ABCC2 p.Gln122Arg
| Predicted by SNAP2: | A: N (61%), C: N (66%), D: D (71%), E: N (66%), F: D (59%), G: N (61%), H: N (82%), I: N (72%), K: N (93%), L: N (82%), M: N (82%), N: N (82%), P: D (53%), R: N (93%), S: N (78%), T: N (72%), V: N (72%), W: D (59%), Y: N (61%), |
| Predicted by PROVEAN: | A: N, C: D, D: N, E: N, F: N, G: D, H: N, I: N, K: N, L: N, M: N, N: N, P: N, R: N, S: N, T: N, V: N, W: D, Y: N, |
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[hide] In silico search for single nucleotide polymorphis... IUBMB Life. 2004 Oct;56(10):615-20. Doring F, Rimbach G, Lodge JK
In silico search for single nucleotide polymorphisms in genes important in vitamin E homeostasis.
IUBMB Life. 2004 Oct;56(10):615-20., [PMID:15814460]
Abstract [show]
Large inter-individual variation exists in the response to vitamin E supplementation, and this may influence the outcome of human studies. It is our hypothesis that genetic heterogeneity is an important determinant of vitamin E homeostasis. Therefore we have performed an in silico search for single nucleotide polymorphisms (SNPs) associated with genes involved in vitamin E homeostasis. Based on function, the following genes were considered as candidates for vitamin E heterogeneity: c-tocopherol transfer protein (TTPA), tocopherol associated protein (TAP), lipoprotein lipase (LPL), multidrug resistance protein 2 (MDR-2), pregnane X receptor (PXR) and members of the cytochrome P450 family (CYP). Searches for coding SNPs were initiated from web based programs of the National Center for Biotechnology Information (NCBI). SNP frequencies were calculated by dividing the number of annotated coding SNPs by the number of base pairs in the open reading frame. Genes for TTPA, TAP and CYP3A5 had calculated SNP frequencies between 503 and 837 base pairs per coding SNP (bp/cSNP) and so are not highly polymorphic. In contrast, cSNP frequencies in LPL, MRP2, PXR, CYP3A4 and CYP4F2 were in the range of 100 bp/cSNP and so are highly polymorphic. Thus proteins involved in specific vitamin E binding are not highly polymorphic, may not influence inter-individual variation and so may not be good candidates for population studies. Proteins involved in drug/lipid metabolism which indirectly influence vitamin E status are highly polymorphic, are likely to influence inter-individual variation and so are good candidates for population studies. We suggest that future studies are aimed at addressing the role of such SNPs in vitamin E homeostasis.
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No. Sentence Comment
74 In addition, identified non-synonymous SNPs of TTPA (W3E), and CYP3A5 (T495R) Table 1 SNP frequencies and non-synonymous SNPs in candidate genes involved in vitamin E homeostasis gene geneID chromosome exonsa ASb bp/cSNPc cSNPd non-synonymous SNP [heterozygosity]e LPL 4032 8p22 10 476 119 12 T427A [0.03] TTPA 7274 8q13.1-q13.3 6 279 837 1 none (W3Ef ) TAP 23541 22q12.2 12 407 610 2 K11R [0.475] MRP2 1244 10q24 32 1546 122 38 P39Y [0.01], G333D [0.01], E495K [0.01], R849L [0.01], L1181D [0.07], E1188V [0.1] PXR 8856 3q12-q13.3 9 435 118 11 T12A [0.1], S27P [0.05], R36G [0.07], Q122R [0.01] CYP3A5 1577 7q21.1 13 503 503 3 none (T495Rf ) CYP3A4 1576 7q21.1 13 504 101 15 E96K [0.003], Q162R [0.02], H174D [0.02] CYP4F2 8529 19p13.11 12 521 82 19 G12W [0.268], D269A [0.288] a number of exons.
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ABCC2 p.Gln122Arg 15814460:74:583
status: NEW