Final answer:
The best explanation is that the substituted nucleotide produces codons that correspond to the same amino acid found in other mice, resulting in no change to the mouse's phenotype.
Step-by-step explanation:
The best explanation for why a nucleotide substitution in the mouse does not change its phenotype is Option 3: The substituted nucleotide produces codons that correspond to the same amino acid that is found in the other mice. Genotype refers to the genetic makeup of an organism, while phenotype refers to the observable traits of an organism. In this case, the nucleotide substitution does not result in a change in amino acid sequence, which means that the protein produced by the gene remains the same. Since phenotypic traits are determined by proteins, the mouse's phenotype will not be affected.