Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?
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
- Variation in Vertebrate Cis-Regulatory Elements in Evolution and Disease
- A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens
- A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig
- Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element [..]