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These are 291 snps definitely relate to CYP2D6
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{{Topic}} The wikipedia article on [http://en.wikipedia.org/wiki/CYP2D6 CYP2D6] is a good resource to learn about this gene, and includes a large table of the drugs known to be metabolized by the CYP2D6 protein. In fact, almost 25% of all drugs are metabolized by [[CYP2D6]], including dextromethorphan (a key ingredient in products such as [[Nyquil]]), beta-blockers, antiarrhythmics, and antidepressants. The authoritative source for defining alleles is the [http://www.cypalleles.ki.se/ CYP Allele Nomenclature Committee]'s [http://www.cypalleles.ki.se/cyp2d6.htm CYP2D6 Allele Nomenclature] page. In articles on CYP2D6 it is common to see the positions described within a reference sequence of the gene rather than SNP IDs or reference genome positions. The reference sequence used is [http://www.ncbi.nlm.nih.gov/nuccore/181303?report=genbank M33388]. The sequence starts at genome build 36.3 position 40856738 or genome build 37.1 position 42526794. It is on the reverse strand, which means that M33388 positions must be subtracted from the start position. In addition, M33388 positions from 601 to 1330 need to be decremented by 1, and positions from 1440 and up incremented by 1 before conversion. It also appears that negative positions need to be adjusted, but it isn't clear what standard is used to do so. Alleles are stated in minus orientation. {{PMID|19817501}} appears to be a good survey of known effects of alleles. Many variants of CYP2D6 are known. The main CYP2D6 alleles are the following: CYP2D6*1 - the most common form, considered 'fully functional'; also known as wild-type, or WT<br> CYP2D6*2 - normal function except CYP2D6*2XN variants<br> CYP2D6*3 - nonfunctioning variant<br> CYP2D6*4 - nonfunctioning variant; the most common variant; [[rs3892097]]<br> CYP2D6*5 - nonfunctioning variant; consists of a complete deletion of the gene<br> CYP2D6*6 - nonfunctioning variant; [[rs5030655]]<br> CYP2D6*9 - partially functioning variant<br> CYP2D6*10 - partially functioning variant; [[rs1065852]]<br> CYP2D6*17 - partially functioning variant<br> [PMID 17115111] [[CYP2D6]] metabolism, as measured by genetic variation and enzyme inhibition, is an independent predictor of [[Breast cancer]] outcome in post-menopausal women receiving [[tamoxifen]] for early breast cancer. Determination of CYP2D6 genotype may be of value in selecting adjuvant hormonal therapy and it appears CYP2D6 inhibitors should be avoided in tamoxifen-treated women. [PMID 1782973] [[Codeine]] is ineffective at typical doses in up to 10% of Caucasians carrying two nonfunctional CYP2D6 alleles. [PMID 16638864] SNPs in [[LIG4]], [[ERCC2]], and [[CYP2D6]] genes were identified as putative markers predicting individuals at risk for complications arising from radiation therapy in [[Prostate cancer]]. [PMID 9012401] Presents a tabulation of allele frequences and phenotypic consequences in a European population. [PMID 18070221] CYP2D6*4 homozygotes should have lower doses of tricyclic [[antidepressants]]. [PMID 16958828] CYP2D6 poor metabolizers (*4, *5, *6 alleles) have more side effects when taking [[antidepressants]], in particular, [[venlafaxine]] ([[Effexor]]) [PMID 18784654] CYP2D6*4 homozygotes taking a [[beta blocker]] like [[metoprolol]] are at 4x increased risk for [[bradycardia]] {{PMID|19541866}} a paper on CYP2D6 CNV profiling in a chinese population. In late 2004, the FDA approved the AmpliChip CYP450, a dedicated microarray test from Roche which allows the automated determination of a patient's [[CYP2D6]] and [[CYP2C19]] genotype. In 2006 the FDA recommended an update in the [[tamoxifen]] label to reflect the increased risk of recurrence in [[breast cancer]] patients who are [[CYP2D6]] poor metabolizers; a 2009 review of several studies since then mostly confirms worse clinical outcome in patients with decreased CYP2D6 metabolism and supports the notion that [[CYP2D6]] genotype may well become a clinically relevant predictive marker.{{PMID|19118028}} A more complete list of [[CYP2D6]] variants includes: {| class="wikitable" |- ! Allele Name ! Code ! Defining Name/Change ! Rs# ! Comments ! Enzyme Activity ! Platforms |- | CYP2D6*1 | | | | Wild-type | normal | |- | CYP2D6*2 | | 2850C>T, 4180G>C (but these also appear in other variants) | [[rs16947]](A) [[rs1135840]](C) | R296C, S486T; has several subvariants | normal (except *2XN subvariant) | {{#show:Rs16947|?On microarray}};{{#show:Rs1135840|?On microarray}} |- | CYP2D6*2XN | | 1661G>C, 2850C>T, 4180G>C with multiple copies | [[rs16947]](A) [[rs1135840]](C) | more than one copy of *2 variant in chromosome, N replaced by copy number | increased | {{#show:Rs16947|?On microarray}};{{#show:Rs1135840|?On microarray}} |- | CYP2D6*3A | | 2549delA | [[rs35742686]](-) | 259frameshift | none | {{#show:Rs35742686|?On microarray}} |- | CYP2D6*3B | | 1749A>G, 2549delA | [[rs1135824]](G) [[rs35742686]](-) | N166D; 259frameshift | none | {{#show:Rs1135824|?On microarray}};{{#show:Rs35742686|?On microarray}} |- | CYP2D6*4 | | 1846G>A | [[rs3892097]](A) | splicing defect; has several subvariants | none | {{#show:Rs3892097|?On microarray}} |- | CYP2D6*4F | | 1846G>A, 1858C>T | [[rs3892097]](A) [[i4001456]](A) | splicing defect, R173C | none | {{#show:Rs3892097|?On microarray}};{{#show:I4001456|?On microarray}} |- | CYP2D6*4G | | 1846G>A, 2938C>T | [[rs3892097]](A) [[i4001467]](A) | splicing defect, P325L | none | {{#show:Rs3892097|?On microarray}};{{#show:I4001467|?On microarray}} |- | CYP2D6*4H | | 1846G>A, 3877G>C | [[rs3892097]](A) [[rs28371733]](C) | splicing defect, E418Q | none | {{#show:Rs3892097|?On microarray}};{{#show:Rs28371733|?On microarray}} |- | CYP2D6*5 | | whole-gene deletion | | CYP2D6 gene deleted | none | |- | CYP2D6*6 | | 1707delT | [[rs5030655]] | 118frameshift | none | {{#show:Rs5030655|?On microarray}} |- | CYP2D6*7 | | 2935A>C | [[rs5030867]] | H324P | none | {{#show:Rs5030867|?On microarray}} |- | CYP2D6*8 | | 1758G>T | [[rs5030865]] | G169X | none | {{#show:Rs5030865|?On microarray}} |- | CYP2D6*9 | | 2615-2617delAAG | [[rs5030656]] | K281del | decreased | {{#show:Rs5030656|?On microarray}} |- | CYP2D6*10 | | 100C>T (but also appears in other variants) | [[rs1065852]] | P34S | decreased | {{#show:Rs1065852|?On microarray}} |- | CYP2D6*11 | | 883G>C | [[rs5030863]] | | none | {{#show:Rs5030863|?On microarray}} |- | CYP2D6*12 | | 124G>A | [[rs5030862]] | G42R | none | {{#show:Rs5030862|?On microarray}} |- | CYP2D6*14 | | 1758G>A | [[rs5030865]] | G169R | none | {{#show:Rs5030865|?On microarray}} |- | CYP2D6*15 | | 137insT; 137_138insT | | in-del; 46 frameshift | none | |- | CYP2D6*17 | | 1023C>T, 2850C>T (but also appear in other variants) | [[rs28371706]](T) [[rs16947]](A) | T107I, R296C | decreased | {{#show:Rs28371706|?On microarray}};{{#show:Rs16947|?On microarray}} |- | CYP2D6*18 | | 4133dupGTGCCCACT | | 468_470dupVPT | none | |- | CYP2D6*19 | | 2539_2542delAACT | | 255frameshift | none | |- | CYP2D6*20 | | 1973_1974insG | [[i4001479]](CC) | 211frameshift | none | {{#show:I4001479|?On microarray}} |- | CYP2D6*21 | | 2573insC | | | none | |- | CYP2D6*29 | | 1659G>A; 1661G>C; 2850C>T; 3183G>A; 4180G>C | | V136M; R296C; V338M; S486T | decreased | |- | CYP2D6*38 | | 2587_2590delGACT | | 271Frameshift | none | |- | CYP2D6*39 | | 1661G>C, 4180G>C | [[rs1135840]] | S486T | normal | {{#show:Rs1135840|?On microarray}} |- | CYP2D6*40 | | 1863_1864ins(TTT CGC CCC)2 | | 174_175ins(FRP)2 | none | |- | CYP2D6*41 | | 2988G>A | [[rs28371725]] | aberrant splicing | decreased | {{#show:Rs28371725|?On microarray}} |- | CYP2D6*42 | | 3259insGT; 3259_3260insGT | | 365frameshift | none | |- | CYP2D6*44 | | 2950G>C | | splicing defect | none | |- | CYP2D6*52 | | 3877G>A | [[rs28371733]](A) | E418K | possibly decreased | {{#show:Rs28371733|?On microarray}} |- | CYP2D6*56 | | 3201C>T | | R344X | none | |- | CYP2D6*1xN | | whole-gene duplication | | Nx active genes | increased | |- | CYP2D6*4xN | | whole-gene duplication (+1846G>A) | | Nx inactive genes | none | |- | CYP2D6*10xN | | whole-gene duplication (+100C>T) | | Nx decreased-activity genes | decreased | |- | CYP2D6*41xN | | whole-gene duplication (+2988G>A) | | Nx decreased- activity genes | decreased | |- | CYP2D6_(rs1080983) | | | [[rs1080983]] | | | {{#show:Rs1080983|?On microarray}} |- | CYP2D6_(rs28360521) | | | [[rs28360521]] | | |{{#show:Rsrs28360521|?On microarray}} |- |} [https://oa.doria.fi/bitstream/handle/10024/42557/pharmaco.pdf?sequence=1 source1] and [http://www.cypalleles.ki.se/cyp2d6.htm source2] *[[rs4078248]] *[[rs79347391]] *[[rs35028622]] *[[rs77827855]] *[[rs4078249]] *[[rs78340630]] *[[rs35183748]] *[[rs71184866]] *[[rs71754064]] *[[rs12169962]] *[[i4001469]] *[[rs28371738]] *[[rs75824064]] *[[i4001451]] *[[rs28371737]] *[[rs77845838]] *[[rs79125935]] *[[rs61731577]] *[[rs1135840]] *[[i4001403]] *[[rs28371736]] *[[i4001398]] *[[rs75467367]] *[[rs74478221]] *[[rs1135839]] *[[rs1135838]] *[[rs1135837]] *[[rs28371735]] *[[i4001394]] *[[rs1135836]] *[[rs1135835]] *[[rs1135833]] *[[rs1135832]] *[[i4001412]] *[[rs79392742]] *[[rs3021084]] *[[rs72549345]] *[[rs28371733]] *[[rs61737947]] *[[rs78762568]] *[[rs28371732]] *[[i4001438]] *[[rs4987144]] *[[rs77867647]] *[[rs28371730]] *[[rs2004511]] *[[rs915947]] *[[i4001474]] *[[rs79596243]] *[[rs28371729]] *[[i4001464]] *[[rs28371728]] *[[rs78139609]] *[[rs28578778]] *[[rs72454628]] *[[rs1985842]] *[[rs9611741]] *[[rs77312092]] *[[rs75386357]] *[[rs61736515]] *[[rs61731586]] *[[rs1065569]] *[[rs61737946]] *[[rs2982055]] *[[rs61745683]] *[[i4001428]] *[[rs1058172]] *[[rs72549346]] *[[rs28371726]] *[[rs79489631]] *[[rs61736517]] *[[rs76088846]] *[[rs72549347]] *[[i4001417]] *[[i4001416]] *[[rs59421388]] *[[i4001411]] *[[rs78209835]] *[[rs72549348]] *[[i4001404]] *[[rs1135831]] *[[rs3915951]] *[[i4001490]] *[[rs28371725]] *[[i4001476]] *[[rs72549349]] *[[i3003610]] *[[i4001471]] *[[rs79292917]] *[[i4001468]] *[[i4001467]] *[[rs28371724]] *[[rs5030867]] *[[i4001466]] *[[rs1135830]] *[[rs1058171]] *[[rs1058170]] *[[i4001434]] *[[rs16947]] *[[rs61736514]] *[[rs1135829]] *[[rs28371723]] *[[i4001426]] *[[rs74516776]] *[[rs28371722]] *[[i4001409]] *[[rs28371721]] *[[rs76015180]] *[[rs77952980]] *[[rs77562994]] *[[rs5030656]] *[[rs28371720]] *[[rs72549350]] *[[rs1135828]] *[[rs77913725]] *[[i4001391]] *[[rs28371719]] *[[rs79441454]] *[[rs72549351]] *[[rs72549352]] *[[i4000487]] *[[rs1135827]] *[[rs28371718]] *[[rs35742686]] *[[rs4986774]] *[[i4000452]] *[[i4001497]] *[[rs72549353]] *[[rs28371717]] *[[i4001478]] *[[i4001477]] *[[rs17002852]] *[[rs17002853]] *[[i4001473]] *[[rs79331140]] *[[rs77593160]] *[[rs1075944]] *[[rs1807313]] *[[rs79650744]] *[[rs28371715]] *[[rs79738337]] *[[i4001440]] *[[rs75203276]] *[[rs5845524]] *[[rs3045547]] *[[rs1807314]] *[[rs4996601]] *[[rs4996602]] *[[rs2899353]] *[[rs5845525]] *[[rs4996603]] *[[rs80262685]] *[[rs6002635]] *[[i4001494]] *[[rs76327133]] *[[rs2267447]] *[[rs58440431]] *[[i4001392]] *[[rs5758596]] *[[rs5758597]] *[[rs9623532]] *[[rs7285233]] *[[rs5758598]] *[[rs28371713]] *[[rs5758599]] *[[rs5030866]] *[[i4001480]] *[[rs72549354]] *[[i4001479]] *[[rs3831704]] *[[rs72549355]] *[[rs28371712]] *[[rs77578877]] *[[rs2267448]] *[[i4001461]] *[[rs72549356]] *[[rs67780109]] *[[i4001456]] *[[i4001454]] *[[rs1800716]] *[[rs3892097]] *[[rs76326664]] *[[rs5030865]] *[[i4001433]] *[[i4001432]] *[[rs1135826]] *[[rs1135825]] *[[rs1135824]] *[[i4001452]] *[[rs74962936]] *[[i4001425]] *[[i4001423]] *[[rs28371710]] *[[i4001421]] *[[rs5030655]] *[[i4001420]] *[[rs78482768]] *[[i4001419]] *[[rs1058164]] *[[rs61736911]] *[[rs61736512]] *[[i4001413]] *[[rs80018788]] *[[rs1135823]] *[[i4001401]] *[[rs61736507]] *[[rs1135822]] *[[i4001397]] *[[rs76060075]] *[[rs67497403]] *[[i4001495]] *[[rs79931073]] *[[rs35029149]] *[[rs1081004]] *[[rs28439001]] *[[rs77449786]] *[[rs78854695]] *[[rs1081003]] *[[i4001386]] *[[rs1135821]] *[[rs78459009]] *[[rs28371706]] *[[i4001501]] *[[rs74802369]] *[[rs76187628]] *[[rs28371705]] *[[rs76802407]] *[[rs28371704]] *[[rs28371703]] *[[i4001486]] *[[i4001483]] *[[rs5030863]] *[[rs79712708]] *[[rs28371702]] *[[rs71328650]] *[[i4001460]] *[[rs28371701]] *[[i4001435]] *[[rs75614915]] *[[rs13056401]] *[[rs769259]] *[[rs28371700]] *[[rs35970455]] *[[rs34291018]] *[[rs28371699]] *[[rs71328651]] *[[rs29001678]] *[[rs76527171]] *[[rs1081000]] *[[rs56011157]] *[[rs1080999]] *[[rs28695233]] *[[rs29001518]] *[[rs75276289]] *[[rs1080998]] *[[rs76312385]] *[[rs1080997]] *[[rs74644586]] *[[rs1080996]] *[[rs71328652]] *[[rs1080995]] *[[rs71328653]] *[[rs79802111]] *[[rs72549357]] *[[rs5030862]] *[[i4001414]] *[[rs1065852]] *[[rs72552269]] *[[rs28448769]] *[[i4001402]] *[[rs28371696]] *[[i4001396]] *[[rs72552262]] *[[rs769258]] *[[rs72549358]] *[[rs72552268]] *[[i4001387]] *[[base]] *[[rs75085559]] *[[i4001489]] *[[rs28371695]] *[[rs28371694]] *[[i4001472]] *[[rs1080993]] *[[rs35481113]] *[[rs35023634]] *[[rs34894147]] *[[rs35046171]] *[[rs34898711]] *[[rs35534760]] *[[rs34167214]] *[[rs1080992]] *[[rs74951492]] *[[rs74966855]] *[[rs77185887]] *[[rs769257]] *[[rs72549359]] *[[rs28633410]] *[[rs79102241]] *[[i4001459]] *[[rs75324300]] *[[rs28624811]] *[[rs60979881]] *[[i4001444]] *[[i4001442]] *[[rs71667834]] *[[rs1080990]] *[[rs1080989]] *[[i4001388]] *[[rs59360719]] *[[i4001400]] *[[i4001499]] *[[rs62625688]] *[[rs1080988]] *[[rs28735595]] *[[rs72233016]] *[[rs71710351]] *[[rs71800336]] *[[rs56358138]] *[[rs58331414]] *[[rs58405804]] *[[rs59099247]] *[[i4001436]] *[[rs78047908]] *[[rs1080987]] *[[rs1080986]] *[[rs28588594]] *[[rs35888064]] *[[rs76210340]] *[[rs75471486]] *[[rs1080985]] *[[i4001488]] *[[rs1080984]] *[[rs58188898]] *[[rs1080983]] *[[rs75112600]] *[[rs28680494]] *[[rs28439297]]
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