A substitution is a mutation in which there is an exchange between two bases (i.e. a change in a single "chemical letter" such as switching a T to a C). Such a substitution could change a codon to one that encodes a different amino acid and cause a change in the protein produced.
Sometimes substitutions may not effects the protein structure, such mutations are called silent mutations and sometimes they may change an amino-acid-coding codon to a single "stop" codon and cause an incomplete protein. This can seriously affect the protein structure which may completely change the organism


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