Haplotype
CYP2D6 *41 with related variants rs16947 rs28371725 rs1135840 -1235A>G -740C>T -678G>A 1661G>C *41 CYP2D7 gene conversion in intron 1

Clinical Annotations

Clinical Variants that meet the highest level of criteria, manually curated by PharmGKB, are shown below. Please follow the link in the "Position" column for more information about a particular variant. Each link in the "Position" column leads to the corresponding PharmGKB Variant Page. The Variant Page contains summary data, including PharmGKB manually curated information about variant-drug pairs based on individual PubMed publications. The PMIDs for these PubMed publications can be found on the Variant Page.

To see more Clinical Variants with lower levels of criteria, click the button at the bottom of the table.

Disclaimer: The PharmGKB's clinical annotations reflect expert consensus based on clinical evidence and peer-reviewed literature available at the time they are written and are intended only to assist clinicians in decision-making and to identify questions for further research. New evidence may have emerged since the time an annotation was submitted to the PharmGKB. The annotations are limited in scope and are not applicable to interventions or diseases that are not specifically identified.

The annotations do not account for individual variations among patients, and cannot be considered inclusive of all proper methods of care or exclusive of other treatments. It remains the responsibility of the health-care provider to determine the best course of treatment for a patient. Adherence to any guideline is voluntary, with the ultimate determination regarding its application to be made solely by the clinician and the patient. PharmGKB assumes no responsibility for any injury or damage to persons or property arising out of or related to any use of the PharmGKB clinical annotations, or for any errors or omissions.

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View the full haplotype translation table for CYP2D6

Variant Alelle
rs769258 C
rs28371696 C
rs1065852 G
rs5030862 C
rs28371703 G
rs28371704 T
rs28371706 G
rs1135822 A
rs1135823 C
rs5030655 A
rs28371710 C
rs1135824 T
rs3892097 C
rs5030866 C
rs28371717 C
rs35742686 T
rs5030656 CTT
rs16947 A (differs from reference)
rs5030867 T
rs28371725 T (differs from reference)
rs59421388 C
rs28371733 C
rs1135840 G (differs from reference)
rs72549357 NO ins
2853A>C T
rs78482768 G
rs61736512 C
-1770 G>A C
'-1601_-1600GA>TT TC
-1584C>G G
-1543 G>A C
'-1426C>T G
-1298G>A C
-1258_-1257insAAAAA NO ins
-1253A>G T
-1245_-1244insGA NO ins
-1238_-1237delAA NO del
-1237_-1236insAA NO ins
-1235A>G C (differs from reference)
-1094_-1093insA NO ins
-1028T>C A
-1011T>C A
-1000G>A C
-750_-749delGA NO del
-740C>T A (differs from reference)
-695_-692delTGTG NO del
-678G>A T (differs from reference)
-629A>G T
-377A>G T
'-175G>A C
19G>A C
73C>T G
82C>T G
125G>A C
214G>C C
221C>A G
223C>G G
227T>C A
310G>T C
601delC NO del
746C>G G
843T>G A
883G>C C
887C>T G
957C>T G
972C>T G
997C>G G
1013G>A C
1039C>T G
1062A>G T
1494T>C A
1513C>T G
1598A>G T
1608G>A C
1661G>C G (differs from reference)
1720A>C T
1724C>T G
1757C>T G
rs5030865 C
1858C>T G
1863_1864ins(TTTCGCCCC) NO ins
1863_1864ins(TTTCGCCCC)2 NO ins
1869T>C A
1887insTA NO ins
1943G>A C
1973_1974insG NO ins
1978C>T G
1979T>C A
2097A>G T
2129A>C T
2291G>A C
2303C>T G
2470T>C A
2480C>T G
2539_2542delAACT NO del
2556C>T G
2573_2574insC NO ins
2575C>A G
2661G>A C
2587_2590delGACT NO del
2938C>T G
2939G>A C
2950G>C C
3030G>G/A C
3172A>C T
3198C>G G
3254T>C A
3259_3260insGT NO ins
3201C>T G
3277T>C A
3288G>A C
3318G>A C
3384A>C T
3491G>A C
3582A>G T
3584G>A C
3609G>T C
3790C>T G
3828G>A C
3835A>C T
3853G>A C
3877G>C C
3887T>C A
4042G>A C
4044C>T G
4045G>A C
4115C>T G
4125_4133dupGTGCCCACT NO DUP
4388C>T G
4401C>T G
4481G>A C
4535insT NO ins
*2A CYP2D7 gene conversion in intron 1 NO
*2M CYP2D7 gene conversion in intron 1 NO
*4N gene conversion to CYP2D7 in exon 9 NO
*10D CYP2D7-like 3'-flanking region NO
*13 CYP2D7/2D6 hybrid gene structure NO
*14B/*21B -intron 1 conversion with CYP2D7 (214-245) NO
*31 CYP2D7 gene conversion in intron 1 NO
*35B CYP2D7 conversion upstream of exon 1 NO
*36 gene conversion to CYP2D7 in exon 9 NO
*41 CYP2D7 gene conversion in intron 1 YES (differs from reference)
*51 CYP2D7 gene conversion in intron 1 NO
*56A CYP2D7 gene conversion in intron 1 NO
*57 gene conversion to CYP2D7 in exon 9 NO
*58 CYP2D7 gene conversion in intron 1 NO
*61 CYP2D7 seq from intron 7 onwards NO
*63/*73(are these the same?) intron 1 conversion with CYP2D7 (214-245) NO
more than 1 copy, unspecified - active genes NO
more than 1 copy: (N=2, 3, 4, 5 or 13) NO
*63 CYP2D7 sequence from exon 8 onwards NO

Haplotype Annotations

PharmGKB haplotype annotations provide information about haplotype-drug pairs based on individual PubMed publications. Each annotation represents information from a single paper and the goal is to report the information that the author states, not an interpretation of the paper. The PMID for supporting PubMed publications is found in the "Evidence" field.

Information presented, including study size, allele frequencies and statistics is taken directly from the publication. However, if the author does not correct p-values in cases of multiple hypotheses, curators may apply a Bonferroni correction. Curators attempt to report study size based on the actual number of participants used for the calculation of the association statistics, so the number may vary slightly from what is reported in the abstract of the paper. OMB Race Category information is derived from the paper and mapped to standardized categories. Category definitions may be found by clicking on the "OMB Race Category" link.

There are direct annotations for this haplotype. Register or sign in to see them.

VIP Annotation

CYP2D6*41 [Article:15289790] is also a reduced functioning haplotype of CYP2D6 [Articles:11037799, 15289790]. This haplotype has been discovered more recently, and thus has not been studied as well as most of the others. CYP2D6*41 likely contributes towards the IM phenotype [Article:15289790] (see table for allele frequencies).


Allele frequency table

Population
\*1 \*2 \*3 \*4 \*5 \*6 \*9 \*10 \*17 \*29 \*41 UM References
European Caucasian
.33-.36 .22-.33 .01-.04 .12-.21 .02-.07 .01 0-.02 .01-.02 0 N/D N/D .02 [Articles:9241659, 9012401, 1681816, 7909282, 7697944, 9511177]
US Caucasian
.36-.40 .26-.37 .01-.02 .18-.23 .02-.05 .01 .02-.03 .02-.08 0 N/D N/D .01 [Articles:8098046, 9918137, 10634130, 11505219]
African American
.29-.35 .18-.27 0 .06-.08 .06-.07 0 0 .03-.08 .15-.23 N/D N/D .01-.05 [Articles:9918137, 11505219, 12152006, 8098046]
Chinese .23 .2 .01 .01 .06 N/D N/D .5-.7 N/D N/D N/D .01 [Article:8097442]
Japanese .42-.43 .09-.12 N/D .01 .05-.06 N/D N/D .38-.41 N/D N/D N/D N/D [Articles:10886115, 10975611, 10340923]
Malay .36
N/D N/D .03 .05 N/D .03 .50 .01 N/D N/D N/D [Article:11422605]
Inuit N/D N/D 0 .08 N/D N/D N/D .02 N/D N/D N/D .01 [Article:9164697]
Mexican .57 .23 .01 .10 .02 N/D N/D .07 .01 N/D N/D .02 [Article:11753272]
Ghanaian .44 .11 0 .07 .01 0 0 .03 .28 N/D N/D N/D [Article:10634134]
Gabonese .32 .44 N/D N/D .01 N/D N/D N/D .24 N/D N/D .03 [Article:10073750]
Zimbabwean N/D N/D 0 .02-.03 .04 N/D 0 .06 .34 N/D N/D N/D [Articles:7908586, 8911874]
Tanzanian .28 .2 0 .01 .06 0 0 .04 .17 N/D N/D .14 [Articles:10634133, 11470994, 11372584]
Ethiopean N/D N/D 0 .01 .03 N/D N/D .09 .1 N/D N/D N/D [Article:8764380]
Amerindian .66 .19 0 .04-.17 .04 .01 0 .02-.18 N/D N/D N/D .03 [Articles:10376769, 9731721]
Subsaharan Africa
.24 .33 0 .03 .06 0 0 .04 .12 .07 .03 .28 [Article:17301689]
North Africa
.12 .28 0 .12 .03 0 0 0 .08 0 .08 .07 [Article:17301689]
Middle Eastern
.35 .25 0 .07 .04 .01 0 .01 .02 0 .17 .02 [Article:17301689]
Europe .34 .29 0 .17 .03 .01 .03 .03 0 0 .07 .01 [Article:17301689]
Central/South Asia
.43 .29 0 .08 .04 0 0 .04 0 0 .11 .01 [Article:17301689]
East Asia
.31 .16 0 .03 .06 0 0 .4 0 0 .02 .12 [Article:17301689]
Oceania .72 0 0 0 .01 0 0 .03 0 0 0 .05 [Article:17301689]
Native American
.60 .30 0 .03 .01 0 0 0 .01 0 0 .05 [Article:17301689]
Drugs / Other Molecules
Diseases Cystic Fibrosis Depression Hypertension Neoplasms Pain Parkinson Disease Schizophrenia

Appendix

How many SNPs, indels, repeats define this haplotype? CYP2D6 haplotypes are typically determined by a genotyping algorithm. For the purposes of this VIP, we will define the SNPs that make up a haplotype from those SNPs which have variant pages. For fully defined CYP2D6 haplotypes, please see http://www.cypalleles.ki.se/cyp2d6.htm

CYP2D6*41 includes CYP2D6 2850C>T (rs16947) and CYP2D6 2988G>A (rs28371725)