Phenotypes List

This page documents all named alleles, phenotypes and activity scores used by PharmCAT.

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ABCG2

Named Variants	CPIC Phenotypes	DPWG Phenotypes
rs2231142 reference (G) rs2231142 variant (T)	Decreased Function Normal Function Poor Function	Decreased Function Normal Function Poor Function

CACNA1S

Named Variants	CPIC Phenotypes
Reference c.520C>T c.3257G>A	Malignant Hyperthermia Susceptibility Uncertain Susceptibility

CFTR

Named Variants	CPIC Phenotypes
711+3A->G 2789+5G->A 3272-26A->G 3849+10kbC->T A455E A1067T D110E D110H D579G D1152H D1270N E56K E193K E831X F1052V F1074L G178R G551D G551S G1069R G1244E G1349D K1060T L206W P67L R74W R117C R117H R347H R352Q R1070Q R1070W S549N S549R(A>C) S549R(T>G) S945L S977F S1251N S1255P ivacaftor non-responsive CFTR sequence	ivacaftor non-responsive in CF patients ivacaftor responsive in CF patients

CYP2B6

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *17 *18 *19 *20 *21 *22 *23 *24 *25 *26 *27 *28 *31 *32 *33 *34 *35 *36 *37 *38 *39 *40 *41 *42 *43 *44 *45 *46 *47 *48 *49 *50	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Rapid Metabolizer Ultrarapid Metabolizer	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

CYP2C19

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *16 *17 *18 *19 *22 *23 *24 *25 *26 *28 *29 *30 *31 *32 *33 *34 *35 *38 *39 *40 *41	Indeterminate Intermediate Metabolizer Likely Intermediate Metabolizer Likely Poor Metabolizer Normal Metabolizer Poor Metabolizer Rapid Metabolizer Ultrarapid Metabolizer	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Ultrarapid Metabolizer

CYP2C9

Named Alleles	CPIC Phenotypes	CPIC Activity Scores	DPWG Phenotypes
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *16 *17 *18 *19 *20 *21 *22 *23 *24 *25 *26 *27 *28 *29 *30 *31 *32 *33 *34 *35 *36 *37 *38 *39 *40 *41 *42 *43 *44 *45 *46 *47 *48 *49 *50 *51 *52 *53 *54 *55 *56 *57 *58 *59 *60 *61 *62 *63 *64 *65 *66 *67 *68 *69 *70 *71 *72 *73 *74 *75 *76 *77 *78 *79 *80 *81 *82 *83 *84 *85 *86 *87 *88	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer	0.0 0.5 1.0 1.5 2.0	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

CYP2D6

Named Alleles	CPIC Phenotypes	CPIC Activity Scores	DPWG Phenotypes	DPWG Activity Scores
*1 *1x2 *1x≥3 *2 *2x2 *2x≥3 *3 *3x2 *4 *4x2 *4x≥3 *5 *6 *6x2 *7 *8 *9 *9x2 *10 *10x2 *11 *12 *13 *13 + *1 *13 + *1x2 *13 + *2 *13 + *68x2 + *4 *14 *15 *17 *17x2 *18 *19 *20 *21 *22 *23 *24 *25 *26 *27 *27x2 *28 *28x2 *29 *29x2 *30 *31 *32 *33 *34 *35 *35x2 *36 *36 + *10 *36 + *10x2 *36x2 *36x2 + *10 *36x2 + *10x2 *37 *38 *39 *40 *41 *41x2 *41x3 *42 *43 *43x2 *44 *45 *45x2 *46 *47 *48 *49 *50 *51 *52 *53 *54 *55 *56 *58 *59 *60 *61 *62 *63 *64 *65 *68 *68 + *2 *68 + *4 *68x2 *69 *70 *71 *72 *73 *74 *75 *81 *82 *83 *84 *85 *86 *87 *88 *89 *90 *91 *92 *93 *94 *95 *96 *97 *98 *99 *100 *101 *102 *103 *104 *105 *106 *107 *108 *109 *110 *111 *112 *113 *114 *115 *116 *117 *118 *119 *120 *121 *122 *123 *124 *125 *126 *127 *128 *129 *130 *131 *132 *133 *134 *135 *136 *137 *138 *139 *140 *141 *142 *143 *144 *145 *146 *146x2 *147 *148 *149 *152 *153 *154 *155 *156 *157 *158 *159 *160 *161 *162 *163	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Ultrarapid Metabolizer	0.0 0.25 0.5 0.75 1.0 1.25 1.5 1.75 2.0 2.25 2.5 2.75 3.0 4.0 ≥3.0 ≥3.25 ≥3.5 ≥3.75 ≥4.0 ≥5.0 ≥6.0	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Ultrarapid Metabolizer	0.0 0.25 0.5 0.75 1.0 1.25 1.5 2.0 2.25 2.5 3.0 4.0 ≥3.0 ≥3.25 ≥3.5 ≥4.0 ≥5.0 ≥6.0

CYP3A4

Named Alleles	DPWG Phenotypes
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *16 *17 *18 *19 *20 *21 *22 *23 *24 *26 *28 *29 *30 *31 *32 *33 *34 *35 *37 *38 *39 *40 *41 *42 *43 *44 *45 *46 *47 *48	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

CYP3A5

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *3 *6 *7 *8 *9	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Possible Intermediate Metabolizer	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

CYP4F2

No recommendations available for this gene.

Named Alleles
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *17 *18 *19 *20 *21 *22 *23

DPYD

Named Variants	CPIC Phenotypes	CPIC Activity Scores	DPWG Phenotypes
Reference c.46C>G c.61C>T c.62G>A c.85T>C (*9A) c.295_298delTCAT (*7) c.313G>A c.343A>G c.451A>G c.496A>G c.498G>A c.525G>A c.557A>G c.601A>C c.632A>G c.703C>T (*8) c.775A>G c.868A>G c.929T>C c.934C>T c.967G>A c.1003G>T (*11) c.1024G>A c.1057C>T c.1108A>G c.1129-5923C>G c.1129-5923C>G, c.1236G>A (HapB3) c.1156G>T (*12) c.1180C>T c.1181G>T c.1218G>A c.1260T>A c.1278G>T c.1294G>A c.1314T>G c.1349C>T c.1358C>G c.1371C>T c.1403C>A c.1475C>T c.1484A>G c.1519G>A c.1543G>A c.1577C>G c.1601G>A (*4) c.1615G>A c.1627A>G (*5) c.1679T>G (*13) c.1682G>T c.1774C>T c.1775G>A c.1777G>A c.1796T>C c.1896T>C c.1898delC (*3) c.1905+1G>A (*2A) c.1905C>G c.1906A>C c.1990G>T c.2021G>A c.2161G>A c.2186C>T c.2194G>A (*6) c.2195T>G c.2279C>T c.2303C>A c.2336C>A c.2482G>A c.2582A>G c.2623A>C c.2639G>T c.2656C>T c.2657G>A (*9B) c.2846A>T c.2872A>G c.2915A>G c.2921A>T c.2933A>G c.2977C>T c.2978T>G c.2983G>T (*10) c.3049G>A c.3061G>C c.3067C>A	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer	0.0 0.5 1.0 1.5 2.0	0.0 (Poor Metabolizer) 0.5 (Phenotyping) 1.0 (Intermediate Metabolizer) 1.0 (Phenotyping) 1.5 (Intermediate Metabolizer) 2.0 (Normal Metabolizer)

G6PD

Named Variants

CPIC Phenotypes

202G>A_376A>G_1264C>G A A- 202A_376G A- 680T_376G A- 968C_376G Aachen Abeno Acrokorinthos Alhambra Amazonia Amiens Amsterdam Anadia Ananindeua Andalus Arakawa Asahi Asahikawa Aures Aveiro B (reference) Bajo Maumere Bangkok Bangkok Noi Bao Loc Bari Belem Beverly Hills, Genova, Iwate, Niigata, Yamaguchi Brighton Buenos Aires Cairo Calvo Mackenna Campinas Canton, Taiwan-Hakka, Gifu-like, Agrigento-like Cassano Chatham Chikugo Chinese-1 Chinese-5 Cincinnati Cleveland Corum Clinic Coimbra Shunde Cosenza Costanzo Covao do Lobo Crispim Dagua Durham Farroupilha Figuera da Foz Flores Fukaya Fushan Gaohe Georgia Gidra Gond Guadalajara Guangzhou Haikou Hammersmith Harilaou Harima Hartford Hechi Hermoupolis Honiara Ierapetra Ilesha Insuli Iowa, Walter Reed, Springfield Iwatsuki Japan, Shinagawa Kaiping, Anant, Dhon, Sapporo-like, Wosera Kalyan-Kerala, Jamnaga, Rohini Kambos Kamiube, Keelung Kamogawa Kawasaki Kozukata Krakow La Jolla Lages Lagosanto Laibin Lille Liuzhou Loma Linda Ludhiana Lynwood Madrid Mahidol Malaga Manhattan Mediterranean, Dallas, Panama, Sassari, Cagliari, Birmingham Metaponto Mexico City Miaoli Minnesota, Marion, Gastonia, LeJeune Mira d'Aire Mizushima Montalbano Montpellier Mt Sinai Munich Murcia Oristano Musashino Namouru Nankang Nanning Naone Nara Nashville, Anaheim, Portici Neapolis Nice Nilgiri No name North Dallas Olomouc Omiya Orissa Osaka Palestrina Papua Partenope Pawnee Pedoplis-Ckaro Piotrkow Plymouth Praha Puerto Limon Quing Yan Radlowo Rehevot Rignano Riley Riverside Roubaix S. Antioco Salerno Pyrgos Santa Maria Santiago Santiago de Cuba, Morioka Sao Borja Seattle, Lodi, Modena, Ferrara II, Athens-like Seoul Serres Shenzen Shinshu Sibari Sierra Leone Sinnai Songklanagarind Split Stonybrook Sugao Sumare Sunderland Surabaya Suwalki Swansea Taipei, Chinese-3 Telti, Kobe Tenri Tokyo, Fukushima Toledo Tomah Tondela Torun Tsukui Ube Konan Union,Maewo, Chinese-2, Kalo Urayasu Utrecht Valladolid Vancouver Vanua Lava Viangchan, Jammu Volendam Wayne West Virginia Wexham Wisconsin Yunan

Deficient Deficient with CNSHA Indeterminate Normal Variable

IFNL3

No recommendations available for this gene.

Named Alleles
rs12979860 reference (C) rs12979860 variant (T)

MT-RNR1

Named Variants	CPIC Phenotypes
Reference m.663A>G m.669T>C m.747A>G m.786G>A m.807A>C m.807A>G m.827A>G m.839A>G m.896A>G m.930A>G m.951G>A m.960C>del m.961T>G m.961T>del m.961T>del+Cn m.988G>A m.1095T>C m.1189T>C m.1243T>C m.1494C>T m.1520T>C m.1537C>T m.1555A>G m.1556C>T	increased risk of aminoglycoside-induced hearing loss normal risk of aminoglycoside-induced hearing loss uncertain risk of aminoglycoside-induced hearing loss

NAT2

No recommendations available for this gene.

Named Alleles
*1 *4 *5 *6 *7 *10 *14 *15 *16 *19 *21 *27 *29 *30 *31 *32 *33 *34 *35 *36 *37 *38 *39 *40 *41 *42 *43 *44 *45 *46 *47 *48 *49 *50 *51 *52 *53 *54 *55 *56 *57 *58 *59 *60 *61 *62 *63 *64 *65 *66 *67 *68 *69 *70 *71 *72 *73 *74 *75

NUDT15

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *16 *17 *18 *19 *20 *21	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Possible Intermediate Metabolizer	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

RYR1

Named Variants

CPIC Phenotypes

Reference c.38T>G c.51_53del c.97A>G c.103T>C c.119G>C c.130C>T c.131G>A c.152C>A c.178G>A c.178G>T c.190T>C c.212C>A c.251C>T c.418G>A c.455C>A c.463C>A c.467G>A c.479A>G c.487C>T c.488G>A c.488G>T c.493G>A c.496G>A c.497A>G c.526G>A c.528G>T c.529C>T c.533A>C c.533A>G c.625G>A c.641C>T c.652G>A c.677T>A c.680A>T c.742G>A c.742G>C c.946C>T c.947G>T c.982C>T c.992_994dup c.1021G>A c.1021G>C c.1024G>A c.1100G>A c.1100G>T c.1144C>A c.1201C>A c.1201C>G c.1201C>T c.1202G>A c.1202G>T c.1209C>G c.1411C>T c.1422G>T c.1453A>G c.1459C>G c.1460T>C c.1475G>A c.1553T>C c.1565A>C c.1565A>G c.1589G>A c.1597C>A c.1597C>T c.1598G>A c.1615T>C c.1615T>G c.1630G>T c.1654C>T c.1834G>C c.1840C>T c.1841G>T c.2050G>C c.2122G>A c.2447C>T c.2537C>T c.2654G>A c.2797G>A c.2924G>A c.2996G>A c.3095G>A c.3127C>T c.3166G>A c.3166G>C c.3172G>A c.3224G>A c.3418C>T c.3527C>T c.3656A>C c.3667G>A c.4024A>G c.4178A>G c.4400A>G c.4711A>G c.4747C>T c.4763C>T c.4775C>T c.5024T>C c.5033A>G c.5036G>A c.5132A>G c.5183C>T c.5186T>G c.5317C>T c.5341T>C c.5360C>T c.5440A>G c.5441T>A c.5890C>T c.6037A>C c.6178G>T c.6302T>A c.6304G>C c.6349G>C c.6377G>A c.6387C>G c.6388G>A c.6478G>A c.6487C>T c.6488G>A c.6488G>C c.6488G>T c.6502G>A c.6544A>T c.6548G>A c.6599C>T c.6612C>G c.6617C>G c.6617C>T c.6628G>T c.6635T>A c.6640G>A c.6670C>T c.6671G>A c.6710G>A c.6742C>T c.6743G>A c.6757C>T c.6838G>A c.6847A>C c.6961A>G c.7007G>A c.7018T>C c.7025A>G c.7032G>C c.7035C>A c.7036G>A c.7042_7044delGAG c.7043A>G c.7048G>A c.7060G>A c.7063C>T c.7073T>A c.7075C>T c.7076G>A c.7084G>A c.7085A>G c.7089C>G c.7090T>G c.7097C>G c.7099G>A c.7112A>G c.7123G>A c.7124G>C c.7199A>G c.7210G>A c.7282G>A c.7291G>A c.7291G>T c.7292A>T c.7300G>A c.7304G>A c.7304G>T c.7307G>A c.7310C>T c.7317G>C c.7354C>T c.7355G>A c.7355G>C c.7358T>C c.7360C>T c.7361G>A c.7372C>T c.7373G>A c.7373G>T c.7385C>T c.7487C>T c.7522C>G c.7522C>T c.7523G>A c.7528T>C c.7760A>G c.7771C>G c.7771C>T c.7777C>G c.7778G>A c.7787C>T c.7816T>A c.7879G>A c.7879G>C c.8005G>A c.8026C>T c.8054C>T c.8188G>C c.8189A>G c.8198G>A c.8290G>A c.8327C>T c.8360C>G c.8518C>T c.8527T>C c.8600T>A c.8638G>A c.8654C>G c.8729C>T c.8926C>T c.9152G>A c.9268G>A c.9310G>A c.9356G>A c.9499C>T c.9635A>G c.9649T>C c.9652G>A c.9676G>C c.9758T>C c.9797T>C c.9848G>A c.9850T>A c.9868G>A c.10042C>T c.10043G>A c.10097G>A c.10100A>G c.10229C>A c.10237A>T c.10252A>G c.10556C>T c.10616G>A c.10747G>C c.10750G>C c.10891G>T c.11086G>C c.11120G>T c.11126C>T c.11132C>T c.11266C>G c.11314C>T c.11315G>A c.11416G>A c.11518G>A c.11708G>A c.11723A>T c.11748T>G c.11798A>G c.11813G>A c.11947C>T c.11953T>C c.11958C>G c.11969G>T c.12028G>A c.12064A>G c.12115A>T c.12121C>T c.12149C>A c.12242C>T c.12310G>C c.12355A>T c.12383C>T c.12398A>G c.12406C>A c.12413T>C c.12532G>A c.12533G>T c.12553G>A c.12689T>G c.12700G>C c.12700G>T c.12848A>T c.12881C>T c.12884C>T c.13505A>G c.13513G>C c.13672C>T c.13673G>A c.13702C>G c.13760C>T c.13913G>A c.13918A>G c.13934G>A c.13990T>C c.13994_13995delTCinsCT c.14002C>T c.14051T>C c.14126C>T c.14168G>A c.14186A>C c.14197T>G c.14201G>A c.14209C>T c.14210G>A c.14270G>A c.14364+1G>T c.14387A>G c.14422_14423delinsAA c.14424C>A c.14449A>T c.14458G>A c.14458G>T c.14471T>C c.14477C>T c.14497C>T c.14509C>G c.14512C>G c.14524G>A c.14539G>C c.14545G>A c.14558C>T c.14567C>G c.14581C>T c.14582G>A c.14627A>G c.14639T>C c.14678G>A c.14680G>A c.14693T>C c.14782A>G c.14803G>A c.14813T>C c.14814C>G c.14817C>A c.14818G>A c.14825G>T c.14879T>A c.14918C>T c.14968A>G c.15059G>C c.15060G>C

Malignant Hyperthermia Susceptibility Uncertain Susceptibility

SLCO1B1

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *2 *3 *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *16 *19 *20 *23 *24 *25 *26 *27 *28 *29 *30 *31 *32 *33 *34 *36 *37 *38 *39 *40 *41 *42 *43 *44 *45 *46 *47 *50 *51 *52 *53 *54	Decreased Function Increased Function Indeterminate Normal Function Poor Function Possible Decreased Function	Decreased Function Normal Function Poor Function

TPMT

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *2 *3A *3B *3C *4 *5 *6 *7 *8 *9 *10 *11 *12 *13 *14 *15 *16 *17 *18 *19 *20 *21 *22 *23 *24 *25 *26 *27 *28 *29 *30 *31 *32 *33 *34 *35 *36 *37 *38 *39 *40 *41 *42 *43 *44	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer Possible Intermediate Metabolizer	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

UGT1A1

Named Alleles	CPIC Phenotypes	DPWG Phenotypes
*1 *6 *27 *28 *36 *37 *80 *80+*28 *80+*37	Indeterminate Intermediate Metabolizer Normal Metabolizer Poor Metabolizer	Intermediate Metabolizer Normal Metabolizer Poor Metabolizer

VKORC1

Named Variants	DPWG Phenotypes
rs9923231 reference (C) rs9923231 variant (T)	-1639 AA -1639 AG -1639 GG

Allele Presence Genes

PharmCAT provides recommendations for these genes based on the presence or absence of specific named alleles.

HLA-A

• *31:01

HLA-B

• *15:02
• *57:01
• *58:01