If a metabolic gene has a synonymous mutation on it, what can that mean?
Here are some hypotheses, please add to it if you think of any-
1. It affects RNA stability and degradation
2. It affects translation rates with rare codon usage
3 .......
A synonymous mutation has no effect at all if it affects non coding regions of DNA.
If it is located in an exon, usually it has no effects on the final product of the gene.
But there are exceptions. For these exceptions read:
Goymer, Patrick (February 2007). "Synonymous mutations break their silence". Nature Reviews Genetics. 8 (2): 92. doi:10.1038/nrg2056.
Synonymous mutations — sometimes called 'silent' mutations — are now widely acknowledged to be able to cause changes in protein expression, conformation and function. The recent increase in knowledge about the association of genetic variants with disease, particularly through genome-wide association studies, has revealed a substantial contribution of synonymous SNPs to human disease risk and other complex traits.
http://www.nature.com/nrg/journal/v12/n10/full/nrg3051.html
ynanonymous mutations can create new binding sites for transcription factors and other DNA BP, and hence affect the expression of other genes.
If the synanmous mutation is transcribed, (90%) of the genome is transcribed, it can also affect the binding of ncRNA and miRNA by similarly acting as RNA sponges.
Lots of Synanymous mutations can create homology between sequences and can result in recombination and chromosomal translocation between duplicated or similar (pseudo)gene , or alleles on different chromosomes.
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