dna - Effect of mutation on phenotype

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

Answer

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