Missense mutation

Template:Short description Template:Cs1 config 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.<ref name=":11">{{#invoke:citation/CS1|citation |CitationClass=web

}}</ref> 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.<ref name=":6" /> These mutations may arise spontaneously from mutagens like UV radiation,<ref name=":5" /> tobacco smoke,<ref name=":4" /> an error in DNA replication,<ref name=":7" /> 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.<ref name="Qin_2019" /> 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.<ref name="Kunkel_2004" /><ref name=":14" /> They can also be repaired by using genetic engineering technologies<ref name="Hou_2024" /> or pharmaceuticals.<ref name="Striessnig_2021" /><ref name="Schulz-Heddergott_2018" /> Some notable examples of human diseases caused by missense mutations are Rett syndrome,<ref name=":8" /> cystic fibrosis,<ref name=":10" /> and sickle-cell disease.<ref name=":1" />

File:Missense Mutation Example.jpg

This image shows an example of missense mutation. One of the nucleotides (adenine) is replaced by another nucleotide (cytosine) in the DNA sequence. This results in an incorrect amino acid (proline) being incorporated into the protein sequence.

Impact on Protein Function

Missense mutation refers to a change in one amino acid in a protein arising from a point mutation in a single nucleotide.<ref name=":11" /> Amino acids are the building blocks of proteins. Missense mutations are a type of nonsynonymous substitution in a DNA sequence.<ref name=":15">Template:Cite book</ref> 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,<ref>Template:Cite journal</ref> and nonstop mutations, in which a stop codon deletion results in a longer but nonfunctional protein.<ref>Template:Cite journal</ref> The latter two types are not considered to be missense mutations.

File:Point mutations-en.png

Point mutation categories. Missense mutations are a type of nonsynonymous point mutation.

Missense mutations can render the resulting protein nonfunctional,<ref name=":6">Template:Cite journal</ref> due to misfolding of the protein.<ref name=":0">Template:Cite journal</ref> These mutations are responsible for human diseases, such as Epidermolysis bullosa,<ref>Template:Cite journal</ref> sickle-cell disease,<ref>Template:Cite journal</ref> SOD1 mediated ALS, and a substantial number of cancers.<ref>Template:Cite journal</ref><ref>Template:Cite news</ref>

Not all missense mutations lead to appreciable protein changes.<ref name=":15" /><ref name=":16" /> 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.<ref name=":16">Template:Cite journal</ref> Alternatively, the amino acid substitution could occur in a region of the protein which does not significantly affect the protein secondary structure or function.<ref name=":15" /> 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,<ref>Template:Cite journal</ref> or a silent mutation, and not a missense mutation.<ref name=":15" />

Origin

Missense mutations may be inherited or arise spontaneously, termed de novo mutations.<ref name=":2">Template:Citation</ref> Well studied diseases arising from inherited missense mutations include sickle cell anemia,<ref>Template:Cite journal</ref> cystic fibrosis,<ref name=":10">Template:Cite journal</ref> and early-onset Alzheimer's<ref>Template:Cite journal</ref> and Parkinson's disease.<ref>Template:Cite journal</ref> De novo mutations that increase or decrease the activity of synapses have been implicated in the development of neurological and developmental disorders,<ref name=":3">Template:Cite journal</ref> such a Autism Spectrum Disorder<ref name=":3" /> and intellectual delay.<ref name=":2" />

Agents of Spontaneous Missense Mutation

Environmental mutagens, such as tobacco smoke or UV radiation, may be a cause of spontaneous missense mutations.<ref name=":4">Template:Cite journal</ref><ref name=":5">Template:Cite journal</ref> 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.<ref name=":4" /> Similarly, numerous studies have shown ultraviolet light induces missense mutations in the p53 gene,<ref name=":5" /><ref>Template:Cite journal</ref>  which when unregulated, reduces the cell's ability to recognize DNA damage and engage in apoptosis, leading to cell proliferation and potential skin carcinogenesis.<ref name=":5" />

File:Adenine-Thymine tautomers.png

Spontaneous tautomerization of adenine, resulting in adenine mispairing with cytosine, rather than thymine, after replication. Future replications would lead to cytosine pairing with guanine, instead of an adenine-thymine pair in that location, resulting in a missense mutation.

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.<ref name=":2" /> Spontaneous DNA polymerase errors are estimated to occur at a frequency of 1/10⁹ base pairs.<ref name=":2" />

Although rarer, tautomerization of bases also creates spontaneous missense mutations.<ref>Template:Cite journal</ref> 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.<ref>Template:Citation</ref> 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.<ref name=":7">Template:Citation</ref> 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.<ref>Template:Cite journal</ref>

Screening

Next Generation Sequencing (NGS)

Next Generation Sequencing (NGS) has changed the world of sequencing by decreasing the cost of sequencing and increasing the throughput.<ref>Template:Cite journal</ref> It does this by utilizing massively parallel sequencing to sequence the genome. This involves clonally amplified DNA fragments that can be spatially separated into second generation sequencing (SGS) or third generation sequencing (TGS) platforms.<ref>Template:Cite book</ref> There is variation between these protocols, but the overall methods are similar. Using massively parallel sequencing allows the NGS platform to produce very large sequences in a single run.<ref name="Valencia_2013">Template:Cite book</ref> The DNA fragments are typically separated by length using gel electrophoresis.

NGS consists of four main steps, DNA isolation, target enrichment, sequencing, and data analysis.<ref name="Valencia_2013" /> The DNA isolation step involves breaking the genomic DNA into many small fragments.<ref name="Qin_2019" /> There are many different mechanisms that can be used to accomplish this such as mechanical methods, enzymatic digestion, and more.<ref name="Qin_2019">Template:Cite journal</ref> This step also consists of adding adaptors to either end of the DNA fragments that are complementary to the flow cell oligos and include primer binding sites for the target DNA.<ref name="Valencia_2013" /> The target enrichment step amplifies the region of interest. This includes creating a complementary strand to the DNA fragments through hybridization to a flow cell oligo.<ref name="Valencia_2013" /> It then gets denatured and bridge amplification occurs before the reverse strand is finally washed and sequencing can occur. The sequencing step involves massive parallel sequencing of all DNA fragments simultaneously using a NGS sequencer. This information is saved and analyzed in the last step, data analysis, using bioinformatics software.<ref name="Qin_2019" /> This compares the sequences to a reference genome to align the fragments and show mutations in the targeted area of the sequence.<ref name="Qin_2019" />

Newborn Screening (NBS)

Newborn screening (NBS) for missense mutations is increasingly incorporating genomic technologies in addition to traditional biochemical methods to improve the detection of genetic disorders early in life. Traditional NBS primarily relies on biochemical assays, such as tandem mass spectrometry,<ref>Template:Cite journal</ref> to detect metabolic abnormalities indicative of conditions like phenylketonuria or congenital hypothyroidism.<ref>Template:Cite journal</ref> However, these methods may miss genetic causes or produce ambiguous results. To address these deficiencies, next-generation sequencing (NGS) is being added to NBS programs.<ref>Template:Cite journal</ref> For instance, targeted gene panels and whole-exome sequencing (WES) are used to identify disease causing missense mutations in genes associated with treatable conditions, such as severe combined immunodeficiency (SCID) and cystic fibrosis. Studies like the BabyDetect project have demonstrated the utility of genomic screening in identifying disorders missed by conventional methods, with actionable results for conditions affecting more than 400 genes.<ref name="Boemer_2025">Template:Cite journal</ref><ref>Template:Cite book</ref> In addition, genomic approaches allow for the detection of rare or recessive conditions that may not manifest biochemically at birth, significantly expanding the scope of diseases screened.<ref name="pmid37656463">Template:Cite journal</ref> These advancements align with the established principles of NBS, which emphasize early detection and intervention to prevent morbidity and mortality.<ref>Template:Cite book</ref>

Prevention and Repair Mechanisms

File:DNA Repair Mechanisms.png

Three mechanisms of DNA repair are represented in simplified form. DNA proofreading and mismatch repair are used to fix missense mutations. Nucleotide excision repair is used to repair large DNA lesions, not missense mutations<ref>Template:Cite journal</ref>.

Cellular mechanisms

DNA polymerases, used in DNA replication, have a high specificity of 10⁴ to 10⁶-fold in base pairing.<ref name="Kunkel_2004" /> They have proofreading abilities to correct incorrect matches, allowing 90-99.9% of mismatches to be excised and repaired.<ref name="Kunkel_2004">Template:Cite journal</ref> The base mismatches that go unnoticed are repaired by the DNA mismatch repair pathway, also inherent in cells.<ref name=":13">Template:Cite journal</ref><ref name=":14">Template:Cite journal</ref> The DNA mismatch repair pathway uses exonucleases that move along the DNA strand and remove the incorrectly incorporated base in order for DNA polymerase to fill in the correct base.<ref name=":13" />Exonuclease1 is involved in many DNA repair systems and moves 5' to 3' on the DNA strand.<ref>Template:Cite journal</ref>

Genetic engineering and drug-based interventions

More recently, research has explored the use of genetic engineering<ref name="Hou_2024">Template:Cite journal</ref> and pharmaceuticals as potential treatments.<ref name="Striessnig_2021">Template:Cite journal</ref><ref name="Schulz-Heddergott_2018">Template:Cite journal</ref> tRNA therapies have emerged in research studies as a potential missense mutation treatment, following evidence supporting their use in nonsense mutation correction.<ref name="Albers_2021">Template:Cite journal</ref> Missense-correcting tRNAs are engineered to identify the mutated codon, but carry the correct charged amino acid which is inserted into the nascent protein.<ref name="Hou_2024" />

Pharmaceuticals that target specific proteins affected by missense mutations have also shown therapeutic potential.<ref name="Striessnig_2021" /><ref name="Schulz-Heddergott_2018" /> Pharmaceutical studies have particularly focused on targeting the p53 mutant protein and Ca²⁺ channel abnormalities, both caused by gain of function missense mutations due to their high prevalence in a number of cancers and genetic diseases respectively.<ref name="Schulz-Heddergott_2018" /><ref name="Albers_2021" /> In cystic fibrosis, most commonly caused by missense mutations,<ref>Template:Cite journal</ref> drugs known as modulators target the defective Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein.<ref>Template:Cite journal</ref> For example, to reduce the defects caused by class III CFTR mutations, Ivacaftor, part of the modulator Kalydeco, forces the chloride channel to remain in an open position.<ref name=":12">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>

Future Technology and Research

Gene therapy is being explored as a treatment for missense mutations. This involves inserting the correct sequence of DNA into an incorrect gene.<ref name=":12" /> Artificial Intelligence programs, such as AlphaFold, are also being developed to predict the effect of missense mutations.<ref name=":17" /> Identifying potential deleterious mutations can assist with disease diagnosis and treatment.<ref name=":17">Template:Cite journal</ref>

Evolution

File:Phylogenetic tree of SNP variations.png

Diverged nucleotide sequence demonstrating how sequences diverge over time. Red letters are nucleotides changed from the original sequence.

If a missense mutation is not deleterious, it will not be selected against and can contribute to species divergence.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref> Over time, mutations occur randomly in individuals and can become fixed in populations if they are not selected against.<ref>Template:Cite journal</ref> Missense mutations are a type of mutation that are not neutral, and therefore can be acted on by selection. Selection cannot act on synonymous mutations (mutations that do not change anything phenotypically).<ref>Template:Cite journal</ref>

Tracking missense mutations, like nonsynonymous SNPs, in ancestral species populations allow genealogies and phylogenetic trees to be created and evolutionary connections to be made.<ref>Template:Cite journal</ref> Missense mutation analysis is often used in evolutionary genetics to create relationships between species, as amino acid changes leading to protein changes are needed for species to diverge from each other.<ref>Template:Cite journal</ref>

Notable Examples

LMNA

File:LMNA protein (1IFR) mutation R527L PMID 22549407.png

Wild type (left) and mutated (right) form of lamin A (pdb id: 1IFR). Normally, Arginine 527 (blue) forms salt bridge with glutamate 537 (magenta), but R527L substitution results in breaking this interaction (leucine has a nonpolar tail and therefore cannot form a static salt bridge).

    DNA: 5' - AAC AGC CTG CGT ACG GCT CTC - 3'
         3' - TTG TCG GAC GCA TGC CGA GAG - 5'
   mRNA: 5' - AAC AGC CUG CGU ACG GCU CUC - 3'
Protein:      Asn Ser Leu Arg Thr Ala Leu

LMNA missense mutation (c.1580G>T) introduced at LMNA gene – position 1580 (nt) in the DNA sequence (CGT) causing the guanine to be replaced with the thymine, yielding CTT in the DNA sequence. This results at the protein level in the replacement of the arginine by the leucine at the position 527.<ref>Template:Cite journal</ref> This leads to destruction of salt bridge and structure destabilization. At phenotype level this manifests with overlapping mandibuloacral dysplasia and progeria syndrome.

The resulting transcript and protein product is:

    DNA: 5' - AAC AGC CTG CTT ACG GCT CTC - 3'
         3' - TTG TCG GAC GAA TGC CGA GAG - 5'
   mRNA: 5' - AAC AGC CUG CUU ACG GCU CUC - 3'
Protein:      Asn Ser Leu Leu Thr Ala Leu

Rett Syndrome

Missense mutations in the MeCP2 protein can cause Rett syndrome, otherwise known as the RTT phenotype.<ref name="Brown_2016">Template:Cite journal</ref> This phenotype primarily effects females, as males do not live with this mutation past infancy.<ref name="Brown_2016" /> T158M, R306C and R133C are the most common missense mutations causing RTT.<ref name="Brown_2016" /> T158M is a mutation of an adenine being substituted for a guanine causing the threonine at amino acid position 158 being substituted with a methionine.<ref>Template:Cite book</ref> R133C is a mutation of a cytosine at base position 417 in the gene encoding the MeCP2 protein being substituted for a thymine, causing an amino acid substitution at position 133 in the protein of arginine with cysteine.<ref name=":8">Template:Cite journal</ref>

Sickle Cell

File:Sickle cell anemia.jpg

(1) Normal red blood cells and (2) sickled-cell red blood cells

Sickle-cell disease changes the shape of red blood cells from round to sickle shaped.<ref name=":9">Template:Cite journal</ref> In the most common variant of sickle-cell disease, the 20th nucleotide of the gene for the beta chain of hemoglobin is altered from the codon GAG to GTG.<ref name=":9" /> Thus, the 6th amino acid, glutamic acid, is substituted by valine—notated as an "E6V" or a "Glu6Val" mutation—which causes the protein to be sufficiently altered with a sickle-cell phenotype.<ref>{{#invoke:citation/CS1|citation

|CitationClass=web }}</ref> The affected cells cause issues in the bloodstream as they can become sticky due to their improper ion transport leading to them being susceptible to water loss.<ref name=":1">Template:Cite journal</ref> This can cause a buildup of blood cells that obstructs blood flow to any organ in the body.<ref name=":1" />

Other conditions that can be caused by missense mutations

• Alzheimers<ref name=":0" />
• X-linked intellectual disability<ref name=":0" />
• Hypocholesterolemia<ref name=":0" />
• Tangier disease<ref name=":0" />
• Congenital nemaline myopathy<ref>Template:Cite journal</ref>

See also

• Ka/Ks ratio
• Missense mRNA