In genetics, a missense mutation is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution. Missense mutations change amino acids, which in turn alter proteins and may alter a protein's function or structure. These mutations may arise spontaneously from mutagens like UV radiation, tobacco smoke, an error in DNA replication, and other factors. Screening for missense mutations can be done by sequencing the genome of an organism and comparing the sequence to a reference genome to analyze for differences. Missense mutations can be repaired by the cell when there are errors in DNA replication by using mechanisms such as DNA proofreading and mismatch repair. They can also be repaired by using genetic engineering technologies or pharmaceuticals. Some notable examples of human diseases caused by missense mutations are Rett syndrome, cystic fibrosis, and sickle-cell disease.

Missense mutation refers to a change in one amino acid in a protein arising from a point mutation in a single nucleotide. Amino acids are the building blocks of proteins. Missense mutations are a type of nonsynonymous substitution in a DNA sequence. Two other types of nonsynonymous substitutions are nonsense mutations, in which a codon is changed to a premature stop codon that results in the resulting protein being cut short, and nonstop mutations, in which a stop codon deletion results in a longer but nonfunctional protein. The latter two types are not considered to be missense mutations.

Missense mutations can render the resulting protein nonfunctional, due to misfolding of the protein. These mutations are responsible for human diseases, such as Epidermolysis bullosa, sickle-cell disease, SOD1 mediated ALS, and a substantial number of cancers.

Not all missense mutations lead to appreciable protein changes. An amino acid may be replaced by a different amino acid of very similar chemical properties in which case the protein may still function normally; this is termed a conservative mutation. Alternatively, the amino acid substitution could occur in a region of the protein which does not significantly affect the protein secondary structure or function. Lastly, when more than one codon codes for the same amino acid (termed "degenerate coding"), the resulting mutation does not produce any change in translation and hence no change in protein is observed; degenerate coding would be classified as a synonymous substitution, or a silent mutation, and not a missense mutation.

Missense mutations may be inherited or arise spontaneously, termed de novo mutations. Well studied diseases arising from inherited missense mutations include sickle cell anemia, cystic fibrosis, and early-onset Alzheimer's and Parkinson's disease. De novo mutations that increase or decrease the activity of synapses have been implicated in the development of neurological and developmental disorders, such a Autism Spectrum Disorder and intellectual delay.

Environmental mutagens, such as tobacco smoke or UV radiation, may be a cause of spontaneous missense mutations. Tobacco smoke has been implicated in transversion mutations in the K-ras gene, with a meta-analysis of lung carcinomas showing 25 tumours containing a G to T mutation causing an amino acid change from glycine to cysteine, and 11 tumours with a G to T mutation causing an amino acid change from glycine to valine. Similarly, numerous studies have shown ultraviolet light induces missense mutations in the p53 gene,  which when unregulated, reduces the cell's ability to recognize DNA damage and engage in apoptosis, leading to cell proliferation and potential skin carcinogenesis.

DNA polymerase replication errors during cell division may lead to spontaneous missense mutations if DNA polymerase's proofreading ability does not detect and repair an error it makes. Spontaneous DNA polymerase errors are estimated to occur at a frequency of 1/10⁹ base pairs.

Although rarer, tautomerization of bases also creates spontaneous missense mutations. Tautomerization occurs when hydrogen atoms on DNA bases spontaneously change locations, impacting the structure of the base, and allowing it to pair with an incorrect base. If this strand of DNA is replicated, the incorrect base will be the template for a new strand, leading to a mutation, possibly changing the amino acid and therefore, the protein. For example, Wang et al., (2011) used X-ray cystallography to demonstrate that a de novo mutation was created when DNA repair mechanisms did not recognize a C-A base mismatch due to tautomerization allowing the base structures to be compatible.