Final answer:
A silent mutation likely caused the substitution of one nucleotide without affecting the polypeptide, due to the redundancy of the genetic code that allows different codons to code for the same amino acid.
Step-by-step explanation:
If a geneticist found that a particular mutation had no effect on the polypeptide coded by a gene, this mutation likely involved a substitution of one nucleotide causing a silent mutation. A silent mutation occurs when a change in the nucleotide sequence results in a codon that still encodes the same amino acid due to the redundancy of the genetic code. Therefore, the protein's amino acid sequence remains unchanged and the mutation passes undetected unless DNA sequencing is conducted. In contrast, a substitution that results in a premature stop codon is a nonsense mutation and would have significant effects, typically resulting in a truncated, often nonfunctional protein.