Abstract: An invention is described which provides a diagnostic approach for diseases, such as HNPCC, that are associated with defects in MMR and provides a method for determining whether any specific genetic sequence of a gene associated with MMR that differs from a consensus sequence is a mutation (i.e., encodes a non-functional protein), a silent polymorphism (i.e., encodes a protein with normal protein function) or an efficiency polymorphism (i.e., encodes a protein with reduced efficiency in MMR). The invention allows the generation of databases of the functional significance of specific amino acid replacements on MMR protein function in vivo, which in turn will allow accurate and unambiguous interpretation of genetic tests of MMR.