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Table 3 Genetic variants in the putative ALOX5 and TGFβ1 promoters.

From: Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission

Gene GenBank Accession no. Common SNPs in the 5' upstream promoter region SNPs found in this study
Arachidonate 5- Lipoxygenase (ALOX5) H51574 rs12762303: -557 T>C (Hoshiko et al, 1990)
-458 T>C (ensembl database)
Both identified in MS and control cohorts
   GGGCGG tandem repeat deletion:
Between -146 and -176 (Hoshiko et al,1990)
Between -48 and -78 (ensembl database)
 
Transforming growth factor beta-1 (TGFβ1) R364674 rs12977628: -18 C>A (Kim et al, 1989)
+181 C>A (ensembl database)
rs1800469 identified in MS and control cohorts
   rs17516265: -257 A>C (Kim et al, 1989)
-59 A>C (ensembl database)
 
   rs35318502: -315 C>T (Kim et al, 1989)
-117 C>T (ensembl database)
 
   rs35775330: -331 TT del (Kim et al, 1989)
-133 TT del (ensembl database)
 
   rs11466314: -448 G>A (Kim et al, 1989)
-250 G>A (ensembl database)
 
   rs1800469: -508 T>C (Kim et al, 1989)
-310 T>C (ensembl database)
 
  1. Sequencing of the 5' upstream promoter region of pooled genomic DNA confirmed the presence of two common genetic variants in the ALOX5 promoter: rs12762303 T>C and a 6 bp deletion of the tandem repeat sequence GGGCGG, in addition to a single common SNP in the TGFβ1 promoter: rs1800469 T>C. Common SNPs and their positions in the 5' promoter region are shown according to nucleotide numbering in the ensembl database and by the authors who first described the promoter regions for ALOX5 (Hoshiko et al, 1990) [66] and TGFβ1 (Kim et al, 1989) [48]. Pooled DNA sequencing only detects common polymorphisms (> 10–15% of sample) [30].