Synonymous SNPs are not so synonymous

Early this week, an excellent paper by Brest, Darfeuille-Michaud, Hofman, et al. in Nature Genetics provides a prime example of going beyond genome-wide association studies (GWAS) to dissect the functional consequences of a genetic variant associated with disease risk. In so doing, the authors provide another case of synonynous SNPs not being so synonymous.

Here are what I find to be the key points of the research presented in this report:

1. The exonic SNP c.313C>T (rs10065172) is in perfect linkage disequilibrium (r²=1.0) with a deletion polymorphism of 20 kbp mapping upstream of the IRGM gene. This deletion has been strongly associated with Crohn's disease in several European populations or those with European ancestry. What is important here is a SNP can act as a tag or proxy for the deletion.

2. The c.313C>T variant alters codon 105 of the IRGM protein from CTG>TTG. Both codons call for leucine upon translation and so this SNP is classified as synonymous. The authors speculate that there could be allele-specific consequences to protein expression. Based on two other reports from other groups, the authors decided to investigate whether allele-specific interactions between the IRGM transcript and a microRNA could be at play here. They observed a predicted binding between microRNA-196 (or miR-196, both miR-196A encoded by A1 and A2 genes and by miR-196B) that was affected by the variation at SNP c.313C>T. Importantly, they show that not only is the miR-196-IRGM interaction real but that expression of miR-196 is elevated in inflammatory epithelia from Crohn's sufferers. These results underscore the point that synonymous SNPs are not so synonymous. The different alleles can exhibit different functions that have health consequences.

3. From GWAS to function. Although this paper does not report original results from GWAS, it builds on those results in an important way. There are four key papers reporting GWAS results for IRGM and Crohn's disease. These papers are by Parkes et al (2007), the Wellcome Trust Case Control Consortium (2007), Barrett et al (2008) and Franke et al (2010). So, in just over three years from the initial discovery of association of this once rather unremarkable gene (only 5 papers were published on IRGM prior to the initial GWAS report of 2007, most reporting a role in autophagy), we now have a much deeper understanding how a synonymous variant leads to the disease condition.

This is very nice work indeed and can be held up as an example of the success of GWAS in laying a foundation for getting at the mechanism of a disease.