Synonymous substitution

[3] The substrate specificity of the tRNA to the rare codon can affect the timing of translation, and in turn the co-translational folding of the protein.

Each of these amino acids is coded for by a sequence of three DNA base pairs called a codon.

When a synonymous or silent mutation occurs, the change is often assumed to be neutral, meaning that it does not affect the fitness of the individual carrying the new gene to survive and reproduce.

For example, when a handful of synonymous changes in the fruit fly alcohol dehydrogenase gene were introduced, changing several codons to sub-optimal synonyms, production of the encoded enzyme was reduced[7] and the adult flies showed lower ethanol tolerance.

[9] Another reason why synonymous changes are not always neutral is the fact that exon sequences close to exon-intron borders function as RNA splicing signals.