A substitution mutation, also known as a point mutation, involves the replacement of a single nucleotide in DNA or RNA, leading to potential changes in protein synthesis without altering the number of bases. There are different types of substitution mutations, including silent, missense, and nonsense mutations, with varying effects on proteins, such as causing diseases like sickle-cell anemia and cystic fibrosis. Factors contributing to these mutations include errors during DNA replication and exposure to mutagens.