Genes

This page describes gene-specific information. PyPGx currently supports genotyping of a total of 88 pharmacogenes.

In order to provide the most accurate information, this page borrows heavily from the works of the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Pharmacogenomics Knowledge Base (PharmGKB). All curated contents published by CPIC and PharmGKB are available free of restriction under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedication and the Creative Commons Attribution-ShareAlike 4.0 International License, repsectively.

Many of the genes are known to have structural variation (SV) including gene deletions, duplications, and hybrids. Please read the Structural variation detection page for more details.

Some genes have a genotype-phenotype table available from CPIC or PharmGKB. Please read the Phenotype prediction page for more details.

Below is a summary table:

Gene	Variants	SV	Phenotype	PharmVar	CPIC	Function	GRCh37	GRCh38	Notes
ABCB1	✅					Disposition	chr7:87130178-87345639	chr7:87500862-87716323
ABCG2	✅		✅		✅	Disposition	chr4:89008420-89082791	chr4:88087268-88161639
ACYP2	✅					Metabolism	chr2:54339751-54535437	chr2:54112614-54308300	NM_138448.4 was used as the main transcript.
ADRA2A	✅					Absorption	chr10:112833786-112843665	chr10:111074028-111083907	NM_000681.4 was used as the main transcript.
ADRB2	✅					Target	chr5:148203173-148211186	chr5:148823610-148831623	NM_000024.6 was used as the main transcript.
ANKK1	✅					Metabolism	chr11:113255500-113274138	chr11:113384778-113403416	NM_178510.2 was used as the main transcript.
APOE	✅					Efficacy	chr19:45406052-45415650	chr19:44902795-44912393	NM_000041.4 was used as the main transcript.
ATM	✅					Efficacy	chr11:108090793-108286161	chr11:108220066-108415434	NM_000051.4 was used as the main transcript.
BCHE	✅					Efficacy	chr3:165487691-165558211	chr3:165769903-165840423	NM_000055.4 was used as the main transcript.
BDNF	✅					Efficacy	chr11:27673439-27725002	chr11:27651892-27703455	NM_001709.5 was used as the main transcript.
CACNA1S	✅		✅		✅	Target	chr1:201005639-201084694	chr1:201036511-201115426
CFTR	✅		✅		✅	Target	chr7:117117016-117311719	chr7:117477024-117671665
COMT	✅					Metabolism	chr22:19917359-19962473	chr22:19929836-19974950
CYP1A1	✅			✅		Metabolism	chr15:75008882-75020951	chr15:74716541-74728528
CYP1A2	✅			✅		Metabolism	chr15:75038183-75051941	chr15:74745844-74759607
CYP1B1	✅			✅		Metabolism	chr2:38291745-38306323	chr2:38064602-38079181
CYP2A6	✅	✅		✅		Metabolism	chr19:41339442-41396352	chr19:40833540-40890447	CYP2A6 has pseudogene (CYP2A7).
CYP2A13	✅			✅		Metabolism	chr19:41574355-41622100	chr19:41068450-41116195
CYP2B6	✅	✅	✅	✅	✅	Metabolism	chr19:41427203-41534301	chr19:40921281-41028398	CYP2B6 has pseudogene (CYP2B7).
CYP2C8	✅			✅		Metabolism	chr10:96793528-96832254	chr10:95033771-95072497
CYP2C9	✅		✅	✅	✅	Metabolism	chr10:96695414-96752148	chr10:94935657-94993091
CYP2C19	✅		✅	✅	✅	Metabolism	chr10:96519437-96615962	chr10:94759680-94858547
CYP2D6	✅	✅	✅	✅	✅	Metabolism	chr22:42512500-42551883	chr22:42116498-42155810	CYP2D6 has pseudogene (CYP2D7).
CYP2E1	✅	✅		✅		Metabolism	chr10:135330866-135362620	chr10:133517362-133549123
CYP2F1	✅			✅		Metabolism	chr19:41617336-41637286	chr19:41111431-41131381
CYP2J2	✅			✅		Metabolism	chr1:60355979-60395470	chr1:59890307-59929773
CYP2R1	✅			✅		Metabolism	chr11:14896554-14916751	chr11:14875008-14895205
CYP2S1	✅			✅		Metabolism	chr19:41696111-41716444	chr19:41190218-41210539
CYP2W1	✅			✅		Metabolism	chr7:1019834-1032276	chr7:980180-992640
CYP3A4	✅			✅		Metabolism	chr7:99351582-99384811	chr7:99753966-99787184
CYP3A5	✅		✅	✅	✅	Metabolism	chr7:99242811-99280649	chr7:99645193-99682996
CYP3A7	✅			✅		Metabolism	chr7:99299659-99335823	chr7:99702035-99738196
CYP3A43	✅			✅		Metabolism	chr7:99422635-99466727	chr7:99825012-99869093
CYP4A11	✅			✅		Metabolism	chr1:47391859-47410148	chr1:46926187-46944476
CYP4A22	✅			✅		Metabolism	chr1:47600112-47618399	chr1:47134440-47152727
CYP4B1	✅			✅		Metabolism	chr1:47261669-47288021	chr1:46796045-46822413
CYP4F2	✅	✅		✅		Metabolism	chr19:15973833-16023930	chr19:15863022-15913074
CYP17A1	✅			✅		Metabolism	chr10:104587287-104600170	chr10:102827530-102840413
CYP19A1	✅			✅		Metabolism	chr15:51497253-51633795	chr15:51205056-51341596
CYP26A1	✅			✅		Metabolism	chr10:94830646-94840641	chr10:93070892-93080885
DBH	✅					Efficacy	chr9:136498484-136527451	chr9:133633362-133662329	NM_000787.4 was used as the main transcript.
DPYD	✅		✅	✅	✅	Excretion	chr1:97540298-98389615	chr1:97074742-97924034
DRD2	✅					Toxicity	chr11:113277326-113349120	chr11:113406604-113478398	NM_000795.4 was used as the main transcript.
F2	✅					Other	chr11:46737762-46764056	chr11:46716212-46742506	NM_000506.5 was used as the main transcript.
F5	✅		✅			Other	chr1:169478188-169558719	chr1:169508950-169589481
G6PD	✅	✅	✅			Disease	chrX:153756604-153778233	chrX:154528389-154550018	G6PD is located on X chromosome.
GRIK1	✅					Metabolism	chr21:30906253-31315314	chr21:29533932-29942996	NM_001330994.2 was used as the main transcript.
GRIK4	✅					Efficacy	chr11:120379456-120862615	chr11:120508747-120991906	NM_014619.5 was used as the main transcript.
GRIN2B	✅					Other	chr12:13687270-14137536	chr12:13534336-13984602	NM_000834.5 was used as the main transcript.
GSTM1	✅	✅				Metabolism	chr1:110227417-110239367	chr1:109684816-109696745
GSTP1	✅					Metabolism	chr11:67348065-67357124	chr11:67580811-67589653
GSTT1		✅				Metabolism	chr22:24373132-24387311	chr22_KI270879v1_alt:267307-281486	GSTT1 is located on different contigs between GRCh37 and GRCh38.
HTR1A	✅					Efficacy	chr5:63250700-63261272	chr5:63954873-63965445	NM_000524.4 was used as the main transcript.
HTR2A	✅					Efficacy	chr13:47402680-47474188	chr13:46828545-46900053	NM_000524.4 was used as the main transcript.
IFNL3	✅		✅			Other	chr19:39731245-39744165	chr19:39240552-39253525
IFNL4	✅					Other	chr19:39733953-39742496	chr19:39243313-39251856	NR_074079.1 was used as the main transcript.
ITGB3	✅					Efficacy	chr17:45328192-45394109	chr17:47250826-47316743	NM_000212.3 was used as the main transcript.
ITPA	✅					Other	chr20:3187143-3207506	chr20:3206497-3226860	NM_033453.4 was used as the main transcript.
MT-RNR1	✅		✅			Disease	chrM:410-1840	chrM:410-1840
MTHFR	✅					Metabolism	chr1:11842779-11869021	chr1:11782722-11808964
NAT1	✅					Metabolism	chr8:18064617-18084198	chr8:18207108-18226689
NAT2	✅					Metabolism	chr8:18245791-18261728	chr8:18388281-18404218
NUDT15	✅		✅	✅	✅	Metabolism	chr13:48608702-48624364	chr13:48034725-48050221
OPRK1	✅					Other	chr8:54135283-54167197	chr8:53222723-53254637	NM_000912.5 was used as the main transcript.
OPRM1	✅					Other	chr6:154357374-154456491	chr6:154036239-154135356	NM_000914.5 was used as the main transcript.
POR	✅			✅		Disease	chr7:75541419-75619173	chr7:75912154-75989855
PTGIS	✅			✅		Other	chr20:48117410-48187674	chr20:49500873-49571137
RARG	✅					Toxicity	chr12:53601352-53628993	chr12:53207568-53235209	NM_000966.6 was used as the main transcript.
RYR1	✅		✅	✅		Disease	chr19:38921339-39081204	chr19:38430690-38590564
SLC6A4	✅					Other	chr17:28518336-28565715	chr17:30191318-30238697	NM_001045.6 was used as the main transcript.
SLC15A2	✅					Excretion	chr3:121610170-121666034	chr3:121891400-121947188
SLC22A2	✅	✅				Excretion	chr6:160627786-160689853	chr6:160206754-160268821
SLC28A3	✅	✅				Excretion	chr9:86887371-86958673	chr9:84272456-84343758	NM_001199633.2 was used as the main transcript.
SLC47A2	✅					Other	chr17:19578629-19622897	chr17:19675316-19719584	NM_001099646.3 was used as the main transcript.
SLCO1B1	✅		✅	✅	✅	Absorption	chr12:21281127-21395730	chr12:21128193-21242796
SLCO1B3	✅					Absorption	chr12:20960637-21072845	chr12:20807704-20919911
SLCO2B1	✅					Absorption	chr11:74859151-74920594	chr11:75148106-75209549
SULT1A1	✅	✅				Metabolism	chr16:28601907-28636365	chr16:28590586-28625044
TBXAS1	✅			✅		Other	chr7:139525951-139723125	chr7:139826263-140023321
TPMT	✅		✅		✅	Metabolism	chr6:18125541-18158400	chr6:18125310-18158169
UGT1A1	✅		✅		✅	Excretion	chr2:234662918-234687945	chr2:233754269-233779300
UGT1A4	✅	✅				Excretion	chr2:234624437-234684945	chr2:233715735-233776300
UGT1A6	✅					Excretion	chr2:234598535-234684946	chr2:233689889-233776300	NM_001072.4 was used as the main transcript.
UGT2B7	✅					Excretion	chr4:69959191-69981705	chr4:69093473-69115987
UGT2B15	✅	✅				Excretion	chr4:69506314-69542494	chr4:68640596-68676652
UGT2B17		✅				Excretion	chr4:69399901-69437245	chr4:68534183-68571527
VKORC1	✅				✅	Target	chr16:31099162-31109320	chr16:31087853-31097797
XPC	✅					Other	chr3:14183646-14223172	chr3:14142146-14181672

ABCG2

Phenotype summary for ABCG2

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Normal Function	Reference/Reference	Normal/Routine/Low Risk
Decreased Function	Reference/rs2231142	Abnormal/Priority/High Risk
Poor Function	rs2231142/rs2231142	Abnormal/Priority/High Risk

Recommendations for ABCG2

• Rosuvastatin

  “Prescribe ≤20mg as a starting dose and adjust doses of rosuvastatin based on disease-specific and specific population guidelines for patients who are SLCO1B1 or ABCG2 poor function phenotype. If dose >20mg needed for desired efficacy, consider combination therapy (i.e. rosuvastatin plus non-statin guideline directed medical therapy). Patients with both ABCG2 poor function and SLCO1B1 poor/decreased function should be prescribed ≤10mg as a starting dose.” (Source: PharmGKB)

Resources for ABCG2

• CPIC® guideline for statins and SLCO1B1, ABCG2, and CYP2C9

• The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms

• PharmGKB: Annotation of CPIC Guideline for rosuvastatin and ABCG2, SLCO1B1

CACNA1S

Phenotype summary for CACNA1S

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Uncertain Susceptibility	Reference/Reference	Normal Risk
Malignant Hyperthermia Susceptibility	Reference/c.520C>T	Abnormal/Priority/High Risk

Recommendations for CACNA1S

• Desflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics uch as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Enflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Halothane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Isoflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Methoxyflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Sevoflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Succinylcholine

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

Resources for CACNA1S

• PharmGKB: Annotation of CPIC Guideline for desflurane and CACNA1S, RYR1

• CPIC® Guideline for Potent Volatile Anesthetic Agents and Succinylcholine and RYR1 and CACNA1S

• Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for the Use of Potent Volatile Anesthetic Agents and Succinylcholine in the Context of RYR1 or CACNA1S Genotypes

CFTR

Phenotype summary for CFTR

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Favorable Response	Reference/G551D	None
Unfavorable Response	F508del/F508del	None
Indeterminate	Reference/F508del	None

Recommendations for CFTR

• Ivacaftor

  “Ivacaftor treatment is recommended only in cystic fibrosis (CF) patients that are either homozygous or heterozygous for certain CFTR variants. See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

Resources for CFTR

• PharmGKB: Annotation of CPIC Guideline for ivacaftor and CFTR

• CPIC® Guideline for Ivacaftor and CFTR

• Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for Ivacaftor Therapy in the Context of CFTR Genotype

CYP1A1

Resources for CYP1A1

• PharmVar CYP1A1 page

CYP1A2

Resources for CYP1A2

• PharmVar CYP1A2 page

CYP1B1

Resources for CYP1B1

• PharmVar CYP1B1 page

CYP2A6

SV summary for CYP2A6

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*2		Model	Profile	Profile	WGS	GeT-RM	NA10831	0.4.1
*4	WholeDel1	*1/*4		Model	Profile	Profile	WGS	GeT-RM	NA18617	0.4.1
*4	WholeDel1Hom	*4/*4		Model	Profile	Profile	WGS	GeT-RM	NA18952	0.4.1
*4	WholeDel2	*1/*4		Model	Profile	Profile	WGS			0.12.0
*4	WholeDel2Hom	*4/*4		Model	Profile	Profile	WGS	1KGP	NA21093	0.15.0
*4	WholeDel3	*4/*9		Model	Profile	Profile	WGS	1KGP	NA18488	0.12.0
*1x2	WholeDup1	*1x2/*25	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA18861	0.4.1
*1x2	WholeDup2	*1x2/*2		Model	Profile	Profile	WGS	1KGP	NA12342	0.12.0
*1x2	WholeDup3	*1x2/*17		Model	Profile	Profile	WGS	1KGP	NA19129	0.12.0
	Hybrid1	Indeterminate		Model	Profile	Profile	WGS	GeT-RM	HG00436	0.4.1
*12	Hybrid2	*1/*12		Model	Profile	Profile	WGS	1KGP	NA11829	0.12.0	*12 has exons 1-2 of CYP2A7 origin and exons 3-9 of CYP2A6 origin (breakpoint in intron 2).
*12	Hybrid2Hom	*12/*12		Model	Profile	Profile	WGS	1KGP	NA19780	0.14.0
*34	Hybrid3	*1/*34		Model	Profile	Profile	WGS	1KGP	NA18516	0.12.0	*34 has exons 1-4 of CYP2A7 origin and exons 5-9 of CYP2A6 origin (breakpoint in intron 4).
	Hybrid4	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA20515	0.14.0
	Hybrid5	Indeterminate		Model	Profile	Profile	WGS	1KGP	HG00155	0.15.0
	Hybrid6	Indeterminate		Model	Profile	Profile	WGS	1KGP	HG00141	0.15.0
	Hybrid7	Indeterminate			Profile	Profile	WGS	1KGP	HG02382	0.16.0
	Tandem1	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA20828	0.14.0
	Tandem2	Indeterminate			Profile	Profile	WGS	1KGP	HG04214	0.16.0
	ParalogWholeDel1	Indeterminate		Model	Profile	Profile	WGS	1KGP	HG00625	0.15.0
	ParalogWholeDup1	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA06985	0.12.0
	Unknown1	Indeterminate			Profile	Profile	WGS	1KGP	HG02081	0.16.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for CYP2A6, and corresponding copy number profiles and allele fraction profiles.

Filtered alleles for CYP2A6

Some alleles in PharmVar will not be called by PyPGx because one or more of their variants have a high false positive rate, likely due to read misalignment to the CYP2A7 pseudogene. Those alleles are listed in below table. If problematic variants are present in gnomAD, their links are provided so that you can look at filtering status, allele imbalance for heterozygotes, etc.

Problematic Variant	Star Alleles	GRCh37	GRCh38
rs143731390 (N438Y)	*35	22-42523514-C-T	22-42127512-C-T

Resources for CYP2A6

• PharmVar CYP2A6 page

CYP2A13

Resources for CYP2A13

• PharmVar CYP2A13 page

CYP2B6

SV summary for CYP2B6

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*2		Model	Profile	Profile	WGS	GeT-RM	NA12813	0.4.1
*22x2	WholeDup1	*6/*22x2		Model	Profile	Profile	WGS	1KGP	NA19190	0.12.0
*29	Hybrid1	*6/*29		Model	Profile	Profile	WGS	GeT-RM	NA19178	0.4.1	*29 has exons 1-4 of CYP2B7 origin and exons 5-9 of CYP2A6 origin (breakpoint in intron 4).
	Tandem1	Indeterminate		Model	Profile	Profile	WGS	1KGP	HG01806	0.16.0
	PartialDup1	Indeterminate			Profile	Profile	WGS	1KGP	HG03784	0.16.0
	PartialDup2	Indeterminate			Profile	Profile	WGS	1KGP	HG02790	0.16.0
	ParalogWholeDel1	Indeterminate			Profile	Profile	WGS	1KGP	HG03235	0.16.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for CYP2B6, and corresponding copy number profiles and allele fraction profiles.

Phenotype summary for CYP2B6

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Ultrarapid Metabolizer	*4/*4	Normal/Routine/Low Risk
Rapid Metabolizer	*1/*4	Normal/Routine/Low Risk
Normal Metabolizer	*1/*2	Normal/Routine/Low Risk
Intermediate Metabolizer	*1/*29	Abnormal/Priority/High Risk
Poor Metabolizer	*6/*6	Abnormal/Priority/High Risk
Indeterminate	*1/*3	None

Recommendations for CYP2B6

• Efavirenz

  “Consider initiating efavirenz with a decreased dose of either 400 or 200 mg/day for patients who are CYP2B6 poor metabolizers. Consider initiating efavirenz with a decreased dose of 400 mg/day for patients who are CYP2B6 intermediate metabolizers.” (Source: PharmGKB)

Resources for CYP2B6

• PharmVar CYP2B6 page

• CPIC® Guideline for Efavirenz based on CYP2B6 genotype

• PharmGKB: Annotation of CPIC Guideline for efavirenz and CYP2B6

CYP2C8

Resources for CYP2C8

• PharmVar CYP2C8 page

CYP2C9

Phenotype summary for CYP2C9

Activity score is used for phenotype prediction.

Phenotype	Activity Score	Example	Priority
Normal Metabolizer	2 == score	*1/*1	Normal/Routine/Low Risk
Intermediate Metabolizer	1 <= score < 2	*1/*2	Abnormal/Priority/High Risk
Poor Metabolizer	0 <= score < 1	*2/*3	Abnormal/Priority/High Risk
Indeterminate	Unknown score	*1/*7	Normal/Routine/Low Risk

Recommendations for CYP2C9

• Celecoxib

  “The CPIC Dosing Guideline for celecoxib, flurbiprofen, ibuprofen and lornoxicam recommends initiating therapy with 25-50% of the lowest recommended starting dose for CYP2C9 poor metabolizers and initiating therapy with lowest recommended starting dose for CYP2C9 intermediate metabolizers with activity score of 1. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Flurbiprofen

  “The CPIC Dosing Guideline for celecoxib, flurbiprofen, ibuprofen and lornoxicam recommends initiating therapy with 25-50% of the lowest recommended starting dose for CYP2C9 poor metabolizers and initiating therapy with lowest recommended starting dose for CYP2C9 intermediate metabolizers with activity score of 1. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Fluvastatin

  “CYP2C9 IMs should avoid fluvastatin doses greater than 40mg while CYP2C9 PMs should avoid doses greater than 20mg. If higher doses are required for desired efficacy, an alternative statin should be considered. Patients with SLCO1B1 poor function should also avoid fluvastatin doses greater than 40mg and and adjust doses of fluvastatin based on disease-specific guidelines. Patients with both SLCO1B1 poor function and CYP2C9 IM/PM should be prescribed an alternative statin depending on the desired potency.” (Source: PharmGKB)

• Ibuprofen

  “The CPIC Dosing Guideline for celecoxib, flurbiprofen, ibuprofen and lornoxicam recommends initiating therapy with 25-50% of the lowest recommended starting dose for CYP2C9 poor metabolizers and initiating therapy with lowest recommended starting dose for CYP2C9 intermediate metabolizers with activity score of 1. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Lornoxicam

  “The CPIC Dosing Guideline for celecoxib, flurbiprofen, ibuprofen and lornoxicam recommends initiating therapy with 25-50% of the lowest recommended starting dose for CYP2C9 poor metabolizers and initiating therapy with lowest recommended starting dose for CYP2C9 intermediate metabolizers with activity score of 1. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Meloxicam

  “The CPIC Dosing Guideline for meloxicam recommends alternative therapy for CYP2C9 poor metabolizers due to markedly prolonged half-life, and initiating therapy with 50% of the lowest recommended starting dose or choose an alternative therapy for CYP2C9 intermediate metabolizers with activity score of 1. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Piroxicam

  “The CPIC Dosing Guideline for piroxicam recommends that CYP2C9 poor metabolizers and intermediate metabolizers with activity score of 1 should choose an alternative therapy not metabolized by CYP2C9 or not significantly impacted by CYP2C9 genetic variants in vivo or choose an NSAID metabolized by CYP2C9 but with a shorter half-life. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Tenoxicam

  “The CPIC Dosing Guideline for tenoxicam recommends that CYP2C9 poor metabolizers and intermediate metabolizers with activity score of 1 should choose an alternative therapy not metabolized by CYP2C9 or not significantly impacted by CYP2C9 genetic variants in vivo or choose an NSAID metabolized by CYP2C9 but with a shorter half-life. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

Resources for CYP2C9

• PharmVar CYP2C9 page

• CPIC® Guideline for NSAIDs based on CYP2C9 genotype

• The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms

CYP2C19

Phenotype summary for CYP2C19

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Ultrarapid Metabolizer	*17/*17	Abnormal/Priority/High Risk
Rapid Metabolizer	*1/*17	Abnormal/Priority/High Risk
Normal Metabolizer	*1/*1	Normal/Routine/Low Risk
Likely Intermediate Metabolizer	*1/*10	Abnormal/Priority/High Risk
Intermediate Metabolizer	*1/*2	Abnormal/Priority/High Risk
Likely Poor Metabolizer	*10/*22	Abnormal/Priority/High Risk
Poor Metabolizer	*2/*2	Abnormal/Priority/High Risk
Indeterminate	*1/*12	None

Recommendations for CYP2C19

• Amitriptyline

  “The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Citalopram

  “The CPIC Dosing Guideline for the selective serotonin reuptake inhibitors citalopram and escitalopram recommends an alternative drug not predominantly metabolized by CYP2C19 for CYP2C19 ultrarapid metabolizers. For CYP2C19 poor metabolizers, consider a 50% reduction of recommended starting dose and titrate to response or select alternative drug not predominantly metabolized by CYP2C19.” (Source: PharmGKB)

• Clomipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including clomipramine. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Clopidogrel

  “The CPIC Dosing Guideline for clopidogrel recommends an alternative antiplatelet therapy for CYP2C19 poor or intermediate metabolizers (cardiovascular indications: prasugrel or ticagrelor if no contraindication; neurovascular indications: alternative P2Y12 inhibitor if clinically indicated and no contraindication.)” (Source: PharmGKB)

• Dexlansoprazole

  “The CPIC Dosing Guideline recommendations for dexlansoprazole are based on the similarity in its metabolism and lansoprazole and extrapolated from the first-generation PPIs. The guideline recommends to increase the starting daily dose and to monitor efficacy in CYP2C19 ultrarapid metabolizer. For CYP2C19 rapid and normal metabolizers in the treatment of H. pylori infection and erosive esophagitis increasing the dose might be considered after initiation with the standard starting daily dose. The recommendations for intermediate and poor metabolizers for chronic therapy (>12 weeks) and efficacy achieved is to consider 50% reduction in daily dose. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Doxepin

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including doxepin. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Escitalopram

  “The CPIC Dosing Guideline for the selective serotonin reuptake inhibitors citalopram and escitalopram recommends an alternative drug not predominantly metabolized by CYP2C19 for CYP2C19 ultrarapid metabolizers. For CYP2C19 poor metabolizers, consider a 50% reduction of recommended starting dose and titrate to response or select alternative drug not predominantly metabolized by CYP2C19.” (Source: PharmGKB)

• Imipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including imipramine. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Lansoprazole

  “The CPIC Dosing Guideline for omeprazole, lansoprazole, pantoprazole recommends to increase the starting daily dose and to monitor efficacy in CYP2C19 ultrarapid metabolizer. For CYP2C19 rapid and normal metabolizers in the treatment of H. pylori infection and erosive esophagitis increasing the dose might be considered after initiation with the standard starting daily dose. The recommendations for intermediate and poor metabolizer for chronic therapy (>12 weeks) and efficacy achieved is to consider 50% reduction in daily dose. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Omeprazole

  “The CPIC Dosing Guideline for omeprazole, lansoprazole, pantoprazole recommends to increase the starting daily dose and to monitor efficacy in CYP2C19 ultrarapid metabolizer. For CYP2C19 rapid and normal metabolizers in the treatment of H. pylori infection and erosive esophagitis increasing the dose might be considered after initiation with the standard starting daily dose. The recommendations for intermediate and poor metabolizer for chronic therapy (>12 weeks) and efficacy achieved is to consider 50% reduction in daily dose. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Pantoprazole

  “The CPIC Dosing Guideline for omeprazole, lansoprazole, pantoprazole recommends to increase the starting daily dose and to monitor efficacy in CYP2C19 ultrarapid metabolizer. For CYP2C19 rapid and normal metabolizers in the treatment of H. pylori infection and erosive esophagitis increasing the dose might be considered after initiation with the standard starting daily dose. The recommendations for intermediate and poor metabolizer for chronic therapy (>12 weeks) and efficacy achieved is to consider 50% reduction in daily dose. See full guideline for further details and supporting evidence.” (Source: PharmGKB)

• Sertraline

  “The CPIC Dosing Guideline for the selective serotonin reuptake inhibitor sertraline recommends to consider a 50% reduction of recommended starting dose and titrate to response or select alternative drug not predominantly metabolized by CYP2C19 for CYP2C19 poor metabolizers.” (Source: PharmGKB)

• Voriconazole

  “The CPIC dosing guideline for voriconazole recommends selecting an alternative agent that is not dependent on CYP2C19 metabolism in adults who are CYP2C19 ultrarapid metabolizers, rapid metabolizers or poor metabolizers. In pediatric patients, an alternative agent should be used in patients who are ultrarapid metabolizers or poor metabolizers. In pediatric rapid metabolizers, therapy should be initiated at recommended standard case dosing, then therapeutic dosing monitoring should be used to titrate dose to therapeutic trough concentrations.” (Source: PharmGKB)

• Trimipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including trimipramine. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

Resources for CYP2C19

• PharmVar CYP2C19 page

• CPIC® Guideline for Voriconazole and CYP2C19

CYP2D6

SV summary for CYP2D6

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*2		Model	Profile	Profile	WGS	GeT-RM	NA11839	0.4.1
*5	WholeDel1	*5/*29		Model	Profile	Profile	WGS	GeT-RM	NA18861	0.4.1
*5	WholeDel1Hom	*5/*5		Model	Profile	Profile	WGS			0.10.0
*4x2	WholeDup1	*2/*4x2		Model	Profile	Profile	WGS	GeT-RM	NA19819	0.4.1
*1x3	WholeMultip1	*1x3/*10		Model	Profile	Profile	WGS	1KGP	NA19190	0.12.0
*68+*4	Tandem1A	*139/*68+*4		Model	Profile	Profile	WGS	GeT-RM	NA11832	0.4.1	*68 has exon 1 of CYP2D6 origin and exons 2-9 of CYP2D7 origin (breakpoint in intron 1).
*68+*4	Tandem1B	*68+*4/*68+*4		Model	Profile	Profile	WGS	1KGP	NA12282	0.12.0
*36+*10	Tandem2A	*2/*36+*10		Model	Profile	Profile	WGS	GeT-RM	NA18564	0.4.1	*36 has exons 1-8 of CYP2D6 origin and exon 9 of CYP2D7 origin (breakpoint in exon 9).
*36x2+*10	Tandem2B	*1/*36x2+*10		Model	Profile	Profile	WGS	GeT-RM	NA18524	0.4.1
*36x3+*10	Tandem2C	*1/*36x3+*10		Model	Profile	Profile	WGS			0.10.0
	Tandem2F	Indeterminate		Model	Profile	Profile	WGS	1KGP	HG00458	0.15.0
*13+*1	Tandem3	*1/*13+*1		Model	Profile	Profile	WGS			0.11.0
	Tandem4	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA19719	0.14.0
*5, *68+*4	WholeDel1+Tandem1A	*5/*68+*4		Model	Profile	Profile	WGS	GeT-RM	HG01190	0.4.1
*2x2, *68+*4	WholeDup1+Tandem1A	*2x2/*68+*4		Model	Profile	Profile	WGS	GeT-RM	NA21781	0.4.1
	ParalogPartialDel1	*2/*41		Model	Profile	Profile	WGS	1KGP	NA19316	0.13.0
	WholeDel1+Tandem3	Indeterminate		Model	Profile	Profile	WGS	1KGP	HG03803	0.16.0
	Unknown1	Indeterminate			Profile	Profile	WGS	1KGP	NA18555	0.12.0
	Unknown2	Indeterminate			Profile	Profile	WGS	1KGP	NA19982	0.14.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for CYP2D6, and corresponding copy number profiles and allele fraction profiles.

Phenotype summary for CYP2D6

Activity score is used for phenotype prediction.

Phenotype	Activity Score	Example	Priority
Ultrarapid Metabolizer	2.5 <= score	*1/*2x2	Abnormal/Priority/High Risk
Normal Metabolizer	1.25 <= score < 2.5	*1/*1	Normal/Routine/Low Risk
Intermediate Metabolizer	0.25 <= score < 1.25	*1/*4	Abnormal/Priority/High Risk
Poor Metabolizer	0 <= score < 0.25	*4/*5	Abnormal/Priority/High Risk
Indeterminate	Unknown score	*1/*22	None

Recommendations for CYP2D6

• Amitriptyline

  “The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Atomoxetine

  “The CPIC Dosing Guideline for atomoxetine provides therapeutic recommendations for CYP2D6 ultrarapid, normal, intermediate, and poor metabolizer, which includes guidance for plasma drug concentration testing, as a means to estimate atomoxetine exposure, if no clinical response and in the absence of adverse events after 2 weeks of therapy.” (Source: PharmGKB)

• Clomipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including clomipramine. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Codeine

  “Alternate non-tramadol analgesics are recommended for CYP2D6 ultrarapid and poor metabolizers. A label recommended age- or weight-specific dose of codeine is warranted for CYP2D6 normal and intermediate metabolizers.” (Source: PharmGKB)

• Desipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline/nortriptyline and CYP2C19, CYP2D6 to other tricyclics including desipramine. The CPIC Dosing Guideline update for nortriptyline recommends a 25% dose reduction for CYP2D6 intermediate metabolizers. For CYP2D6 ultrarapid or poor metabolizers, an alternative drug should be considered. If nortriptyline is warranted, consider a 50% dose reduction in CYP2D6 poor metabolizers.” (Source: PharmGKB)

• Doxepin

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including doxepin. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Fluvoxamine

  “The CPIC Dosing Guideline for the selective serotonin reuptake inhibitor fluvoxamine recommends to consider a 25-50% reduction of recommended starting dose and titrate to response or use an alternative drug not metabolized by CYP2D6 for CYP2D6 poor metabolizers.” (Source: PharmGKB)

• Hydrocodone

  “CYP2D6 intermediate and poor metabolizers should initiate hydrocodone therapy using the label recommended age- or weight-specific dosing. However, if there is no response to hydrocodone in these patients, an alternative analgesic should be considered.

  There is insufficient evidence to provide a dosing recommendation for hydrocodone in CYP2D6 ultrarapid metabolizers.” (Source: PharmGKB)

• Imipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including imipramine. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Nortriptyline

  “The CPIC Dosing Guideline update for nortriptyline recommends a 25% dose reduction for CYP2D6 intermediate metabolizers. For CYP2D6 ultrarapid or poor metabolizers, an alternative drug should be considered. If nortriptyline is warranted, consider a 50% dose reduction in CYP2D6 poor metabolizers.” (Source: PharmGKB)

• Ondansetron

  “The CPIC dosing guideline for ondansetron recommends selecting an alternate drug for CYP2D6 ultrarapid metabolizers. It is recommended that the alternate drug not be predominantly metabolized by CYP2D6 (eg. granisetron).” (Source: PharmGKB)

• Paroxetine

  “The CPIC Dosing Guideline for the selective serotonin reuptake inhibitor paroxetine recommends an alternative drug not predominantly metabolized by CYP2D6 for CYP2D6 ultrarapid metabolizers and for CYP2D6 poor metabolizers. For CYP2D6 poor metabolizers, if paroxetine use is warranted, consider a 50% reduction of recommended starting dose and titrate to response.” (Source: PharmGKB)

• Tamoxifen

  “The CPIC Dosing Guideline for tamoxifen recommends the use of alternative hormonal therapy such as an aromatase inhibitor for postmenopausal women or aromatase inhibitor along with ovarian function suppression in premenopausal women for CYP2D6 poor metabolizer, if aromatase inhibitor use is not contraindicated. For CYP2D6 intermediate metabolizers and CYP2D6 allele combinations resulting in an activity score (AS) of 1 the recommendation is to consider the recommendations stated for the CYP2D6 poor metabolizer. If aromatase inhibitor use is contraindicated, consideration should be given to use a higher but FDA approved tamoxifen dose for CYP2D6 intermediate metabolizers and CYP2D6 allele combinations resulting in an AS of 1. For poor metabolizer, higher dose tamoxifen (40 mg/day) increases but does not normalize endoxifen concentrations and can be considered if there are contraindications to aromatase inhibitor therapy.” (Source: PharmGKB)

• Tramadol

  “Alternate non-codeine analgesics are recommended for CYP2D6 ultrarapid and poor metabolizers. A label recommended age- or weight-specific dose of tramadol is warranted for CYP2D6 normal and intermediate metabolizers.” (Source: PharmGKB)

• Trimipramine

  “Tricyclic antidepressants have comparable pharmacokinetic properties, it may be reasonable to apply the CPIC Dosing Guideline for amitriptyline and CYP2C19, CYP2D6 to other tricyclics including trimipramine. The CPIC Dosing Guideline update for amitriptyline recommends an alternative drug for CYP2D6 ultrarapid or poor metabolizers and CYP2C19 ultrarapid, rapid or poor metabolizers. If amitriptyline is warranted, consider a 50% dose reduction in CYP2D6 or CYP2C19 poor metabolizers. For CYP2D6 intermediate metabolizers, a 25% dose reduction should be considered.” (Source: PharmGKB)

• Tropisetron

  “The CPIC dosing guideline for tropisetron recommends selecting an alternate drug for CYP2D6 ultrarapid metabolizers. It is recommended that the alternate drug not be predominantly metabolized by CYP2D6 (eg. granisetron).” (Source: PharmGKB)

Filtered alleles for CYP2D6

Some alleles in PharmVar will not be called by PyPGx because one or more of their variants have a high false positive rate, likely due to read misalignment to the CYP2D7 pseudogene. Those alleles are listed in below table. If problematic variants are present in gnomAD, their links are provided so that you can look at filtering status, allele imbalance for heterozygotes, etc.

Problematic Variant	Star Alleles	GRCh37	GRCh38
rs769157652 (E410K)	*27, *32	22-42522940-C-T	22-42126938-C-T
rs61745683 (V370I)	*122	22-42523514-C-T	22-42127512-C-T
rs1058172 (R365H)	*139	22-42523528-C-T	22-42127526-C-T
rs202102799 (Y355C)	*127	22-42523558-T-C	22-42127556-T-C
rs17002853 (L231P)	*131	22-42524327-A-G	22-42128325-A-G

Resources for CYP2D6

• PharmVar CYP2D6 page

• CPIC® Guideline for Tamoxifen based on CYP2D6 genotype

CYP2E1

SV summary for CYP2E1

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*7	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA10831	0.4.1
	WholeDel1	Indeterminate			Profile	Profile	WGS	1KGP	HG03445	0.16.0
*1x2	WholeDup1	*1/*1x2		Model	Profile	Profile	WGS			0.4.1
*7x2	WholeDup1	*1/*7x2	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA19095	0.4.1
*1x2	WholeDup2	*1x2/*7		Model	Profile	Profile	WGS	1KGP	NA19225	0.12.0
*S1	PartialDup1	*1/*S1	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA19920	0.4.1	*S1 is linked to *7.
*S1	PartialDup1Hom	*S1/*S1		Model	Profile	Profile	WGS	1KGP	NA19309	0.13.0
*7x3	WholeMultip1	*7/*7x3		Model	Profile	Profile	WGS	GeT-RM	NA19908	0.4.1
	WholeMultip2	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA20291	0.14.0
	WholeDup1+PartialDup1	Indeterminate			Profile	Profile	WGS	1KGP	HG03401	0.16.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for CYP2E1, and corresponding copy number profiles and allele fraction profiles.

Resources for CYP2E1

• PharmVar CYP2E1 page

CYP2F1

Resources for CYP2F1

• PharmVar CYP2F1 page

CYP2J2

Resources for CYP2J2

• PharmVar CYP2J2 page

CYP2R1

Resources for CYP2R1

• PharmVar CYP2R1 page

CYP2S1

Resources for CYP2S1

• PharmVar CYP2S1 page

CYP2W1

Resources for CYP2W1

• PharmVar CYP2W1 page

CYP3A4

Resources for CYP3A4

• PharmVar CYP3A4 page

CYP3A5

Phenotype summary for CYP3A5

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Normal Metabolizer	*1/*1	Abnormal/Priority/High Risk
Intermediate Metabolizer	*1/*3	Abnormal/Priority/High Risk
Possible Intermediate Metabolizer	*1/*2	Abnormal/Priority/High Risk
Poor Metabolizer	*6/*6	Normal/Routine/Low Risk
Indeterminate	*2/*2	None

Recommendations for CYP3A5

• Tacrolimus

  “The CPIC dosing guideline for tacrolimus recommends increasing the starting dose by 1.5 to 2 times the recommended starting dose in patients who are CYP3A5 intermediate or extensive metabolizers, though total starting dose should not exceed 0.3 mg/kg/day. Therapeutic drug monitoring should also be used to guide dose adjustments.” (Source: PharmGKB)

Resources for CYP3A5

• PharmVar CYP3A5 page

• CPIC® Guideline for Tacrolimus and CYP3A5

• PharmGKB: Annotation of CPIC Guideline for tacrolimus and CYP3A5

CYP3A7

Resources for CYP3A7

• PharmVar CYP3A7 page

CYP3A43

Resources for CYP3A43

• PharmVar CYP3A43 page

CYP4A11

Resources for CYP4A11

• PharmVar CYP4A11 page

CYP4A22

Resources for CYP4A22

• PharmVar CYP4A22 page

CYP4B1

Resources for CYP4B1

• PharmVar CYP4B1 page

CYP4F2

SV summary for CYP4F2

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*3		Model	Profile	Profile	WGS	GeT-RM	HG01190	0.11.0
*DEL	WholeDel1	*1/*DEL		Model	Profile	Profile	WGS			0.11.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for CYP4F2, and corresponding copy number profiles and allele fraction profiles.

Resources for CYP4F2

• PharmVar CYP4F2 page

CYP17A1

Resources for CYP17A1

• PharmVar CYP17A1 page

CYP19A1

Resources for CYP19A1

• PharmVar CYP19A1 page

CYP26A1

Resources for CYP26A1

• PharmVar CYP26A1 page

DPYD

Phenotype summary for DPYD

Activity score is used for phenotype prediction.

Phenotype	Activity Score	Example	Priority
Normal Metabolizer	2 == score	Reference/Reference	Normal/Routine/Low Risk
Intermediate Metabolizer	1 <= score < 2	Reference/c.1905+1G>A (*2A)	Abnormal/Priority/High Risk
Poor Metabolizer	0 <= score < 1	c.295_298delTCAT (*7)/c.703C>T (*8)	Abnormal/Priority/High Risk

Recommendations for DPYD

• Capecitabine

  “The CPIC Dosing Guideline for 5-fluorouracil and capecitabine recommends an alternative drug for patients who are DPYD poor metabolizers with an activity score of 0. In those who are poor metabolizers with an activity score of 0.5, an alternative drug is also recommended, but if this is not considered a suitable therapeutic option, 5-fluorouracil or capecitabine should be administered at a strongly reduced dose with early therapeutic drug monitoring. Patients who are intermediate metabolizers with an activity score of 1 or 1.5 should receive a dose reduction of 50%. Patients with the c.[2846A>T];[2846A>T] genotype may require a >50% dose reduction.” (Source: PharmGKB)

• Fluorouracil

  “The CPIC Dosing Guideline for 5-fluorouracil and capecitabine recommends an alternative drug for patients who are DPYD poor metabolizers with an activity score of 0. In those who are poor metabolizers with an activity score of 0.5, an alternative drug is also recommended, but if this is not considered a suitable therapeutic option, 5-fluorouracil or capecitabine should be administered at a strongly reduced dose with early therapeutic drug monitoring. Patients who are intermediate metabolizers with an activity score of 1 or 1.5 should receive a dose reduction of 50%. Patients with the c.[2846A>T];[2846A>T] genotype may require a >50% dose reduction.” (Source: PharmGKB)

Resources for DPYD

• PharmVar DPYD page

• CPIC® Guideline for Fluoropyrimidines and DPYD

F5

Phenotype summary for F5

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Favorable Response	Reference/Reference	None
Unfavorable Response	Reference/Leiden	None

Recommendations for F5

• Hormonal contraceptives

  “In individuals who carry the Factor V Leiden allele (rs6025 T) and have a family history of thrombotic events, estrogen-containing oral contraceptives should be avoided and alternative forms of contraception used.” (Source: PharmGKB)

Resources for F5

• PharmGKB: Annotation of DPWG Guideline for hormonal contraceptives for systemic use and F5

G6PD

SV summary for G6PD

Since the gene is located on X chromosome, its copy number differs between females (N=2) and males (N=1). Technically speaking, this difference is not a SV event, but it is treated as such by PyPGx for genotyping purposes (i.e. sex determination).

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Female	B (reference)/B (reference)		Model	Profile	Profile	WGS	GeT-RM	HG00276	0.12.0
MALE	Male	MALE/B (reference)		Model	Profile	Profile	WGS	GeT-RM	HG00436	0.12.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for G6PD, and corresponding copy number profiles and allele fraction profiles.

Phenotype summary for G6PD

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
G6PD Normal	A/B (reference)	Normal Risk
G6PD Deficient with CNSHA	Alhambra/Bari	Abnormal/Priority/High Risk
G6PD Variable	202G>A_376A>G_1264C>G/B (reference)	Abnormal/Priority/High Risk
G6PD Deficient	202G>A_376A>G_1264C>G/A- 680T_376G	Abnormal/Priority/High Risk
G6PD Indeterminate	A- 202A_376G/Dagua	Abnormal/Priority/High Risk

GSTM1

SV summary for GSTM1

This gene is known to have an extremely high rate of gene deletion polymorphism in the population and thus requires SV analysis.

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*A/*B		Model	Profile	Profile	WGS	GeT-RM	NA06991	0.4.1
*0	WholeDel1	*0/*A	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA18855	0.4.1
*0	WholeDel1Hom	*0/*0	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA10831	0.4.1
*0	WholeDel2	*0/*A		Model	Profile	Profile	WGS	GeT-RM	NA21097	0.15.0
*Ax2	WholeDup1	*A/*Ax2	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA19908	0.4.1
*Bx2	WholeDup1	*A/*Bx2		Model	Profile	Profile	WGS			0.4.1
	NoncodingDel1	*A/*B		Model	Profile	Profile	WGS	1KGP	NA19005	0.12.0
*0	WholeDel1+NoncodingDel1	*0/*A		Model	Profile	Profile	WGS	1KGP	NA06984	0.12.0
	PartialDup1	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA19908	0.14.0
	WholeDel1+WholeDel2	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA20506	0.14.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for GSTM1, and corresponding copy number profiles and allele fraction profiles.

GSTT1

GRCh38 data for GSTT1

GSTT1 is located on chr22 for GRCh37 but on chr22_KI270879v1_alt for GRCh38. Therefore, if you are interested in genotyping this gene with GRCh38 data, then you must have sequence reads mapped to the ALT contig. For more details, please read the GRCh37 vs. GRCh38 page.

SV summary for GSTT1

This gene is known to have an extremely high rate of gene deletion polymorphism in the population and thus requires SV analysis.

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*A/*A		Model	Profile	Profile	WGS	GeT-RM	NA07055	0.4.1
*0	WholeDel1	*0/*A	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA19908	0.4.1
*0	WholeDel1Hom	*0/*0	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA11832	0.4.1

IFNL3

Phenotype summary for IFNL3

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Favorable Response	Reference/Reference	None
Unfavorable Response	Reference/rs12979860	None
Indeterminate	Reference/rs8099917	None

Recommendations for IFNL3

• Peginterferon alfa-2a

“IFNL3 (IL28B) variation (rs12979860) is the strongest baseline predictor of response to PEG-interferon-alpha-containing regimens in HCV genotype 1 patients. Patients with the favorable response genotype (rs12979860 CC) have increased likelihood of response (higher SVR rate) to PEG-interferon-alpha- containing regimens as compared to patients with unfavorable response genotype (rs12979860 CT or TT). Consider implications before initiating PEG-IFN alpha and RBV containing regimens.” (Source: PharmGKB)

• Peginterferon alfa-2b

“IFNL3 (IL28B) variation (rs12979860) is the strongest baseline predictor of response to PEG-interferon-alpha-containing regimens in HCV genotype 1 patients. Patients with the favorable response genotype (rs12979860 CC) have increased likelihood of response (higher SVR rate) to PEG-interferon-alpha- containing regimens as compared to patients with unfavorable response genotype (rs12979860 CT or TT). Consider implications before initiating PEG-IFN alpha and RBV containing regimens.” (Source: PharmGKB)

• Ribavirin

“IFNL3 (IL28B) variation (rs12979860) is the strongest baseline predictor of response to PEG-interferon-alpha-containing regimens in HCV genotype 1 patients. Patients with the favorable response genotype (rs12979860 CC) have increased likelihood of response (higher SVR rate) to PEG-interferon-alpha- containing regimens as compared to patients with unfavorable response genotype (rs12979860 CT or TT). Consider implications before initiating PEG-IFN alpha and RBV containing regimens.” (Source: PharmGKB)

Resources for IFNL3

• PharmGKB: Annotation of CPIC Guideline for peginterferon alfa-2a,peginterferon alfa-2b,ribavirin and IFNL3

• CPIC® Guideline for PEG Interferon-Alpha-Based Regimens and IFNL3

MT-RNR1

Phenotype summary for MT-RNR1

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Normal Risk of Aminoglycoside-Induced Hearing Loss	Reference/Reference	None
Increased Risk of Aminoglycoside-Induced Hearing Loss	m.1494C>T/m.1494C>T	None
Uncertain Risk of Aminoglycoside-Induced Hearing Loss	m.663A>G/m.663A>G	None

NUDT15

Phenotype summary for NUDT15

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Normal Metabolizer	*1/*1	Normal/Routine/Low risk
Intermediate Metabolizer	*1/*2	Abnormal/Priority/High Risk
Possible Intermediate Metabolizer	*3/*4	Abnormal/Priority/High Risk
Poor Metabolizer	*2/*3	Abnormal/Priority/High Risk
Indeterminate	*1/*4	Abnormal/Priority/High Risk

Recommendations for NUDT15

• Azathioprine

  “Consider an alternate agent or extreme dose reduction of azathioprine for patients who are TPMT or NUDT15 poor metabolizers. Start at 30-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers.” (Source: PharmGKB)

• Mercaptopurine

  “Consider an alternate agent or extreme dose reduction of mercaptopurine for patients who are TPMT or NUDT15 poor metabolizers. Start at 30-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers.” (Source: PharmGKB)

• Thioguanine

  “Consider an alternate agent or extreme dose reduction of thioguanine for patients who are TPMT or NUDT15 poor metabolizers. Start at 50-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers.” (Source: PharmGKB)

Resources for NUDT15

• PharmVar NUDT15 page

• CPIC® Guideline for Thiopurines and TPMT and NUDT15

POR

Resources for POR

• PharmVar POR page

PTGIS

Resources for PTGIS

• PharmVar PTGIS page

RYR1

Phenotype summary for RYR1

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Uncertain Susceptibility	Reference/Reference	Normal Risk
Malignant Hyperthermia Susceptibility	Reference/c.103T>C	Abnormal/Priority/High Risk

Recommendations for RYR1

• Desflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics uch as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Enflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Halothane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Isoflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Methoxyflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Sevoflurane

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

• Succinylcholine

  “The CPIC Dosing Guideline recommends that halogenated volatile anesthetics such as desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane and the depolarizing muscle relaxants succinylcholine are relatively contraindicated in persons with malignant hyperthermia susceptibility (MHS). See full guideline for disclaimers, further details and supporting evidence.” (Source: PharmGKB)

Resources for RYR1

• PharmGKB: Annotation of CPIC Guideline for desflurane and CACNA1S, RYR1

• CPIC® Guideline for Potent Volatile Anesthetic Agents and Succinylcholine and RYR1 and CACNA1S

• Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for the Use of Potent Volatile Anesthetic Agents and Succinylcholine in the Context of RYR1 or CACNA1S Genotypes

SLC22A2

SV summary for SLC22A2

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*3		Model	Profile	Profile	WGS	GeT-RM	HG01190	0.4.1
*S1	NoncodingDel1	*1/*S1	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA18855	0.4.1
*S1	NoncodingDel1Hom	*S1/*S1		Model	Profile	Profile	WGS	1KGP	HG02337	0.16.0
*S2	PartialDel1	*1/*S2	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA19819	0.4.1
*S1, *S2	NoncodingDel1+PartialDel1	*S1/*S2		Model	Profile	Profile	WGS	1KGP	NA19030	0.13.0
	PartialDup1	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA20813	0.14.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for SLC22A2, and corresponding copy number profiles and allele fraction profiles.

SLCO1B1

Phenotype summary for SLCO1B1

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Increased Function	*14/*14	None
Normal Function	*1/*1	Normal/Routine/Low Risk
Possible Decreased Function	*2/*15	Abnormal/Priority/High Risk
Decreased Function	*1/*5	Abnormal/Priority/High Risk
Poor Function	*5/*5	Abnormal/Priority/High Risk
Indeterminate	*2/*38	None

Recommendations for SLCO1B1

• Atorvastatin

  “Prescribe ≤20mg for patients with SLCO1B1 poor function phenotype and ≤40mg for patients with SLCO1B1 decreased or possible decreased phenotype as a starting dose. Adjust doses of atorvastatin based on disease-specific guidelines. Prescriber should be aware of possible increased risk for myopathy especially for 40mg dose.” (Source: PharmGKB)

• Fluvastatin

  “CYP2C9 IMs should avoid fluvastatin doses greater than 40mg while CYP2C9 PMs should avoid doses greater than 20mg. If higher doses are required for desired efficacy, an alternative statin should be considered. Patients with SLCO1B1 poor function should also avoid fluvastatin doses greater than 40mg and and adjust doses of fluvastatin based on disease-specific guidelines. Patients with both SLCO1B1 poor function and CYP2C9 IM/PM should be prescribed an alternative statin depending on the desired potency.” (Source: PharmGKB)

• Lovastatin

  “Prescribe an alternative statin depending on the desired potency for patients with SLCO1B1 decreased function, possible decreased function or poor function phenotype. If lovastatin therapy is warranted in patients with SLCO1B1 decreased or possible decreased phenotype, limit dose to <20mg/day.” (Source: PharmGKB)

• Pitavastatin

  “Prescribe ≤1mg as a starting dose for patients with SLCO1B1 poor function phenotype. Prescribe ≤2mg as a starting dose for patients with SLCO1B1 decreased or possible decreased phenotype. Adjust doses of pitavastatin based on disease-specific guidelines. Consider an alternative statin or combination therapy if higher doses are needed.” (Source: PharmGKB)

• Pravastatin

  “Prescribe ≤40mg as a starting dose and adjust doses of pravastatin based on disease-specific guidelines for patients with SLCO1B1 poor function phenotype. Prescribe desired starting dose and adjust doses of pravastatin based on disease-specific guidelines for patients with SLCO1B1 decreased or possible decreased phenotype. Prescriber should be aware of possible increased risk for myopathy with pravastatin especially with doses >40mg per day.” (Source: PharmGKB)

• Rosuvastatin

  “Prescribe ≤20mg as a starting dose and adjust doses of rosuvastatin based on disease-specific and specific population guidelines for patients who are SLCO1B1 or ABCG2 poor function phenotype. If dose >20mg needed for desired efficacy, consider combination therapy (i.e. rosuvastatin plus non-statin guideline directed medical therapy). Patients with both ABCG2 poor function and SLCO1B1 poor/decreased function should be prescribed ≤10mg as a starting dose.” (Source: PharmGKB)

• Simvastatin

  “Prescribe an alternative statin depending on the desired potency for patients with SLCO1B1 decreased function, possible decreased function or poor function phenotype. If simvastatin therapy is warranted in patients with SLCO1B1 decreased or possible decreased phenotype, limit dose to <20mg/day.” (Source: PharmGKB)

Resources for SLCO1B1

• PharmVar SLCO1B1 page

• CPIC® Guideline for Simvastatin and SLCO1B1

• The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms

• PharmGKB: Annotation of CPIC Guideline for rosuvastatin and ABCG2, SLCO1B1

SULT1A1

SV summary for SULT1A1

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*2		Model	Profile	Profile	WGS	GeT-RM	NA06991	0.11.0
*DEL	WholeDel1	*1/*DEL		Model	Profile	Profile	WGS	GeT-RM	NA18942	0.11.0
*DEL	WholeDel1Hom	*DEL/*DEL		Model	Profile	Profile	WGS	1KGP	NA20874	0.14.0
*1x2	WholeDup1	*1x2/*2		Model	Profile	Profile	WGS	GeT-RM	NA18509	0.11.0
*1x3	WholeMultip1	*1x3/*2		Model	Profile	Profile	WGS	GeT-RM	NA18868	0.11.0
*1x4	WholeMultip2	*1x4/*2		Model	Profile	Profile	WGS	GeT-RM	NA18484	0.11.0
*1x3, *2x2	WholeMultip2	*1x3/*2x2		Model	Profile	Profile	WGS	GeT-RM	NA19143	0.11.0
	Unknown1	Indeterminate		Model	Profile	Profile	WGS	GeT-RM	HG01085	0.15.0
	Unknown2	Indeterminate			Profile	Profile	WGS	1KGP		0.16.0
	Unknown3	Indeterminate			Profile	Profile	WGS	1KGP	HG03854	0.16.0
	Unknown4	Indeterminate			Profile	Profile	WGS	1KGP	HG03742	0.16.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for SULT1A1, and corresponding copy number profiles and allele fraction profiles.

TBXAS1

Resources for TBXAS1

• PharmVar TBXAS1 page

TPMT

Phenotype summary for TPMT

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Normal Metabolizer	*1/*1	Normal/Routine/Low Risk
Possible Intermediate Metabolizer	*3A/*12	Abnormal/Priority/High Risk
Intermediate Metabolizer	*1/*2	Abnormal/Priority/High Risk
Poor Metabolizer	*2/*3A	Abnormal/Priority/High Risk
Indeterminate	*1/*18	Abnormal/Priority/High Risk

Recommendations for TPMT

• Azathioprine

  “Consider an alternate agent or extreme dose reduction of azathioprine for patients who are TPMT or NUDT15 poor metabolizers. Start at 30-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers.” (Source: PharmGKB)

• Mercaptopurine

  “Consider an alternate agent or extreme dose reduction of mercaptopurine for patients who are TPMT or NUDT15 poor metabolizers. Start at 30-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers.” (Source: PharmGKB)

• Thioguanine

  “Consider an alternate agent or extreme dose reduction of thioguanine for patients who are TPMT or NUDT15 poor metabolizers. Start at 50-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers.” (Source: PharmGKB)

Resources for TPMT

• CPIC® Guideline for Thiopurines and TPMT and NUDT15

UGT1A1

Phenotype summary for UGT1A1

Diplotype-phenotype mapping is used for phenotype prediction.

Phenotype	Example	Priority
Normal Metabolizer	*1/*1	Normal/Routine/Low Risk
Intermediate Metabolizer	*1/*6	Normal/Routine/Low Risk
Poor Metabolizer	*6/*27	Abnormal/Priority/High Risk
Indeterminate	*28/*80	None

Recommendations for UGT1A1

• Atazanavir

  “The CPIC dosing guideline recommends considering advising individuals who carry two decreased function UGT1A1 alleles about a substantial likelihood of developing jaundice, which may cause non-adherence. The dosing guideline recommends that alternative agents be considered if the risk of non-adherence due to jaundice is high. The risk of discontinuation is low and very low for individuals carrying one, or no decreased function UGT1A1 alleles, respectively.” (Source: PharmGKB)

Resources for UGT1A1

• CPIC® Guideline for Atazanavir and UGT1A1

UGT1A4

SV summary for UGT1A4

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*2		Model	Profile	Profile	WGS	GeT-RM	NA11993	0.9.0
*S1	NoncodingDel1	*1/*S1		Model	Profile	Profile	WGS	GeT-RM	NA19908	0.9.0
*S1	NoncodingDel1Hom	*S1/*S1		Model	Profile	Profile	WGS	1KGP	HG03479	0.16.0
*S2	NoncodingDel2	*1/*S2		Model	Profile	Profile	WGS			0.10.0
*S3	NoncodingDup1	*1/*S3		Model	Profile	Profile	WGS	1KGP	NA18632	0.13.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for UGT1A4, and corresponding copy number profiles and allele fraction profiles.

UGT2B15

SV summary for UGT2B15

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*2	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	HG00589	0.4.1
*S4	WholeDel1	*2/*S4		Model	Profile	Profile	WGS	1KGP	NA19024	0.13.0
	WholeDel2	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA19786	0.14.0
	WholeDup1	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA19776	0.14.0
*S1	PartialDel1	*4/*S1	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA11993	0.4.1
*S2	PartialDel2	*2/*S2		Model	Profile	Profile	WGS	1KGP	NA19160	0.12.0
*S3	PartialDel3	*1/*S3		Model	Profile	Profile	WGS	1KGP	NA19189	0.13.0
	PartialDup1	Indeterminate		Model	Profile	Profile	WGS	1KGP	NA20821	0.14.0
	PartialDup2	Indeterminate			Profile	Profile	WGS	1KGP	HG03082	0.16.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for UGT2B15, and corresponding copy number profiles and allele fraction profiles.

UGT2B17

SV summary for UGT2B17

This gene is known to have an extremely high rate of gene deletion polymorphism in the population and thus requires SV analysis.

Below is comprehensive summary of SV described from real NGS studies:

SV Alleles	SV Name	Genotype	Reference	Gene Model	GRCh37	GRCh38	Data Type	Source	Coriell ID	Version	Description
	Normal	*1/*1	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA19178	0.4.1
*2	WholeDel1	*1/*2	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA18855	0.4.1
*2	WholeDel1Hom	*2/*2	Lee et al., 2019	Model	Profile	Profile	WGS	GeT-RM	NA18617	0.4.1
*S2	PartialDel2	*1/*S2			Profile	Profile	WGS	1KGP	HG03127	0.16.0
*S3	PartialDel3	*1/*S3		Model	Profile	Profile	WGS	1KGP	NA20886	0.14.0
*2, *S1	WholeDel1+PartialDel1	*2/*S1		Model	Profile	Profile	WGS	1KGP	NA19160	0.12.0
*2, *S2	WholeDel1+PartialDel2	*2/*S2		Model	Profile	Profile	WGS	1KGP	NA19189	0.13.0
*2, *S3	WholeDel1+PartialDel3	*2/*S3		Model	Profile	Profile	WGS	1KGP	NA21090	0.15.0

PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP (N=2,504). Click here to see individual SV calls for UGT2B17, and corresponding copy number profiles and allele fraction profiles.