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Silent mutations, also called synonymous or samesense mutations, are mutations in DNA that do not have an observable effect on the organism's phenotype. The phrase silent mutation is often used interchangeably with the phrase synonymous mutation ; however, synonymous mutations are not always silent, nor vice versa.
A synonymous mutation can affect transcription, splicing, mRNA transport, and translation, any of which could alter the resulting phenotype, rendering the synonymous mutation non-silent. [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. [1]
Not all missense mutations lead to appreciable protein changes. An amino acid may be replaced by an amino acid of very similar chemical properties, in which case, the protein may still function normally; this is termed a neutral, "quiet", "silent" or conservative mutation.
These are both examples of a non-conservative (missense) mutation. Silent mutations code for the same amino acid (a "synonymous substitution"). A silent mutation does not affect the functioning of the protein. A single nucleotide can change, but the new codon specifies the same amino acid, resulting in an unmutated protein.
A nonsynonymous substitution is a nucleotide mutation that alters the amino acid sequence of a protein.Nonsynonymous substitutions differ from synonymous substitutions, which do not alter amino acid sequences and are (sometimes) silent mutations.
Many mutations are silent mutations, causing no visible effects at all, either because they occur in non-coding or non-functional sequences, or they do not change the amino-acid sequence due to the redundancy of codons. [33] Some mutagens can cause aneuploidy and change the number of chromosomes in the cell. They are known as aneuploidogens. [34]
A nucleotide substitution at a 4-fold degenerate site is always a synonymous mutation with no change on the amino acid. [2]: 521–522 A less degenerate site would produce a nonsynonymous mutation on some of the substitutions. An example (and the only) 3-fold degenerate site is the third position of an isoleucine codon.
For example, the effect of a nonsense mutation depends on the proximity of the nonsense mutation to the original stop codon, and the degree to which functional subdomains of the protein are affected. [3] As nonsense mutations leads to premature termination of polypeptide chains; they are also called chain termination mutations. [4]