A deletion mutation is a chromosomal mutation that occurs with the loss of one or more base pairs from a sequence of base pairs that normally comprise a gene or segment of a chromosome. After a deletion mutation, a chromosome is considered genetically deficient and is often termed a deletion chromosome.

For example, if the base sequence of DNA nucleotides was ATCGAT (adenine-thymine-cytosine-guanine-adenine-thymine) and a single base deletion took place at the third position (i.e. a deletion of the nucleotide with a cytosine nitrogenous base) the sequence would then read ATGAT (adenine-thymine-guanine-adenine-thymine). In a similar manner, a chromosomal deletion may involve a segment of chromosome that carries many genes.

Because the genetic code contained in the base sequence ultimately codes for the sequence of amino acids in a protein, most deletions have an adverse impact on either the synthesis of the protein or on the functional ability of the protein produced.

The identification of deletion mutations is also important to the construction of deletion maps -- a form of genetic mapping that uses known deletion mutants to identify and characterize an unknown point mutation. Following the introduction of a known deletion mutation to DNA containing an unknown point mutation, the recombination between the normal and mutated chromosome is examined for evidence of recombination. If recombination is evident the point mutation must lie outside the deletion area.

It is possible for a large amount of DNA to be deleted without affecting normal gene function. As long as the deleted portions of the chromosome are essentially intergenic or contain non-essential genes.

Although deletions certainly arise form chromosomal breakage, deletions also arise from natural sources. Recombination between repeated sequences of DNA (especially those that exist in the same cell following DNA replication but before cell division may lead to deletion mutations. In such deletion mutations one of the daughter cells may end up with a deletion mutation and the other with both copies of the repeated sequence carried in tandem combination.

Deletion mutations that include essential genes are almost always profound (i.e., they are lethal or causes dramatic changes in phenotype. The loss of genetic material usually precludes normal genetic regulation and function. A deletion mutation will normally result in the inactivation of the gene affected.

Because there is an outright loss of genetic material with deletion mutations, normal DNA repair mechanisms are ineffective and the mutation becomes permanent (i.e., the mutation is incapable of reversion).