Editing Single-nucleotide polymorphism (section)

== Types ==
[[File:Types of SNP new1.png|thumb|400 px|Types of single-nucleotide polymorphism (SNPs)]]

Single-nucleotide [[Polymorphism (biology)|polymorphisms]] may fall within coding sequences of [[gene]]s, [[Noncoding DNA|non-coding regions of genes]], or in the [[intergenic region]]s (regions between genes). SNPs within a coding sequence do not necessarily change the [[amino acid]] sequence of the [[protein]] that is produced, due to [[Genetic code#Degeneracy|degeneracy of the genetic code]].<ref>{{Cite journal |last1=Spencer |first1=Paige S. |last2=Barral |first2=José M. |date=2012 |title=Genetic code redundancy and its influence on the encoded polypeptides |journal=Computational and Structural Biotechnology Journal |volume=1 |pages=e201204006 |doi=10.5936/csbj.201204006 |issn=2001-0370 |pmc=3962081 |pmid=24688635}}</ref>

SNPs in the coding region are of two types: synonymous SNPs and nonsynonymous SNPs. Synonymous SNPs do not affect the protein sequence, while nonsynonymous SNPs change the amino acid sequence of protein.<ref>{{Cite journal |last1=Chu |first1=Duan |last2=Wei |first2=Lai |date=2019-04-16 |title=Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation |journal=BMC Cancer |volume=19 |issue=1 |pages=359 |doi=10.1186/s12885-019-5572-x |issn=1471-2407 |pmc=6469204 |pmid=30991970 |doi-access=free }}</ref>
* SNPs in [[non-coding region]]s can manifest in a higher risk of cancer,<ref>{{cite journal|vauthors=Li G, Pan T, Guo D, Li LC|date=2014|title=Regulatory Variants and Disease: The E-Cadherin -160C/A SNP as an Example|journal=Molecular Biology International|volume=2014|pages=967565|doi=10.1155/2014/967565|pmc=4167656|pmid=25276428|doi-access=free}}</ref> and may affect mRNA structure and disease susceptibility.<ref>{{cite journal|vauthors=Lu YF, Mauger DM, Goldstein DB, Urban TJ, Weeks KM, Bradrick SS|date=November 2015|title=IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance|journal=Scientific Reports|volume=5|pages=16037|bibcode=2015NatSR...516037L|doi=10.1038/srep16037|pmc=4631997|pmid=26531896}}</ref> Non-coding SNPs can also alter the level of [[gene expression|expression]] of a gene, as an [[eQTL]] (expression quantitative trait locus).
* SNPs in [[coding region]]s:
** [[synonymous substitution]]s by definition do not result in a change of amino acid in the protein, but still can affect its function in other ways. An example would be a seemingly silent mutation in the multidrug resistance gene 1 ([[P-glycoprotein|MDR1]]), which codes for a cellular membrane pump that expels drugs from the cell, can slow down translation and allow the peptide chain to fold into an unusual conformation, causing the mutant pump to be less functional (in MDR1 protein e.g. C1236T polymorphism changes a GGC codon to GGT at amino acid position 412 of the polypeptide (both encode glycine) and the C3435T polymorphism changes ATC to ATT at position 1145 (both encode isoleucine)).<ref>{{cite journal|vauthors=Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM|date=January 2007|title=A "silent" polymorphism in the MDR1 gene changes substrate specificity|url=https://zenodo.org/record/1230874|journal=Science|volume=315|issue=5811|pages=525–8|bibcode=2007Sci...315..525K|doi=10.1126/science.1135308|pmid=17185560|s2cid=15146955|doi-access=free}}</ref>
** [[nonsynonymous substitution]]s:
*** [[Missense mutation|missense]] – single change in the base results in change in amino acid of protein and its malfunction which leads to disease (e.g. c.1580G>T SNP in [[LMNA]] gene&nbsp;– position 1580 (nt) in the DNA sequence (CGT codon) causing the [[guanine]] to be replaced with the [[thymine]], yielding CTT codon in the DNA sequence, results at the protein level in the replacement of the [[arginine]] by the [[leucine]] in the position 527,<ref>{{cite journal|vauthors=Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, Bujnicki JM, Yahia S, Abdel-Hadi D, Shams A, Ahmad N, Hamed S, Puzianowska-Kuznicka M|date=November 2012|title=A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome|journal=European Journal of Human Genetics|volume=20|issue=11|pages=1134–40|doi=10.1038/ejhg.2012.77|pmc=3476705|pmid=22549407}}</ref> at the [[phenotype]] level this manifests in overlapping [[mandibuloacral dysplasia]] and [[progeria syndrome]])
*** [[Nonsense mutation|nonsense]] – [[point mutation]] in a sequence of DNA that results in a premature [[stop codon]], or a ''nonsense codon'' in the [[transcription (genetics)|transcribed]] [[mRNA]], and in a [[truncation|truncated]], incomplete, and usually nonfunctional protein product (e.g. [[Cystic fibrosis]] caused by the G542X mutation in the [[cystic fibrosis transmembrane conductance regulator]] gene).<ref>{{cite journal|vauthors=Cordovado SK, Hendrix M, Greene CN, Mochal S, Earley MC, Farrell PM, Kharrazi M, Hannon WH, Mueller PW|date=February 2012|title=CFTR mutation analysis and haplotype associations in CF patients|journal=Molecular Genetics and Metabolism|volume=105|issue=2|pages=249–54|doi=10.1016/j.ymgme.2011.10.013|pmc=3551260|pmid=22137130}}</ref>

SNPs that are not in protein-coding regions may still affect [[gene splicing]], [[transcription factor]] binding, [[messenger RNA]] degradation, or the sequence of noncoding RNA. Gene expression affected by this type of SNP is referred to as an eSNP (expression SNP) and may be upstream or downstream from the gene.