Phenotypes List

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

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ABCG2

Named Variants	CPIC Phenotypes
rs2231142 reference (G) rs2231142 variant (T)	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 A120T A234D A349V A455E A1067T D110E D110H D192G D579G D924N D1152H D1270N E56K E193K E822K E831X F311L F311del F508C F508C,S1251N F1052V F1074L G178E G178R G194R(G>A) G194R(G>C) G314E G551D G551S G576A G970D G1069R G1244E G1249R(G>A) G1249R(G>C) G1349D H939R H1375P I148T I175V I807M I1027T I1139V K1060T L206W L320V L967S L997F(G>C) L997F(G>T) L1480P M152V M952I(G>A) M952I(G>C) M952I(G>T) M952T P67L Q237E Q237H Q359R Q1291R R74W R75Q R117C R117G R117H R117L R117P R170H R347H R347L R352Q R553Q R668C R792G R933G R1070Q R1070W R1162L R1283M S549N S549R(A>C) S549R(T>G) S589N S737F S945L S977F S1159F S1159P S1251N S1255P T338I T1053I V232D V562I V754M V1293G W1282R Y1014C Y1032C ivacaftor non-responsive CFTR sequence

ivacaftor non-responsive in CF patients ivacaftor responsive in CF patients

CYP2B6

Named Alleles	CPIC 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

CYP2C19

Named Alleles	CPIC 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

CYP2C9

Named Alleles	CPIC Phenotypes	CPIC Activity Scores
*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

CYP2D6

Named Alleles	CPIC Phenotypes	CPIC 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

CYP3A4

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

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.930G>A 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

Named Alleles	CPIC Phenotypes
*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	Indeterminate Intermediate Metabolizer Poor Metabolizer Rapid Metabolizer

NUDT15

Named Alleles	CPIC 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

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
*1 *2 *4 *5 *6 *8 *9 *10 *11 *14 *15 *16 *19 *20 *23 *24 *25 *26 *27 *28 *29 *30 *31 *32 *33 *34 *36 *37 *39 *40 *41 *42 *43 *44 *45.001 *45.002 *47 *50 *51 *52 *53 *54 *55 *56 *57 *58	Decreased Function Increased Function Indeterminate Normal Function Poor Function Possible Decreased Function

TPMT

Named Alleles	CPIC 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

UGT1A1

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

VKORC1

Named Variants	CPIC 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