Editing Point mutation (section)

==General consequences==
Point mutations that occur in non-coding sequences are most often without consequences, although there are exceptions. If the mutated base pair is in the [[promoter (biology)|promoter]] sequence of a gene, then the expression of the gene may change. Also, if the mutation occurs in the splicing site of an [[intron]], then this may interfere with correct splicing of the transcribed [[pre-mRNA]].

By altering just one amino acid, the entire [[peptide]] may change, thereby changing the entire protein. The new protein is called a [[protein variant]]. If the original protein functions in cellular reproduction then this single point mutation can change the entire process of cellular reproduction for this organism.

Point [[germline mutation]]s can lead to beneficial as well as harmful traits or diseases. This leads to [[adaptation]]s based on the environment where the organism lives. An advantageous mutation can create an advantage for that organism and lead to the trait's being passed down from generation to generation, improving and benefiting the entire population.  The scientific theory of [[evolution]] is greatly dependent on point mutations in [[cell (biology)|cells]]. The theory explains the diversity and history of living organisms on Earth. In relation to point mutations, it states that beneficial mutations allow the organism to thrive and reproduce, thereby passing its positively affected mutated genes on to the next generation. On the other hand, harmful mutations cause the organism to die or be less likely to reproduce in a phenomenon known as [[natural selection]].

There are different short-term and long-term effects that can arise from mutations. Smaller ones would be a halting of the cell cycle at numerous points. <!--the way the cell structure is base then the DNA and RNA will function by the codon.-->  This means that a codon coding for the amino acid [[glycine]] may be changed to a stop codon, causing the proteins that should have been produced to be deformed and unable to complete their intended tasks. Because the mutations can affect the DNA and thus the [[chromatin]], it can prohibit mitosis from occurring due to the lack of a complete chromosome.  Problems can also arise during the processes of transcription and replication of DNA.  These all prohibit the cell from reproduction and thus lead to the death of the cell.  Long-term effects can be a permanent changing of a chromosome, which can lead to a mutation.  These mutations can be either beneficial or detrimental.  [[Cancer]] is an example of how they can be detrimental.<ref>{{cite journal |author=Hoeijmakers JH |title=Genome maintenance mechanisms for preventing cancer |journal=Nature |volume=411 |issue=6835 |pages=366–74 |date=May 2001  |pmid=11357144 |doi=10.1038/35077232 |bibcode=2001Natur.411..366H |s2cid=4337913 |doi-access= }}</ref>

Other effects of point mutations, or single nucleotide polymorphisms in DNA, depend on the location of the mutation within the gene.  For example, if the mutation occurs in the region of the gene responsible for coding, the amino acid sequence of the encoded protein may be altered, causing a change in the function, protein localization, stability of the protein or protein complex.  Many methods have been proposed to predict the effects of missense mutations on proteins. Machine learning algorithms train their models to distinguish known disease-associated from neutral mutations whereas other methods do not explicitly train their models but almost all methods exploit the evolutionary conservation assuming that changes at conserved positions tend to be more deleterious. While majority of methods provide a binary classification of effects of mutations into damaging and benign, a new level of annotation is needed to offer an explanation of why and how these mutations damage proteins.<ref>{{Cite book|last1=Li|first1=Minghui|last2=Goncearenco|first2=Alexander|last3=Panchenko|first3=Anna R.|title=Proteomics |chapter=Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols |date=2017|volume=1550|pages=235–260|doi=10.1007/978-1-4939-6747-6_17|issn=1940-6029|pmc=5388446|pmid=28188534|series=Methods in Molecular Biology|isbn=978-1-4939-6745-2}}</ref>

Moreover, if the mutation occurs in the region of the gene where transcriptional machinery binds to the protein, the mutation can affect the binding of the transcription factors because the short nucleotide sequences recognized by the transcription factors will be altered.  Mutations in this region can affect rate of efficiency of gene transcription, which in turn can alter levels of mRNA and, thus, protein levels in general.

Point mutations can have several effects on the behavior and reproduction of a protein depending on where the mutation occurs in the amino acid sequence of the protein. If the mutation occurs in the region of the gene that is responsible for coding for the protein, the amino acid may be altered.  This slight change in the sequence of amino acids can cause a change in the function, activation of the protein meaning how it binds with a given enzyme, where the protein will be located within the cell, or the amount of free energy stored within the protein.

If the mutation occurs in the region of the gene where transcriptional machinery binds to the protein, the mutation can affect the way in which transcription factors bind to the protein.  The mechanisms of transcription bind to a protein through recognition of short nucleotide sequences.  A mutation in this region may alter these sequences and, thus, change the way the transcription factors bind to the protein.  Mutations in this region can affect the efficiency of gene transcription, which controls both the levels of mRNA and overall protein levels.<ref>{{cite web |title=A Shortcut to Personalized Medicine |date=18 June 2008 |publisher=Genetic Engineering & Biotechnology News |url=http://www.genengnews.com/gen-articles/snps-a-shortcut-to-personalized-medicine/2507/}}</ref>