Silent mutations are
mutations in
DNA that do not significantly alter the
phenotype of the organism in which they occur. Silent mutations can occur in
non-coding regions (outside of
genes or within
introns), or they may occur within
exons. When they occur within exons they either do not result in a change to the
amino acid sequence of a
protein (a "
synonymous substitution"), or result in the insertion of an alternative amino acid with similar properties to that of the original amino acid; in either case there is no significant change in
phenotype. The phrase
silent mutation is often used interchangeably with the phrase
synonymous mutation; however, synonymous mutations only occur within exons, and are not always silent mutations. Synonymous mutations can affect
transcription,
splicing,
mRNA transport, and
translation, any of which could alter phenotype, rendering the synonymous mutation non-silent. 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. This is reflected in the
codon usage bias that is observed in many species. Mutations that cause the altered codon to produce an amino acid with similar functionality (
e.g. a mutation producing
leucine instead of
isoleucine) are often classified as silent; if the properties of the amino acid are conserved, this mutation does not usually significantly affect protein function.