Deletion Mutation Definition

A deletion mutation is a mistake in the DNA replication process which removes nucleotides from the genome. A deletion mutation can remove a single nucleotide, or entire sequences of nucleotides. Deletions are thought to occur when the enzyme that synthesizes new DNA slips on the template DNA strand, effectively missing a nucleotide. This enzyme, polymerase, must attach the template DNA nucleotides in its active site for DNA replication to occur. Larger strands of DNA can undergo a deletion mutation during crossing-over, which takes place in meiosis. If the segments of DNA that are exchanged are not the same size, large sections may experience a deletion mutation, as seen below.

Deletion vectorized

A deletion mutation can be a serious mutation, or a harmless mutation. The effect of the deletion mutation will be determined by where in the gene it takes place, and how many nucleotides are deleted. The genetic code is read in triplets by protein producing enzymes. If three or more nucleotides are lost in a gene, entire amino acids can be missing from protein created which can have serious functional effect. Losing a single nucleotide is often not better, as a frameshift mutation can occur. A frameshift mutation shifts the entire gene, and changes all of the original triplet codons. A mutation of this type can cause a gene to produce a completely non-functional gene, as it seriously alters the chain of amino acids the gene produces.

A deletion mutation may take place more often than we can measure, but mutations which are inherited in offspring are typically rare. In asexually reproducing animals the rate of mutations is kept relatively low. In part this is due to the specificity and accuracy of polymerase. However, cells also have another enzyme, exonuclease, which follows polymerase and cuts out sections of DNA which do not match their nucleotide counterpart on the template DNA. Due to this and other regulatory mechanisms, deletion mutations that cause phenotypic change are rare.

Examples of Deletion Mutation

A Simple Mutation

The following is an example of a single nucleotide deletion mutation. The short sequences of DNA are not representative of actual DNA, which contains many hundreds or thousands of base pairs. The top string represents the original strand of DNA, while the bottom strand lacks the nucleotide pair removed by the deletion mutation. The triplet codons are separated, to see the effects of the deletion mutation.


5’ TAC CCA GG 3’
3’ ATG GGT CC 5’

As you can see, if this were the end of the DNA molecule, the last amino acid would not be produced. Instead, a deletion mutation will usually occur in the middle of a chromosome or gene. This will cause the deleted nucleotide to be filled by shifting the DNA and causing a frameshift mutation, or inserting a new nucleotide in a mutation known as an insertion. This mutation can only be passed on if the organism’s mechanisms for repairing DNA do not catch the mistake, and the DNA exists in a cell that will produce offspring. In asexual organisms, this is every cell and mutations are more likely to persist. In sexually reproducing organisms, mutations can only be passed on if they arise in the gamete producing tissues of the sex organs.

Discovering the Genetic Code

Before the 1950s, the nature of the genetic code was not well understood. That all changed when Francis Crick and Sydney Brenner began experimenting on mutant strain of bacterial virus. Crick and Brenner analyzed the DNA of viruses that were exposed to a toxin known to cause mutations. During their trials, the noticed that the function of certain genes could be restored by a combination of mutations, which we know now to insertion and deletion mutations. While the DNA between the two mutations would become nonsense, the insertion would offset the deletion. This would reset the reading frame of the gene, and cause a frameshift mutation to be avoided. This interaction between mutations was termed intragenic suppression. By comparing how individual mutations affected the proteins and amino acids produced, Crick and Brenner were able to formally theorize about existence of the triplet genetic code, and its universal use in organisms.

  • Substitution – When the wrong nucleotide is copied during DNA replication.
  • Insertion – Instead of deleting nucleotides, an insertion mutation adds nucleotides to a genome.
  • Inversion – A segment of DNA becomes rotated 180 degrees within the gene.
  • Reciprocal Translocation – Two different chromosomes (non-homologous) exchange pieces of DNA.


1. A complex protein has thousands of amino acids, but only a few of them exist in the active site. The active site requires a specific sequence of amino acids, to bind to a substrate. If a deletion mutation of 3 nucleotides removes one of these amino acids, will the protein still function?
A. No
B. Yes, just not as well
C. Maybe, it depends on the protein.

Answer to Question #1
C is correct. Protein specificity is ability of a protein to bind to a substrate. This specificity has evolved over billions of years to produce proteins that are highly adapted to the molecules they operate on. A change of a single amino acid could completely change the shape of the protein, and render it unable to grasp the substrate. Or, the deletion mutation could lead to a more specific protein which works better than the original. This could actually make the protein work better than it had previously. It all depends on the environment and what the organism needs.

2. While replicating a gene, polymerase accidently slips on the template strand, and skips a nucleotide. The resulting DNA produced is missing that nucleotide counterpart, and forms a mismatch in the DNA. Exonuclease senses the lump in the DNA, and cuts the strand open, allowing polymerase to insert the proper nucleotide and reseal the DNA. What just happened?
A. A deletion mutation, and an insertion mutation
B. Normal DNA replication
C. A deletion mutation

Answer to Question #2
B is correct. While this appears to be a deletion mutation, the DNA was corrected before the mutation could be proliferated or create protein. Many “almost” mutations are corrected by DNA monitoring enzymes as the DNA is replicated. If this mutation survives to another round of DNA replication, the strands of DNA will separate, and the mutation will become its own DNA template. All cells created after this cell will also have the deletion mutation.

3. Look at the following single strand of DNA:


Which of the following would be a deletion mutation?

Answer to Question #3
B is correct. B is the only answer in which a nucleotide is missing from the original sequence. In answer A, an extra T is inserted in the middle of the sequence. In answer C, the beginning of the sequence has undergone an inversion mutation, in which a sequence is rotated completely.