Editing Single-nucleotide polymorphism (section)

== Programs for prediction of SNP effects ==
An important group of SNPs are those that corresponds to [[missense mutations]] causing amino acid change on protein level. [[Point mutation]] of particular residue can have different effect on protein function (from no effect to complete disruption its function). Usually, change in amino acids with similar size and physico-chemical properties (e.g. substitution from leucine to valine) has mild effect, and opposite. Similarly, if SNP disrupts [[secondary structure]] elements (e.g. substitution to proline in [[alpha helix]] region) such mutation usually may affect whole protein structure and function. Using those simple and many other [[machine learning]] derived rules a group of programs for the prediction of SNP effect was developed:<ref>{{Cite journal|last=Johnson|first=Andrew D.|date=October 2009|title=SNP bioinformatics: a comprehensive review of resources|journal=Circulation: Cardiovascular Genetics|volume=2|issue=5|pages=530–536|doi=10.1161/CIRCGENETICS.109.872010|issn=1942-325X|pmc=2789466|pmid=20031630}}</ref>
* [http://sift-dna.org SIFT] This program provides insight into how a laboratory induced missense or nonsynonymous mutation will affect protein function based on physical properties of the amino acid and sequence homology.
* [https://gsponerlab.msl.ubc.ca/software/list/ LIST] (Local Identity and Shared Taxa)<ref>{{cite journal | vauthors = Malhis N, Jones SJ, Gsponer J | title = Improved measures for evolutionary conservation that exploit taxonomy distances | journal = Nature Communications | volume = 10 | issue = 1 | pages = 1556 | date = April 2019 | pmid = 30952844 | pmc = 6450959 | doi = 10.1038/s41467-019-09583-2 | bibcode = 2019NatCo..10.1556M }}</ref><ref>{{cite journal |author1=Nawar Malhis |author2= Matthew Jacobson |author3=Steven J. M. Jones |author4=Jörg Gsponer | year = 2020 | title = LIST-S2: Taxonomy Based Sorting of Deleterious Missense Mutations Across Species | journal = Nucleic Acids Research | volume =48|issue=W1|pages=W154–W161| doi=10.1093/nar/gkaa288| pmc = 7319545| pmid=32352516| doi-access=free}}</ref> estimates the potential deleteriousness of mutations resulted from altering their protein functions. It is based on the assumption that variations observed in closely related species are more significant when assessing conservation compared to those in distantly related species.
* [https://rostlab.org/services/snap SNAP2]
* [http://www.sbg.bio.ic.ac.uk/suspect/index.html SuSPect]
* [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2]
* [http://loschmidt.chemi.muni.cz/predictsnp/ PredictSNP]
* [[MutationTaster]]: [http://www.mutationtaster.org/ official website]
* [http://www.ensembl.org/info/docs/tools/vep/index.html Variant Effect Predictor] from the [[Ensembl]] project
* [https://genomicscomputbiol.org/ojs3/GCB/article/view/48/182 SNPViz] {{Webarchive|url=https://web.archive.org/web/20200807085537/https://genomicscomputbiol.org/ojs3/GCB/article/view/48/182 |date=2020-08-07 }}:<ref>{{Cite journal|url=https://genomicscomputbiol.org/ojs3/GCB/article/view/48/182|title=View of SNPViz - Visualization of SNPs in proteins|website=genomicscomputbiol.org|doi=10.18547/gcb.2018.vol4.iss1.e100048|language=en-US|access-date=2018-10-20|doi-access=free|archive-date=2020-08-07|archive-url=https://web.archive.org/web/20200807085537/https://genomicscomputbiol.org/ojs3/GCB/article/view/48/182|url-status=dead}}</ref> This program provides a 3D representation of the protein affected, highlighting the amino acid change so doctors can determine pathogenicity of the mutant protein.
* [http://provean.jcvi.org/index.php PROVEAN]
* [http://phyrerisk.bc.ic.ac.uk PhyreRisk] is a database which maps variants to experimental and predicted protein structures.<ref name="OfoegbuDavid2019">{{cite journal | vauthors = Ofoegbu TC, David A, Kelley LA, Mezulis S, Islam SA, Mersmann SF, Strömich L, Vakser IA, Houlston RS, Sternberg MJ | display-authors = 6 | title = PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants | journal = Journal of Molecular Biology | volume = 431 | issue = 13 | pages = 2460–2466 | date = June 2019 | pmid = 31075275 | pmc = 6597944 | doi = 10.1016/j.jmb.2019.04.043 }}</ref>
* [http://www.sbg.bio.ic.ac.uk/~missense3d/ Missense3D] is a tool which provides a stereochemical report on the effect of missense variants on protein structure.<ref name="IttisoponpisanIslam2019">{{cite journal | vauthors = Ittisoponpisan S, Islam SA, Khanna T, Alhuzimi E, David A, Sternberg MJ | title = Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? | journal = Journal of Molecular Biology | volume = 431 | issue = 11 | pages = 2197–2212 | date = May 2019 | pmid = 30995449 | pmc = 6544567 | doi = 10.1016/j.jmb.2019.04.009 }}</ref>