Editing Silent mutation (section)

{{Short description|DNA mutation with no observable effect on an organism's phenotype}}
[[File:Point mutations-en.png|thumb|350px|Point substitution mutations of a codon, classified by their impact on protein sequence]]
'''Silent mutations''', also called synonymous or samesense mutations, are [[mutation]]s 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.<ref name="pmid17185560">{{cite journal | vauthors = Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM | title = A "silent" polymorphism in the MDR1 gene changes substrate specificity | journal = Science | volume = 315 | issue = 5811 | pages = 525–8 | date = January 2007 | pmid = 17185560 | doi = 10.1126/science.1135308 | bibcode = 2007Sci...315..525K | s2cid = 15146955 | url = https://zenodo.org/record/1230874 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Chamary JV, Parmley JL, Hurst LD | title = Hearing silence: non-neutral evolution at synonymous sites in mammals | journal = Nature Reviews. Genetics | volume = 7 | issue = 2 | pages = 98–108 | date = February 2006 | pmid = 16418745 | doi = 10.1038/nrg1770 | s2cid = 25713689 }}</ref><ref name=Goymer2007>{{cite journal |last=Goymer |first=Patrick | name-list-style = vanc |title=Synonymous mutations break their silence |journal=Nature Reviews Genetics |date=February 2007 |volume=8 |issue=2 |page=92 |doi=10.1038/nrg2056|s2cid=29882152 |doi-access=free }}</ref><ref>{{cite journal | vauthors = Zhou T, Ko EA, Gu W, Lim I, Bang H, Ko JH | title = Non-silent story on synonymous sites in voltage-gated ion channel genes | journal = PLOS ONE | volume = 7 | issue = 10 | pages = e48541 | date = 31 October 2012 | pmid = 23119053 | pmc = 3485311 | doi = 10.1371/journal.pone.0048541 | bibcode = 2012PLoSO...748541Z | doi-access = free }}</ref><ref>{{cite book |last=Graur |first=Dan | name-list-style = vanc |chapter=Single Base Mutation |chapter-url=http://nsmn1.uh.edu/dgraur/ArticlesPDFs/encyclopediahumangenome93.pdf |publisher=MacMillan |title=Nature Encyclopedia of the Human Genome |isbn=978-0333803868 |year=2003 |editor-first=David N. |editor-last=Cooper }}</ref> Synonymous mutations can affect [[Transcription (genetics)|transcription]], [[Splicing (genetics)|splicing]], [[mRNA]] transport, and [[Translation (biology)|translation]], any of which could alter phenotype, rendering the synonymous mutation non-silent.<ref name=Goymer2007 /> The substrate specificity of the [[tRNA]] to the rare [[Genetic_code#Codons|codon]] can affect the timing of translation, and in turn the co-translational folding of the protein.<ref name="pmid17185560"/> 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.<ref name=mboc>{{cite book |first1=Bruce |last1=Alberts |first2=Alexander |last2=Johnson |first3=Julian |last3=Lewis |first4=Martin |last4=Raff |first5=Keith |last5=Roberts |first6=Peter |last6=Walter | name-list-style = vanc |title=Molecular Biology of the Cell |url=https://books.google.com/books?id=DjMmAgAAQBAJ&pg=PA264 |year=2007 |publisher=Garland Science |isbn=978-1-136-84442-3 |page=264}}</ref>