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:
- 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.
- 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).
- 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?