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Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?

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Yes. It is actually the case of most mutations that affect the phenotype!

Only 1.5% of the human genome codes for proteins. About 5-10% of the human genome are regulatory sequences which do not produce any protein but greatly impact the phenotype by regulating the expression of coding sequences. A mutation in a regulatory sequence does not directly impact the protein sequence but can have drastic impact on the phenotype (and fitness).

There are a lot of such mutations that have been identified. Here are a few quick examples

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    $\begingroup$ Do you have a reference for the statement that most phenotypic changes are caused by mutations in regulatory sequences? And what is the definition of 'regulatory sequence' in the context of the 5-10% number? $\endgroup$
    – Alan Boyd
    Aug 10, 2017 at 11:00
  • $\begingroup$ @Remi - Nice answer. $\endgroup$ Aug 10, 2017 at 13:05
  • $\begingroup$ @AlanBoyd: Read the cired papers. For silky feathers, "The causative mutation is located 103 base pairs upstream of the coding sequence of prenyl (decaprenyl) diphosphate synthase, subunit 2" which is a regulatory protein. $\endgroup$ Aug 10, 2017 at 13:06
  • $\begingroup$ @anongoodnurse I wasn't really asking about specific examples - obviously these exist - I was asking for a supporting reference for the 'most mutations' statement. $\endgroup$
    – Alan Boyd
    Aug 10, 2017 at 13:09
  • $\begingroup$ @AlanBoyd - Ah, sorry. $\endgroup$ Aug 10, 2017 at 13:10

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