The new nucleotide alters the codon to create an altered amino acid in the protein referred as missense mutation. However, they do not have an effect on the phenotype of the organism if the additional amino acid is in a non-critical region of the protein or having comparable chemical properties to the previous amino acid. But, sometimes the new amino acids can possess remarkable results like protein folding, protein targeting or post-translational modifications if the substitution takes place in an essential area of the protein.
When an amino acid substitution takes place in the active site of an enzyme or an important area for the structure of protein, the changes are significant. In some situations, the mutation can direct to a new or enhanced function in the protein, but usually the results are unfavourable.