More will probably be identified soon. Highly-reactive oxygen radicals produced during normal cellular respiration as well as by other biochemical pathways. Chemicals in the Environment many hydrocarbons, including some found in cigarette smoke Link to description of a test measuring the mutations caused by the hydrocarbon benzopyrene. Mismatches of the normal bases because of a failure of proofreading during DNA replication . Breaks in the backbone.
Ionizing radiation is a frequent cause, but some chemicals produce breaks as well.
There are three modes of excision repair, each of which employs specialized sets of enzymes. Some of these can be removed by a protein encoded by our MGMT gene. However, the protein can only do it once, so the removal of each methyl group requires another molecule of protein. Each of the myriad types of chemical alterations to bases requires its own mechanism to correct. What the cell needs are more general mechanisms capable of correcting all sorts of chemical damage with a limited toolbox.