Altering nucleotide sequences most often results in nonfunctioning proteins. Mutations cause changes in the genetic code that lead to genetic variation and the potential to develop disease. Gene mutations can be generally categorized into two types: point mutations and base-pair insertions or deletions.Point mutations are the most common type of gene mutation. Also called a base-pair substitution, this type of mutation changes a single nucleotide base pair. Silent Mutation: Although a change in the DNA sequence occurs, this type of mutation does not change the protein that is to be produced. 2  This is because multiple genetic codons can encode for the same amino acid. 3  Amino acids are coded for by three nucleotide sets called codons.