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Several sources all caution that silent mutations and synonymous substitutions are not the same thing and should not be confused. But they seem to draw different actual distinctions between the terms:

  1. This Wikipedia page and this biology dictionary entry define a silent mutation as a point substitution that replaces a single codon by another codon that codes for the same amino acid, and therefore does not directly change the amino acid sequence that is coded for. It defines a synonymous substitution as a silent mutation that occurs in an exon. Under these definitions, a synonymous substitution is a special case of a silent mutation.
  2. This Wikipedia page and this blog post define a silent mutation as any mutation that does not have any phenotypic effects, and defines a synonymous substitution as a point substitution to a degenerate codon (anywhere in the genome, as far as I can tell). It points out that such synonymous substitutions can still have indirect phenotypic ("nonsilent") effects by affecting translation and transcription. Under these definitions, a silent mutation is a special case of a synonymous substitution (namely, one that doesn't have any indirect phenotypic effects).
  3. This Wikipedia page uses similar definitions to the one in #2, except it explicitly requires that a synonymous substitution occurs in an exon.

Clearly these definitions are not all compatible. (#2 and #3 are very similar and could perhaps be excused as minor variants on the same definition, but they clearly conflict strongly with #1 - they disagree on which of "silent mutation" and "synonymous substitution" is a special case of the other!) Is there a standardized distinction in the biology community between these terms, or is it just the case that everyone uses conflicting definitions and we should ask people to clarify the senses in which they're using these terms?

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Silent mutations are those which have no phenotypic effect and it seems important to note that these could occur in coding regions and non-coding regions alike. Synonymous mutations, on the other and, are confined to coding regions. Because these mutations, by definition, do not change the amino acid sequence, they are nominally silent. However, due to codon bias, etc.,, a synonymous mutation may not always be silent. Therefore, my non-authoritative opinion is that it is not entirely accurate to classify one as a subset of the other. All you can really say is that silent mutations have no phenotypic effect, and synonymous mutations can be silent or not.

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  • $\begingroup$ "Silent mutations are those which have no phenotypic effect".. the definition should have ideally been so. However, the existing definition pertains only to changes in amino acid sequences. In fact, you can have non-synonymous mutations that are "silent". $\endgroup$ – WYSIWYG Apr 23 '18 at 13:27
  • $\begingroup$ @WYSIWYG I seemed to remember, for some reason, that silent mutations need not necessarily refer to mutations in a coding sequence, but I struggled in vain to find more than a few papers that used it this way. Your answer certainly captures its actual usage better than mine. $\endgroup$ – canadianer Apr 23 '18 at 13:33
  • $\begingroup$ Your definition does make real sense but unfortunately the real definition is a bit obsolete. $\endgroup$ – WYSIWYG Apr 23 '18 at 13:34
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I would say that silent mutations, as they have been defined, are a subset (or perhaps even same as) of synonymous mutations. However, the term, "silent mutation", is not used so much these days. Almost every research paper that I have read pertaining to this topic has always used the term "synonymous mutation" irrespective of whether or not it has a phenotypic effect. It seems that the term, "silent mutation", is confined only to textbooks.

If you consider silent mutations are mutations that are not reflected in the phenotype then there some points that you should consider.

  • As canadianer mentioned, these mutations can be present in non-coding region. However, mutations in non-coding regions can also affect the phenotype. Moroever, as they mention, synonymous mutations can cause changes in translation rates because of the codon bias which in turn can lead to phenotypic differences (Kimchi-Sarfaty et al, 2007; Waldman et al, 2011; Buhr et al, 2016). These phenotypic differences can arise due to altered protein concentration or altered folding states. So a synonymous mutation is not essentially "silent"
  • A non-synonymous mutation may not affect the phenotype (neutral mutation).

I would say that this definition should not be used unless the majority of the scientific community agrees on redefining the term. Till then, you can possibly use the term, "neutral mutations", to mean mutations that do not affect the phenotype. Remember that neutrality of "neutral mutations" is defined with respect to fitness. However, if your measure of fitness pertains to the molecular function of the gene then this definition works.

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  • $\begingroup$ I don't understand your last paragraph, I thought that there's a standardized definition that "neutral mutation" only means neutral with respect to evolutionary fitness, not to phenotype. What do you mean "your measure of fitness pertains to the molecular function of the gene"? $\endgroup$ – tparker Apr 23 '18 at 13:46
  • $\begingroup$ @tparker Fitness is a relative term. If you are selecting for the molecular function of a gene, lets say an enzyme, then the enzyme activity is your fitness. Check this out. $\endgroup$ – WYSIWYG Apr 23 '18 at 13:53
  • $\begingroup$ Oh, I thought that "fitness" always refers to reproductive success. $\endgroup$ – tparker Apr 23 '18 at 13:56
  • $\begingroup$ @tparker Let's say in a lab you want to engineer an enzyme with high activity and you are selecting the E.coli cells that show high activity of this enzyme. In that case the fitness (under the selection) is proportional to enzyme activity (unless there are pleiotropic effects). In fact there are (many?) research articles that have used the term in the context of molecular phenotypes. $\endgroup$ – WYSIWYG Apr 23 '18 at 13:59
  • $\begingroup$ I meant to say that I thought that "fitness" always refers to reproductive success under natural selection. But I suppose that if you also include reproductive success under artificial selection, then indeed any trait (even normally "bad" ones) could improve fitness. $\endgroup$ – tparker Apr 23 '18 at 14:03
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But the following sites (Nature and Science) use the "silent mutation" as synonymous mutation.

https://www.nature.com/scitable/definition/silent-mutation-10 https://www.sciencemag.org/news/2006/12/sound-silent-mutation

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We're looking for long answers that provide some explanation and context. Don't just give a one-line answer; explain why your answer is right, ideally with citations. Answers that don't include explanations may be removed.

  • $\begingroup$ Please provide more ocntext in case your links go dead. If possible, please include the formal citations of each article you link as well as a quote or page number where you are pulling from. Thanks. $\endgroup$ – theforestecologist Apr 2 at 16:13

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