I am currently working on the ADORA2a gene coding for the A2a adenosine receptor. The SNP rs5751876 is commonly found in the ADORA2a sequence. Even if this SNP leads to a synonymous mutation (tyrosine-tyrosine) it has been associated to syncopes and altered response to moderate level of caffeine. Could anyone suggest any bionformatic tools to evaluate the SNP putative effect on gene transcription and translation ?
Synonymous snp can affect transcription factor binding, thus affecting gene expression.
Also I came across a paper suggesting an important role of synonymous snp on the transcript , as it might affect splicing for example.
For the bioinformatics tools, you can find a collection here along with nice review of synonymous snp effects (including interesting aspects related to protein structure) . Article Predicting Functional Effects of Synonymous Variants: A Syst...
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Did not understand properly your question. However, you can check GWAS catalogue.
Thank you all really for your response. It was really very helpful for me.
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