 c-0.89 [-] 0.39 [-] 0.32 g-0.28 g-0.98 g-0.38 g-0.77 t-0.16 t-0.40 g-0.17 g-0.71 n Number of subjects, wt wild type, het heterozygote, var variant, p wild-type allele frequency, q variant allele frequency, [+] presence of indel, [-] absence of indel Table 3 Genetic variants in NR1I2 with allele frequencies above 10% Allele frequency SNP location [alternative name] SNP Source African American European Asian -3151 C/T Resequencing 0.16 T 0.0 T 0.0 T -2797 T/C Resequencing 0.43 C 0.0 C 0.0 C -2098 T/C Resequencing 0.28 C 0.70 C 0.67 C -1997 G/A Resequencing 0.16 A 0.0 A 0.01 A -1570 [-25385] C/T [34] 0.32 T 0.39 T N/E -1570 [-25385] C/T [4] N/E 0.36 T N/E -1570 C/T Resequencing 0.34 T 0.50 T 0.21 T -941[-24756] G/A [34] 0.14 A 0.01 A N/E -941[-24756] G/A [4] N/E 0.01 A N/E -941 G/A Resequencing 0.13 A 0.0 A 0.0 A -566 [-24381] A/C [34] 0.73 C 0.41 C N/E -566 [-24381] A/C [4] N/E 0.54 C N/E -566 A/C Resequencing 0.50 C 0.69 C 0.33 C -298 [-24113] G/A [34] 0.32 A 0.39 A N/E -298 G/A Resequencing 0.32 A 0.41 A 0.28 A -205 [-206 DEL] -/GAGAAG [29] N/E N/E 0.72 GAGAAG IVS1-20 [-42] T/C [34] 0.23 C 0.0 C N/E IVS1-20 T/C Resequencing 0.10 C 0.0 C 0.063 C 196 [PXR*2; P66S] C/T [34] 0.20 T 0.0 T N/E 196 [PXR*2; P66S] C/T Resequencing 0.03 T 0.0 T 0.0 T 196 [PXR*2; P66S] C/T [13] 0.15 Ta 0.0 T N/E 196 [PXR*2; P66S] C/T [4] N/E 0.0 T N/E IVS2+55 [+252] A/G [34] 0.64 G 0.28 G N/E IVS2+55 [+252] A/G [4] N/E 0.34 G N/E IVS2+55 A/G Resequencing 0.76 G 0.25 G 0.40 G IVS2+78 A/G Resequencing 0.77 G 0.28 G 0.34 G IVS2+78 [+275] A/G [4] N/E 0.34 G N/E IVS4+285 [+4760] G/A [4] N/E 0.69 A N/E IVS5-93 [+7635] A/G [34] 0.77 G 0.35 G N/E IVS5-93 [+7635] A/G [4] N/E 0.32 G N/E IVS5-93 A/G Resequencing 0.80 G 0.33 G 0.48 G IVS5-53 [+7675] C/T [34] 0.05 T 0.04 T N/E IVS5-53 [+7675] C/T [4] N/E 0.05 T N/E IVS5-53 C/T Resequencing 0.25 T 0.0 T 0.0 T IVS6-17 [+8055] C/T [34] 0.18 T 0.15 T N/E IVS6-17 [+8055] C/T [4] N/E 0.16 T N/E IVS6-17 C/T Resequencing 0.20 T 0.39 T 0.51 T 1437 [+9976] G/A [34] 0.36 A 0.0 A N/E 1437 G/A Resequencing 0.05 A 0.0 A 0.02 A 1792 A/G Resequencing 0.69 G 0.33G 0.59 G 1792 [+10331] A/G [4] N/E 0.20 G N/E 1922 C/A Resequencing 0.06 A 0.0 A 0.10 A 1922 [+10461] C/A [4] N/E 0.12 A N/E 1944 T/C Resequencing 0.69 C 0.23 C 0.65 C 1944 [+10483] T/C [4] N/E 0.24 C N/E 2081 [+10620] C/T [34] 0.14 T 0.11 T N/E 2081 [+10620] C/T [4] N/E 0.08 T N/E 2081 C/T Resequencing 0.03 T 0.01 T 0.0 T 2180 [+10719] A/G [34] 0.0 G 0.05 G N/E 2180 [+10719] A/G [4] N/E 0.05 G N/E 2180 A/G Resequencing 0.18 G 0.0 G 0.0 G 2260 [+10799] G/A [34] 0.14 A 0.13 A N/E 2260 [+10799] G/A [4] N/E 0.12 A N/E 2260 G/A Resequencing 0.06 A 0.05 A 0.0 A 2617 [+11156] A/C [34] 0.33 C 0.16 C N/E 2617 A/C Resequencing 0.43 C 0.09 C 0.50 C 2654 [+11193] T/C [34] 0.30 C 0.16 C N/E 2654 T/C Resequencing 0.54 C 0.14 C 0.53 C 3104 G/A Resequencing 0.24 A 0.0A 0.06 A Previously published naming is included in brackets in the SNP location column [4, 13, 29, 34]. Login to comment 109 ABCB1 p.Pro66Ser Only one of the six SNPs, P66S, had an allele frequency above 10% in the African population alone. Login to comment 110 ABCB1 p.Pro66Ser ABCB1 p.Val179Met P66S was not found to alter basal CYP3A4 and/or induce its transactivation (as were V179M, D202G, and A409T) [13]. Login to comment 111 ABCB1 p.Pro66Ser ABCB1 p.Val179Met Of the six polymorphisms examined, four were found to be specific to the African population (E57K, P66S, D202G, and A409T), and two were specific to the European population (G75R and V179M) [13]. Login to comment 112 ABCB1 p.Pro66Ser Two of these six polymorphisms were found through resequencing in the current study (P66S and G75R). Login to comment 113 ABCB1 p.Pro66Ser P66S was monomorphic in European and Asian populations, however allele frequencies of 0.20 T, 0.15 T, and 0.03 T were found in African and African American populations by Zhang et al [34], Hustert et al. [13], and resequencing, respectively. Login to comment