Final answer:
A base substitution mutation can be silent and have no effect on the protein due to the mutation occurring in a non-coding region or resulting in a synonymous codon that does not change the amino acid in the protein.
Step-by-step explanation:
A base substitution mutation in a gene sometimes has no effect on the protein the gene codes for because of several possible reasons. One reason is that the mutation occurred in a non-coding region of the DNA which does not result in a change in the amino acid sequence of the protein. Another possibility is that the mutation results in a silent mutation where the new codon still codes for the same amino acid due to the redundancy of the genetic code. This means there is no change in the final protein.
A frameshift mutation is a different type of mutation that involves the insertion or deletion of nucleotides, not a base substitution, and would not result in a silent mutation. Instead, it typically causes a major change in the protein's amino acid sequence, potentially rendering the protein non-functional.
The misconception that a mutation always affects the protein or that it is in a vital gene region does not hold true for silent mutations. Although substitution mutations can potentially change an amino acid, causing significant changes in a protein's function or structure, a silent mutation does not alter the amino acid sequence and thereby has no impact on the protein's functionality.