Silent mutations are DNA mutations 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 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 (i.e. a synonymous substitution), or result in the insertion of an alternative amino acid with similar properties to that of the original amino acid, and 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 tranport, 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 (i.e. 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. 
Silent mutations and the genetic code
Most amino acids are specified by multiple codons demonstrating that the genetic code is degenerate. Codons that code for the same amino acid are termed synonyms. Silent mutations are base substitutions that result in no change of the amino acid or amino acid functionality when the altered messenger RNA (mRNA) is translated. For example, if the codon AAA is altered to become AAG, the same amino acid--lysine--will be incorporated into the peptide chain. Silent mutations can also be produced by insertions or deletions, which cause a shift in the reading frame. An example of this is shown with modification to the sequence AUGAAAGAGACGU. If a deletion occurred at the sixth position, the sequence would be converted to AUGAAGAGACGU. If the reading frame begins at the first position of the peptide chain, in either sequence given, the amino acid following the start codon AUG would be lysine. Such frameshift mutations can lead to deleterious effects on the peptide chain, including insertion of different amino acids or premature truncation of the protein. 
Because silent mutations do not alter protein function they are often treated as though they are evolutionarily neutral. Many organisms are known to exhibit codon usage biases, suggesting that there is selection for the use of particular codons due to the need for translational stability. Transfer RNA (tRNA) availability is one of the reasons that silent mutations might not be as silent as conventionally believed. 
There is a different tRNA molecule for each codon. For example, there is a specific tRNA molecule for the codon UCU and another specific for the codon UCC, both of which code for the amino acid serine. In this instance, if there was a thousand times less UCC tRNA than UCU tRNA, then the incorporation of serine into a polypeptide chain would happen a thousand times more slowly when a mutation causes the codon to change from UCU to UCC. If amino acid transport to the ribosome is delayed, translation will be carried out at a much slower rate. This can result in lower expression of a particular gene containing that silent mutation if the mutation occurs within an exon. Additionally, if the ribosome has to wait too long to receive the amino acid, the ribosome could terminate translation prematurely. 
Structural consequences of silent mutations
I. Primary structure
A nonsynonymous mutation that occurs at the genomic or transcriptional levels is one that results in an alteration to the amino acid sequence in the protein product. A protein’s primary structure refers to its amino acid sequence. A substitution of one amino acid for another can impair protein function and structure, or its effects may be minimal or tolerated depending on how closely the properties of the amino acids involved in the swap correlate. The premature insertion of a stop codon, a nonsense mutation, can alter the primary structure of a protein. In this case, a truncated protein is produced. Protein function and folding is dependent on the position in which the stop codon was inserted and the amount and composition of the sequence lost.
Conversely, silent mutations are mutations in which the amino acid sequence is not altered. Silent mutations lead to a change of one of the letters in the triplet code that represents a codon, but despite the single base change, the amino acid that is coded for remains unchanged or similar in biochemical properties. This is permitted by the degeneracy of the genetic code.
Historically, silent mutations were thought to be of little to no significance. However, recent research suggests that such alterations to the triplet code do effect protein translation efficiency and protein folding and function.
II. Secondary structure
Silent mutations alter the secondary structure of mRNA. mRNA has a secondary structure that is not necessarily linear like that of DNA, thus the shape that accompanies complementary bonding in the structure can have significant effects. For example, if the mRNA molecule is relatively unstable, then it can be rapidly degraded by enzymes in the cytoplasm. If the RNA molecule is highly stable, and the complementary bonds are strong and resistant to unpacking prior to translation, then the gene may be underexpressed. Codon usage influences mRNA stability.
If the oncoming ribosome pauses because of a knot in the RNA, then the polypeptide could potentially have enough time to fold into a non-native structure before the tRNA molecule can add another amino acid. Silent mutations may also affect splicing, or transcriptional control.
III. Tertiary structure
Silent mutations affect protein folding and function. Recent research suggests that silent mutations can have an effect on subsequent protein structure and activity. The timing and rate of protein folding can be altered, which can lead to functional impairments.
Research and clinical applications
Silent mutations have been employed as an experimental strategy and can have clinical implications.
Steffen Mueller at the Stony Brook University designed a live virus vaccine for polio in which the pathogen was engineered to have synonymous codons replace naturally-occurring ones in the genome. As a result, the virus was still able to infect and reproduce, albeit more slowly. Mice that were vaccinated with this vaccine and exhibited resistance against the natural polio strain.
Mental disorders can be caused by silent mutations. One silent mutation causes the dopamine receptor D2 gene to be less stable and degrade faster, underexpressing the gene.
A silent mutation in the multidrug resistance gene 1 (MDR1), which codes for a cellular membrane pump that expels drugs from the cell, can slow down translation in a specific location to allow the peptide chain to bend into an unusual conformation. Thus, the mutant pump is less functional.
Deviations from average pain sensitivity (APS) are caused by both an ATG to GTG mutation (nonsynonymous), and a CAT to CAC mutation (synonymous). Ironically, these two mutations are both shared by the Low pain sensitivity (LPS) and High pain sensitivity (HPS) gene. LPS has an additional CTC to CTG silent mutation, while HPS does not and shares the CTC sequence at this location with APS 
- Degeneracy of the genetic code
- Genealogical DNA test
- Missense mutation
- Nonsense mutation
- Point mutation
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- Overview article in Scientific American
- An online tool for silent mutagenesis
- Mueller lab - recoding viral genomes through silent mutagnesis