diff --git a/CHANGELOG.rst b/CHANGELOG.rst index bdd0906..e8da343 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,11 @@ Changelog ********* +0.25.0 (2024-06-16) +------------------- + +* Add 26 new genes: ACYP2, ADRA2A, ADRB2, ANKK1, APOE, ATM, BCHE, BDNF, DBH, DRD2, F2, GRIK1, GRIK4, GRIN2B, HTR1A, HTR2A, IFNL4, ITGB3, ITPA, OPRK1, OPRM1, RARG, SLC6A4, SLC28A3, SLC47A2, UGT1A6. + 0.24.0 (2024-03-31) ------------------- diff --git a/README.rst b/README.rst index 13bc105..3a4c64f 100644 --- a/README.rst +++ b/README.rst @@ -52,58 +52,83 @@ glossary.html#structural-variation-sv>`__ using a machine learning-based approach. Finally, note that PyPGx is compatible with both of the Genome Reference Consortium Human (GRCh) builds, GRCh37 (hg19) and GRCh38 (hg38). -There are currently 61 pharmacogenes in PyPGx: +There are currently 87 pharmacogenes in PyPGx: .. list-table:: * - ABCB1 - ABCG2 - - CACNA1S + - ACYP2 + - ADRA2A + - ADRB2 + * - ANKK1 + - APOE + - ATM + - BCHE + - BDNF + * - CACNA1S - CFTR - COMT - * - CYP1A1 + - CYP1A1 - CYP1A2 - - CYP1B1 + * - CYP1B1 - CYP2A6/CYP2A7 - CYP2A13 - * - CYP2B6/CYP2B7 + - CYP2B6/CYP2B7 - CYP2C8 - - CYP2C9 + * - CYP2C9 - CYP2C19 - CYP2D6/CYP2D7 - * - CYP2E1 + - CYP2E1 - CYP2F1 - - CYP2J2 + * - CYP2J2 - CYP2R1 - CYP2S1 - * - CYP2W1 + - CYP2W1 - CYP3A4 - - CYP3A5 + * - CYP3A5 - CYP3A7 - CYP3A43 - * - CYP4A11 + - CYP4A11 - CYP4A22 - - CYP4B1 + * - CYP4B1 - CYP4F2 - CYP17A1 - * - CYP19A1 + - CYP19A1 - CYP26A1 + * - DBH - DPYD + - DRD2 + - F2 - F5 - - G6PD - * - GSTM1 - - GSTP1 + * - G6PD + - GRIK1 + - GRIK4 + - GRIN2B + - GSTM1 + * - GSTP1 - GSTT1 + - HTR1A + - HTR2A - IFNL3 + * - IFNL3 + - ITGB3 + - ITPA - MTHFR - * - NAT1 - - NAT2 + - NAT1 + * - NAT2 - NUDT15 + - OPRK1 + - OPRM1 - POR - - PTGIS - * - RYR1 + * - PTGIS + - RARG + - RYR1 + - SLC6A4 - SLC15A2 - - SLC22A2 + * - SLC22A2 + - SLC28A3 + - SLC47A2 - SLCO1B1 - SLCO1B3 * - SLCO2B1 @@ -112,12 +137,12 @@ There are currently 61 pharmacogenes in PyPGx: - TPMT - UGT1A1 * - UGT1A4 + - UGT1A6 - UGT2B7 - UGT2B15 - UGT2B17 - - VKORC1 - * - XPC - - + * - VKORC1 + - XPC - - - diff --git a/docs/create.py b/docs/create.py index 9247a54..3cb650c 100644 --- a/docs/create.py +++ b/docs/create.py @@ -79,58 +79,83 @@ approach. Finally, note that PyPGx is compatible with both of the Genome Reference Consortium Human (GRCh) builds, GRCh37 (hg19) and GRCh38 (hg38). -There are currently 61 pharmacogenes in PyPGx: +There are currently 87 pharmacogenes in PyPGx: .. list-table:: * - ABCB1 - ABCG2 - - CACNA1S + - ACYP2 + - ADRA2A + - ADRB2 + * - ANKK1 + - APOE + - ATM + - BCHE + - BDNF + * - CACNA1S - CFTR - COMT - * - CYP1A1 + - CYP1A1 - CYP1A2 - - CYP1B1 + * - CYP1B1 - CYP2A6/CYP2A7 - CYP2A13 - * - CYP2B6/CYP2B7 + - CYP2B6/CYP2B7 - CYP2C8 - - CYP2C9 + * - CYP2C9 - CYP2C19 - CYP2D6/CYP2D7 - * - CYP2E1 + - CYP2E1 - CYP2F1 - - CYP2J2 + * - CYP2J2 - CYP2R1 - CYP2S1 - * - CYP2W1 + - CYP2W1 - CYP3A4 - - CYP3A5 + * - CYP3A5 - CYP3A7 - CYP3A43 - * - CYP4A11 + - CYP4A11 - CYP4A22 - - CYP4B1 + * - CYP4B1 - CYP4F2 - CYP17A1 - * - CYP19A1 + - CYP19A1 - CYP26A1 + * - DBH - DPYD + - DRD2 + - F2 - F5 - - G6PD - * - GSTM1 - - GSTP1 + * - G6PD + - GRIK1 + - GRIK4 + - GRIN2B + - GSTM1 + * - GSTP1 - GSTT1 + - HTR1A + - HTR2A - IFNL3 + * - IFNL3 + - ITGB3 + - ITPA - MTHFR - * - NAT1 - - NAT2 + - NAT1 + * - NAT2 - NUDT15 + - OPRK1 + - OPRM1 - POR - - PTGIS - * - RYR1 + * - PTGIS + - RARG + - RYR1 + - SLC6A4 - SLC15A2 - - SLC22A2 + * - SLC22A2 + - SLC28A3 + - SLC47A2 - SLCO1B1 - SLCO1B3 * - SLCO2B1 @@ -139,12 +164,12 @@ - TPMT - UGT1A1 * - UGT1A4 + - UGT1A6 - UGT2B7 - UGT2B15 - UGT2B17 - - VKORC1 - * - XPC - - + * - VKORC1 + - XPC - - - diff --git a/docs/genes.rst b/docs/genes.rst index e568775..b1e970a 100644 --- a/docs/genes.rst +++ b/docs/genes.rst @@ -2,7 +2,7 @@ Genes ***** This page describes gene-specific information. PyPGx currently supports -genotyping of a total of 61 pharmacogenes. +genotyping of a total of 87 pharmacogenes. In order to provide the most accurate information, this page borrows heavily from the works of the :ref:`glossary:Clinical Pharmacogenetics Implementation @@ -56,6 +56,86 @@ Below is a summary table: - `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. * - :ref:`genes:CACNA1S` - ✅ - @@ -356,6 +436,16 @@ Below is a summary table: - `chr10:94830646-94840641 `__ - `chr10:93070892-93080885 `__ - + * - DBH + - ✅ + - + - + - + - + - Efficacy + - `chr9:136498484-136527451 `__ + - `chr9:133633362-133662329 `__ + - NM_000787.4 was used as the main transcript. * - :ref:`genes:DPYD` - ✅ - @@ -366,6 +456,26 @@ Below is a summary table: - `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. * - :ref:`genes:F5` - ✅ - @@ -386,6 +496,36 @@ Below is a summary table: - `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. * - :ref:`genes:GSTM1` - ✅ - ✅ @@ -416,6 +556,26 @@ Below is a summary table: - `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. * - :ref:`genes:IFNL3` - ✅ - @@ -426,6 +586,36 @@ Below is a summary table: - `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. * - MTHFR - ✅ - @@ -466,6 +656,26 @@ Below is a summary table: - `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. * - :ref:`genes:POR` - ✅ - @@ -486,6 +696,16 @@ Below is a summary table: - `chr20:48117410-48187674 `__ - `chr20:49500873-49571137 `__ - + * - RARG + - ✅ + - + - + - + - + - Toxicity + - `chr12:53601352-53628993 `__ + - `chr12:53207568-53235209 `__ + - NM_000966.6 was used as the main transcript. * - :ref:`genes:RYR1` - ✅ - @@ -496,6 +716,16 @@ Below is a summary table: - `chr19:38921339-39081204 `__ - `chr19:38430690-38590564 `__ - + * - SLC6A4 + - ✅ + - + - + - + - + - Other + - `chr17:28518336-28565715 `__ + - `chr17:30191318-30238697 `__ + - NM_001045.6 was used as the main transcript. * - SLC15A2 - ✅ - @@ -516,6 +746,26 @@ Below is a summary table: - `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. * - :ref:`genes:SLCO1B1` - ✅ - @@ -596,6 +846,16 @@ Below is a summary table: - `chr2:234624437-234684945 `__ - `chr2:233715735-233776300 `__ - + * - UGT1A6 + - ✅ + - + - + - + - + - Excretion + - `chr2:234598535-234684946 `__ + - `chr2:233689889-233776300 `__ + - NM_001072.4 was used as the main transcript. * - UGT2B7 - ✅ - diff --git a/pypgx/api/data/allele-table.csv b/pypgx/api/data/allele-table.csv index 8332968..c222503 100644 --- a/pypgx/api/data/allele-table.csv +++ b/pypgx/api/data/allele-table.csv @@ -3,6 +3,25 @@ ABCB1,*1,N/A,Normal Function,"7-87138645-A-G,7-87160618-A-C,7-87179601-A-G",N/A, ABCB1,*2,N/A,Increased Function,N/A,N/A,N/A,N/A,FALSE ABCG2,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE ABCG2,rs2231142,N/A,Decreased Function,4-89052323-G-T,N/A,4-88131171-G-T,N/A,FALSE +ACYP2,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ACYP2,rs1872328,N/A,Unknown Function,2-54395259-G-A,2-54168122-G-A,N/A,N/A,FALSE +ADRA2A,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ADRA2A,rs1800544,N/A,Unknown Function,10-112836503-G-C,N/A,10-111076745-G-C,N/A,FALSE +ADRB2,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ADRB2,rs1042713,N/A,Unknown Function,5-148206440-G-A,N/A,5-148826877-G-A,N/A,FALSE +ANKK1,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ANKK1,Taq1A,N/A,Unknown Function,11-113270828-G-A,N/A,11-113400106-G-A,N/A,FALSE +APOE,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +APOE,E2,N/A,Unknown Function,19-45412079-C-T,N/A,19-44908822-C-T,N/A,FALSE +APOE,E3,N/A,Unknown Function,"19-45411941-T-C,19-45412079-C-T",N/A,"19-44908684-T-C,19-44908822-C-T",N/A,FALSE +APOE,E4,N/A,Unknown Function,19-45411941-T-C,N/A,19-44908684-T-C,N/A,FALSE +ATM,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ATM,rs11212617,N/A,Unknown Function,11-108283161-C-A,N/A,11-108412434-C-A,N/A,FALSE +BCHE,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +BCHE,rs1803274,N/A,Unknown Function,3-165491280-C-T,N/A,3-165773492-C-T,N/A,FALSE +BCHE,rs1799807,N/A,Unknown Function,3-165548529-T-C,N/A,3-165830741-T-C,N/A,FALSE +BDNF,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +BDNF,rs6265,N/A,Unknown Function,11-27679916-C-T,N/A,11-27658369-C-T,N/A,FALSE CACNA1S,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE CACNA1S,c.520C>T,N/A,Malignant Hyperthermia Associated,1-201061121-G-A,N/A,1-201091993-G-A,N/A,FALSE CACNA1S,c.3257G>A,N/A,Malignant Hyperthermia Associated,1-201029943-C-T,N/A,1-201060815-C-T,N/A,FALSE @@ -663,6 +682,8 @@ CYP26A1,*1,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE CYP26A1,*2,N/A,Unknown Function,10-94834638-C-A,N/A,10-93074881-C-A,N/A,FALSE CYP26A1,*3,N/A,Unknown Function,10-94834679-C-A,N/A,10-93074922-C-A,N/A,FALSE CYP26A1,*4,N/A,Unknown Function,10-94836373-T-C,N/A,10-93076616-T-C,N/A,FALSE +DBH,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +DBH,rs1611115,N/A,Unknown Function,9-136500515-T-C,N/A,9-133635393-T-C,N/A,FALSE DPYD,Reference,1,Normal Function,1-98348885-G-A,N/A,N/A,N/A,FALSE DPYD,c.1905+1G>A (*2A),0,No Function,1-97915614-C-T,N/A,1-97450058-C-T,N/A,FALSE DPYD,c.1898delC (*3),0,No Function,1-97915621-TG-T,N/A,1-97450065-TG-T,N/A,FALSE @@ -746,6 +767,10 @@ DPYD,c.3061G>C,1,Normal Function,1-97544549-C-G,N/A,1-97078993-C-G,N/A,FALSE DPYD,c.3067C>A,1,Normal Function,1-97544543-G-T,N/A,1-97078987-G-T,N/A,FALSE DPYD,c.525G>A,1,Normal Function,1-98165062-C-T,N/A,1-97699506-C-T,N/A,FALSE DPYD,c.1371C>T,1,Normal Function,1-98015269-G-A,N/A,1-97549713-G-A,N/A,FALSE +DRD2,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +DRD2,rs1799978,N/A,Unknown Function,11-113346351-T-C,N/A,11-113475629-T-C,N/A,FALSE +F2,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +F2,G20210A,N/A,Unknown Function,11-46761055-G-A,N/A,11-46739505-G-A,N/A,FALSE F5,Reference,N/A,Normal Function,1-169519049-T-C,N/A,N/A,N/A,FALSE F5,Leiden,N/A,Unknown Function,N/A,N/A,1-169549811-C-T,N/A,FALSE G6PD,B (reference),N/A,Class IV (Normal),N/A,N/A,N/A,N/A,FALSE @@ -936,6 +961,12 @@ G6PD,Laibin,N/A,Unknown Function,X-153760446-T-G,N/A,X-154532231-T-G,N/A,FALSE G6PD,Insuli,N/A,Class IV (Normal),X-153761219-C-T,N/A,X-154533004-C-T,N/A,FALSE G6PD,Mira d'Aire,N/A,Class IV (Normal),X-153761160-C-G,N/A,X-154532945-C-G,N/A,FALSE G6PD,Farroupilha,N/A,Class II (Deficient),X-153761231-G-T,N/A,X-154533016-G-T,N/A,FALSE +GRIK1,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +GRIK1,rs2832407,N/A,Unknown Function,21-30967508-C-A,N/A,21-29595188-C-A,N/A,FALSE +GRIK4,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +GRIK4,rs1954787,N/A,Unknown Function,11-120663363-T-C,N/A,11-120792654-T-C,N/A,FALSE +GRIN2B,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +GRIN2B,rs2058878,N/A,Unknown Function,12-13953118-T-A,N/A,12-13800184-T-A,N/A,FALSE GSTM1,*A,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE GSTM1,*0,N/A,No Function,N/A,N/A,N/A,N/A,TRUE GSTM1,*B,N/A,Unknown Function,1-110233138-G-C,N/A,1-109690516-G-C,N/A,FALSE @@ -945,10 +976,22 @@ GSTP1,*C,N/A,Unknown Function,"11-67352689-A-G,11-67353579-C-T",N/A,"11-67585218 GSTP1,*D,N/A,Unknown Function,11-67353579-C-T,N/A,11-67586108-C-T,N/A,FALSE GSTT1,*A,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE GSTT1,*0,N/A,No Function,N/A,N/A,N/A,N/A,TRUE +HTR1A,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +HTR1A,rs6295,N/A,Unknown Function,5-63258565-C-G,N/A,5-63962738-C-G,N/A,FALSE +HTR2A,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +HTR2A,rs7997012,N/A,Unknown Function,13-47411985-A-G,N/A,13-46837850-A-G,N/A,FALSE +HTR2A,rs6311,N/A,Unknown Function,13-47471478-C-T,N/A,13-46897343-C-T,N/A,FALSE IFNL3,Reference,N/A,Favorable Response,N/A,N/A,N/A,N/A,FALSE IFNL3,rs12979860,N/A,Unfavorable Response,19-39738787-C-T,N/A,19-39248147-C-T,N/A,FALSE IFNL3,rs8099917,N/A,Unknown Function,19-39743165-T-G,N/A,19-39252525-T-G,N/A,FALSE IFNL3,rs12980275,N/A,Unknown Function,19-39731783-A-G,N/A,19-39241143-A-G,N/A,FALSE +IFNL4,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +IFNL4,rs12979860,N/A,Unknown Function,19-39738787-C-T,N/A,19-39248147-C-T,N/A,FALSE +ITGB3,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ITGB3,rs5918,N/A,Unknown Function,17-45360730-T-C,N/A,17-47283364-T-C,N/A,FALSE +ITPA,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +ITPA,rs1127354,N/A,Unknown Function,20-3193842-C-A,N/A,20-3213196-C-A,N/A,FALSE +ITPA,rs7270101,N/A,Unknown Function,20-3193893-A-C,N/A,20-3213247-A-C,N/A,FALSE MTHFR,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE MTHFR,rs1801131,N/A,Unknown Function,1-11854476-T-G,N/A,1-11794419-T-G,N/A,FALSE MTHFR,rs1801133,N/A,Unknown Function,1-11856378-G-A,N/A,1-11796321-G-A,N/A,FALSE @@ -1007,6 +1050,10 @@ NUDT15,*17,N/A,Uncertain Function,13-48615249-G-T,N/A,13-48041113-G-T,N/A,FALSE NUDT15,*18,N/A,Uncertain Function,13-48615113-GA-G,N/A,13-48040977-GA-G,N/A,FALSE NUDT15,*19,N/A,Uncertain Function,13-48611885-G-C,N/A,13-48037749-G-C,N/A,FALSE NUDT15,*20,N/A,Uncertain Function,13-48619826-C-G,N/A,13-48045690-C-G,N/A,FALSE +OPRK1,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +OPRK1,rs6473797,N/A,Unknown Function,8-54152982-T-C,N/A,8-53240422-T-C,N/A,FALSE +OPRM1,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +OPRM1,rs1799971,N/A,Unknown Function,6-154360797-A-G,N/A,6-154039662-A-G,N/A,FALSE POR,*1,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE POR,*2,N/A,No Function,7-75614497-G-A,N/A,7-75985179-G-A,N/A,FALSE POR,*3,N/A,Decreased Function,7-75610925-G-A,N/A,7-75981607-G-A,N/A,FALSE @@ -1064,6 +1111,8 @@ PTGIS,*3,N/A,Unknown Function,20-48164401-A-T,N/A,20-49547864-A-T,N/A,FALSE PTGIS,*4,N/A,Unknown Function,20-48129688-G-T,N/A,20-49513151-G-T,N/A,FALSE PTGIS,*5,N/A,Unknown Function,20-48127584-C-T,N/A,20-49511047-C-T,N/A,FALSE PTGIS,*6,N/A,Unknown Function,20-48130848-C-A,N/A,20-49514311-C-A,N/A,FALSE +RARG,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +RARG,rs2229774,N/A,Unknown Function,12-53605545-G-A,N/A,12-53211761-G-A,N/A,FALSE RYR1,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE RYR1,c.103T>C,N/A,Malignant Hyperthermia Associated,19-38931442-T-C,N/A,19-38440802-T-C,N/A,FALSE RYR1,c.130C>T,N/A,Malignant Hyperthermia Associated,19-38931469-C-T,N/A,19-38440829-C-T,N/A,FALSE @@ -1113,6 +1162,8 @@ RYR1,c.14512C>G,N/A,Malignant Hyperthermia Associated,19-39071010-C-G,N/A,19-385 RYR1,c.14545G>A,N/A,Malignant Hyperthermia Associated,19-39071043-G-A,N/A,19-38580403-G-A,N/A,FALSE RYR1,c.14582G>A,N/A,Malignant Hyperthermia Associated,19-39071080-G-A,N/A,19-38580440-G-A,N/A,FALSE RYR1,c.14693T>C,N/A,Malignant Hyperthermia Associated,19-39075629-T-C,N/A,19-38584989-T-C,N/A,FALSE +SLC6A4,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +SLC6A4,rs25531,N/A,Unknown Function,17-28564346-T-C,N/A,17-30237328-T-C,N/A,FALSE SLC15A2,*1,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE SLC15A2,*2,N/A,Unknown Function,"3-121643804-C-T,3-121647286-C-T,3-121648168-G-A",N/A,"3-121924957-C-T,3-121928439-C-T,3-121929321-G-A",N/A,FALSE SLC22A2,*1,N/A,Normal Function,"6-160645832-C-T,6-160670282-A-C",N/A,"6-160224800-C-T,6-160249250-A-C",N/A,FALSE @@ -1126,6 +1177,10 @@ SLC22A2,*8,N/A,Unknown Function,6-160671584-G-A,N/A,6-160250552-G-A,N/A,FALSE SLC22A2,*K432Q,N/A,Unknown Function,6-160663420-T-G,N/A,6-160242388-T-G,N/A,FALSE SLC22A2,*S1,N/A,Unknown Function,6-160663420-T-G,N/A,6-160242388-T-G,N/A,TRUE SLC22A2,*S2,N/A,Unknown Function,N/A,N/A,N/A,N/A,TRUE +SLC28A3,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +SLC28A3,rs7853758,N/A,Unknown Function,9-86900926-G-A,N/A,9-84286011-G-A,N/A,FALSE +SLC47A2,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +SLC47A2,rs12943590,N/A,Unknown Function,17-19619998-G-A,N/A,17-19716685-G-A,N/A,FALSE SLCO1B1,*1,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE SLCO1B1,*2,N/A,Uncertain Function,12-21325716-T-C,N/A,12-21172782-T-C,N/A,FALSE SLCO1B1,*3,N/A,Uncertain Function,"12-21327529-T-C,12-21329817-A-G",N/A,"12-21174595-T-C,12-21176883-A-G",N/A,FALSE @@ -1255,6 +1310,8 @@ UGT1A4,*8,N/A,Unknown Function,2-234628334-G-T,N/A,2-233719688-G-T,N/A,FALSE UGT1A4,*S1,N/A,Unknown Function,N/A,N/A,N/A,N/A,TRUE UGT1A4,*S2,N/A,Unknown Function,N/A,N/A,N/A,N/A,TRUE UGT1A4,*S3,N/A,Unknown Function,N/A,N/A,N/A,N/A,TRUE +UGT1A6,Reference,N/A,Normal Function,N/A,N/A,N/A,N/A,FALSE +UGT1A6,rs17863783,N/A,Unknown Function,2-234602277-G-T,N/A,2-233693631-G-T,N/A,FALSE UGT2B7,*1,N/A,Normal Function,4-69964338-T-C,N/A,4-69098620-T-C,N/A,FALSE UGT2B7,*2,N/A,Unknown Function,N/A,N/A,N/A,N/A,FALSE UGT2B7,*3,N/A,Unknown Function,4-69962449-G-T,N/A,4-69096731-G-T,N/A,FALSE diff --git a/pypgx/api/data/gene-table.csv b/pypgx/api/data/gene-table.csv index 65c8ee9..0f1ff49 100644 --- a/pypgx/api/data/gene-table.csv +++ b/pypgx/api/data/gene-table.csv @@ -1,6 +1,14 @@ Gene,Target,Control,Paralog,Variants,SV,PhenotypeMethod,RefAllele,GRCh37Default,GRCh38Default,Strand,GRCh37Region,GRCh38Region,GRCh37ExonStarts,GRCh37ExonEnds,GRCh38ExonStarts,GRCh38ExonEnds 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SLC15A2,TRUE,FALSE,N/A,TRUE,FALSE,N/A,*1,*1,*1,+,3:121610170-121666034,3:121891400-121947188,"121613170,121615252,121616234,121630420,121631867,121634073,121634462,121641066,121641621,121641886,121642068,121643197,121643791,121646604,121647267,121647828,121648148,121649686,121650485,121658195,121659230,121659677,","121613428,121615340,121616376,121630513,121631967,121634164,121634540,121641149,121641708,121641976,121642113,121643230,121643880,121646686,121647402,121647993,121648195,121649797,121650582,121658342,121659335,121663034,","121894400,121896405,121897387,121911573,121913020,121915226,121915615,121922219,121922774,121923039,121923221,121924350,121924944,121927757,121928420,121928981,121929301,121930839,121931638,121939348,121940383,121940830,","121894581,121896493,121897529,121911666,121913120,121915317,121915693,121922302,121922861,121923129,121923266,121924383,121925033,121927839,121928555,121929146,121929348,121930950,121931735,121939495,121940488,121944188," SLC22A2,TRUE,FALSE,N/A,TRUE,TRUE,N/A,*1,*3,*3,-,6:160627786-160689853,6:160206754-160268821,"160637793,160645736,160662505,160663325,160664603,160666470,160668215,160670247,160671579,160677645,160679375,","160638530,160645836,160662618,160663434,160664818,160666577,160668330,160670416,160671734,160677749,160679963,","160216754,160224704,160241473,160242293,160243571,160245438,160247183,160249215,160250547,160256613,160258343,","160217498,160224804,160241586,160242402,160243786,160245545,160247298,160249384,160250702,160256717,160258821," +SLC28A3,TRUE,FALSE,N/A,TRUE,FALSE,N/A,Reference,Reference,Reference,-,9:86887371-86958673,9:84272456-84343758,"86890371,86894179,86894889,86895715,86900259,86900857,86902962,86905068,86907582,86909109,86912135,86912820,86914495,86917114,86920168,86924543,86928273,86955488,","86893259,86894300,86894988,86895797,86900457,86901026,86903093,86905194,86907663,86909190,86912213,86912934,86914640,86917304,86920260,86924629,86928369,86955673,","84275456,84279264,84279974,84280800,84285344,84285942,84288047,84290153,84292667,84294194,84297220,84297905,84299580,84302199,84305253,84309628,84313358,84340573,","84278344,84279385,84280073,84280882,84285542,84286111,84288178,84290279,84292748,84294275,84297298,84298019,84299725,84302389,84305345,84309714,84313454,84340758," +SLC47A2,TRUE,FALSE,N/A,TRUE,FALSE,N/A,Reference,Reference,Reference,-,17:19578629-19622897,17:19675316-19719584,"19581629,19583264,19584679,19584850,19605917,19606404,19607382,19608748,19609960,19611058,19611614,19612028,19616015,19617137,19618033,19618428,19619745,","19582219,19583352,19584774,19584983,19605987,19606480,19607491,19608816,19610074,19611156,19611712,19612073,19616058,19617286,19618102,19618530,19619897,","19678316,19679951,19681366,19681537,19702604,19703091,19704069,19705435,19706647,19707745,19708301,19708715,19712702,19713824,19714720,19715115,19716432,","19678906,19680039,19681461,19681670,19702674,19703167,19704178,19705503,19706761,19707843,19708399,19708760,19712745,19713973,19714789,19715217,19716584," SLCO1B1,TRUE,FALSE,N/A,TRUE,FALSE,Diplotype,*1,*1,*1,+,12:21281127-21395730,12:21128193-21242796,"21284127,21294447,21325583,21327510,21329709,21331509,21331855,21349879,21353441,21355424,21358801,21370052,21375233,21377655,21391912,","21284170,21294592,21325725,21327643,21329831,21331656,21331954,21350122,21353606,21355620,21358967,21370237,21375298,21377773,21392730,","21131193,21141513,21172649,21174576,21176775,21178575,21178921,21196945,21200507,21202490,21205867,21217118,21222299,21224721,21238978,","21131236,21141658,21172791,21174709,21176897,21178722,21179020,21197188,21200672,21202686,21206033,21217303,21222364,21224839,21239796," SLCO1B3,TRUE,FALSE,N/A,TRUE,FALSE,N/A,Reference,Reference,Reference,+,12:20960637-21072845,12:20807704-20919911,"20963637,20966457,20968607,21007961,21011372,21013950,21015345,21015689,21028168,21030705,21032369,21033788,21036351,21051369,21054283,21068937,","20963698,20966572,20968756,21008103,21011505,21014072,21015492,21015788,21028411,21030870,21032565,21033954,21036536,21051434,21054401,21069845,","20810704,20813523,20815673,20855027,20858438,20861016,20862411,20862755,20875234,20877771,20879435,20880854,20883417,20898435,20901349,20916003,","20810764,20813638,20815822,20855169,20858571,20861138,20862558,20862854,20875477,20877936,20879631,20881020,20883602,20898500,20901467,20916911," SLCO2B1,TRUE,FALSE,N/A,TRUE,FALSE,N/A,*1,*1,*1,+,11:74859151-74920594,11:75148106-75209549,"74862151,74873699,74875007,74876831,74880217,74880710,74883423,74899180,74904262,74907558,74911268,74913945,74914351,74915444,","74862442,74873830,74875145,74876994,74880451,74880809,74883614,74899283,74904620,74907724,74911432,74914010,74914472,74917594,","75151106,75162654,75163962,75165786,75169172,75169665,75172378,75188135,75193217,75196513,75200223,75202900,75203306,75204399,","75151397,75162785,75164100,75165949,75169406,75169764,75172569,75188238,75193575,75196679,75200387,75202965,75203427,75206549," @@ -59,6 +84,7 @@ TBXAS1,TRUE,FALSE,N/A,TRUE,FALSE,N/A,*1,*3,*1,+,7:139525951-139723125,7:13982626 TPMT,TRUE,FALSE,N/A,TRUE,FALSE,Diplotype,*1,*1,*1,-,6:18125541-18158400,6:18125310-18158169,"18128541,18132363,18134034,18139193,18139895,18143826,18148053,18149218,18155263,","18131011,18132408,18134120,18139268,18139948,18143959,18148146,18149402,18155400,","18128310,18132132,18133803,18138962,18139664,18143595,18147822,18148987,18155032,","18130780,18132177,18133889,18139037,18139717,18143728,18147915,18149171,18155169," UGT1A1,TRUE,FALSE,N/A,TRUE,FALSE,Diplotype,*1,*1,*1,+,2:234662918-234687945,2:233754269-233779300,"234668918,234675679,234676494,234676865,234680907,","234669797,234675811,234676582,234677085,234681945,","233760269,233767033,233767848,233768219,233772261,","233761151,233767165,233767936,233768439,233773300," UGT1A4,TRUE,FALSE,N/A,TRUE,TRUE,N/A,*1,*1,*1,+,2:234624437-234684945,2:233715735-233776300,"234627437,234675679,234676494,234676865,234680907,","234628333,234675811,234676582,234677085,234681945,","233718735,233767033,233767848,233768219,233772261,","233719687,233767165,233767936,233768439,233773300," +UGT1A6,TRUE,FALSE,N/A,TRUE,FALSE,N/A,Reference,Reference,Reference,+,2:234598535-234684946,2:233689889-233776300,"234601535,234675679,234676494,234676865,234680907,","234602511,234675811,234676582,234677085,234681946,","233692889,233767033,233767848,233768219,233772261,","233693865,233767165,233767936,233768439,233773300," UGT2B7,TRUE,FALSE,N/A,TRUE,FALSE,N/A,*1,*2,*2,+,4:69959191-69981705,4:69093473-69115987,"69962191,69964257,69968524,69972892,69973820,69978174,","69962959,69964406,69968656,69972980,69974040,69978705,","69096473,69098539,69102806,69107174,69108102,69112456,","69097241,69098688,69102938,69107262,69108322,69112987," UGT2B15,TRUE,FALSE,N/A,TRUE,TRUE,N/A,*1,*2,*2,-,4:69506314-69542494,4:68640596-68676652,"69512314,69519754,69520812,69528725,69533757,69535612,","69513101,69519974,69520900,69528857,69533906,69536494,","68646596,68654036,68655094,68663007,68668039,68669894,","68647383,68654256,68655182,68663139,68668188,68670652," UGT2B17,TRUE,FALSE,N/A,FALSE,TRUE,N/A,*1,*1,*1,-,4:69399901-69437245,4:68534183-68571527,"69402901,69416394,69417541,69426254,69431289,69433478,","69403622,69416614,69417629,69426386,69431438,69434245,","68537183,68550676,68551823,68560536,68565571,68567760,","68537904,68550896,68551911,68560668,68565720,68568527," diff --git a/pypgx/api/data/variant-table.csv b/pypgx/api/data/variant-table.csv index 6090c21..8390516 100644 --- a/pypgx/api/data/variant-table.csv +++ b/pypgx/api/data/variant-table.csv @@ -3,6 +3,16 @@ ABCB1,7-87138645-A-G,7-87509329-A-G,rs1045642,7,87138645,87509329,A,A,G,N/A,N/A, ABCB1,7-87160618-A-C,7-87531302-A-C,rs2032582,7,87160618,87531302,A,A,C,A893S,N/A,N/A ABCB1,7-87179601-A-G,7-87550285-A-G,rs1128503,7,87179601,87550285,A,A,G,N/A,N/A,N/A ABCG2,4-89052323-G-T,4-88131171-G-T,rs2231142,4,89052323,88131171,G,G,T,Q141K,N/A,N/A +ACYP2,2-54395259-G-A,2-54168122-G-A,rs1872328,2,54395259,54168122,G,G,A,N/A,N/A,N/A +ADRA2A,10-112836503-G-C,10-111076745-G-C,rs1800544,10,112836503,111076745,G,G,C,N/A,N/A,N/A +ADRB2,5-148206440-G-A,5-148826877-G-A,rs1042713,5,148206440,148826877,G,G,A,G16R,N/A,N/A +ANKK1,11-113270828-G-A,11-113400106-G-A,rs1800497,11,113270828,113400106,G,G,A,E713K,N/A,N/A +APOE,19-45411941-T-C,19-44908684-T-C,rs429358,19,45411941,44908684,T,T,C,C130R,N/A,N/A +APOE,19-45412079-C-T,19-44908822-C-T,rs7412,19,45412079,44908822,C,C,T,R176C,N/A,N/A +ATM,11-108283161-C-A,11-108412434-C-A,rs11212617,11,108283161,108412434,C,C,A,N/A,N/A,N/A +BCHE,3-165491280-C-T,3-165773492-C-T,rs1803274,3,165491280,165773492,C,C,T,A567T,N/A,N/A +BCHE,3-165548529-T-C,3-165830741-T-C,rs1799807,3,165548529,165830741,T,T,C,D98G,N/A,N/A +BDNF,11-27679916-C-T,11-27658369-C-T,rs6265,11,27679916,27658369,C,C,T,V66M,N/A,N/A CACNA1S,1-201061121-G-A,1-201091993-G-A,rs772226819,1,201061121,201091993,G,G,A,R174W,N/A,N/A CACNA1S,1-201029943-C-T,1-201060815-C-T,rs1800559,1,201029943,201060815,C,C,T,R1086H,N/A,N/A CFTR,7-117149089-G-A,7-117509035-G-A,rs397508256,7,117149089,117509035,G,G,A,E56K,N/A,N/A @@ -630,6 +640,7 @@ CYP19A1,15-51534995-A-G,15-51242798-A-G,rs2236722,15,51534995,51242798,A,A,G,W39 CYP26A1,10-94834638-C-A,10-93074881-C-A,rs61735552,10,94834638,93074881,C,C,A,R173S,N/A,N/A CYP26A1,10-94834679-C-A,10-93074922-C-A,rs1376885914,10,94834679,93074922,C,C,A,F186L,N/A,N/A CYP26A1,10-94836373-T-C,10-93076616-T-C,rs146619916,10,94836373,93076616,T,T,C,C358R,N/A,N/A +DBH,9-136500515-T-C,9-133635393-T-C,rs1611115,9,136500515,133635393,T,T,C,N/A,N/A,N/A DPYD,1-98058899-C-A,1-97593343-C-A,rs72549306,1,98058899,97593343,C,C,A,V335L,N/A,N/A DPYD,1-98058878-C-T,1-97593322-C-T,rs183385770,1,98058878,97593322,C,C,T,D342N,N/A,N/A DPYD,1-98058845-G-A,1-97593289-G-A,rs143154602,1,98058845,97593289,G,G,A,R353C,N/A,N/A @@ -713,6 +724,8 @@ DPYD,1-98060705-T-C,1-97595149-T-C,rs146356975,1,98060705,97595149,T,T,C,K290E,N DPYD,1-98060644-A-G,1-97595088-A-G,rs150437414,1,98060644,97595088,A,A,G,L310S,N/A,N/A DPYD,1-98060639-G-A,1-97595083-G-A,rs145112791,1,98060639,97595083,G,G,A,L312F,N/A,N/A DPYD,1-98058935-C-T,1-97593379-C-T,rs201018345,1,98058935,97593379,C,C,T,A323T,N/A,N/A +DRD2,11-113346351-T-C,11-113475629-T-C,rs1799978,11,113346351,113475629,T,T,C,N/A,N/A,N/A +F2,11-46761055-G-A,11-46739505-G-A,rs1799963,11,46761055,46739505,G,G,A,N/A,N/A,N/A F5,1-169519049-T-C,1-169549811-C-T,rs6025,1,169519049,169549811,T,C,T,R534Q,N/A,N/A G6PD,X-153760261-A-C,X-154532046-A-C,N/A,X,153760261,154532046,A,A,C,F501C,N/A,N/A G6PD,X-153760272-CTTC-C,X-154532057-CTTC-C,N/A,X,153760272,154532057,CTTC,CTTC,C,K497del,N/A,N/A @@ -897,12 +910,22 @@ G6PD,X-153774276-T-C,X-154546061-T-C,rs137852340,X,153774276,154546061,T,T,C,H32 G6PD,X-153774331-C-T,X-154546116-C-T,N/A,X,153774331,154546116,C,C,T,G14R,N/A,N/A G6PD,X-153774337-C-A,X-154546122-C-A,rs797043472,X,153774337,154546122,C,C,A,V12L,N/A,N/A G6PD,X-153774346-G-A,X-154546131-G-A,rs1273138455,X,153774346,154546131,G,G,A,R9W,N/A,N/A +GRIK1,21-30967508-C-A,21-29595188-C-A,rs2832407,21,30967508,29595188,C,C,A,N/A,N/A,N/A +GRIK4,11-120663363-T-C,11-120792654-T-C,rs1954787,11,120663363,120792654,T,T,C,N/A,N/A,N/A +GRIN2B,12-13953118-T-A,12-13800184-T-A,rs2058878,12,13953118,13800184,T,T,A,N/A,N/A,N/A GSTM1,1-110233138-G-C,1-109690516-G-C,rs1065411,1,110233138,109690516,G,G,C,K173N,N/A,N/A GSTP1,11-67352689-A-G,11-67585218-A-G,rs1695,11,67352689,67585218,A,A,G,I105V,N/A,N/A GSTP1,11-67353579-C-T,11-67586108-C-T,rs1138272,11,67353579,67586108,C,C,T,A114V,N/A,N/A +HTR1A,5-63258565-C-G,5-63962738-C-G,rs6295,5,63258565,63962738,C,C,G,N/A,N/A,N/A +HTR2A,13-47411985-A-G,13-46837850-A-G,rs7997012,13,47411985,46837850,A,A,G,N/A,N/A,N/A +HTR2A,13-47471478-C-T,13-46897343-C-T,rs6311,13,47471478,46897343,C,C,T,N/A,N/A,N/A IFNL3,19-39731783-A-G,19-39241143-A-G,rs12980275,19,39731783,39241143,A,A,G,N/A,N/A,N/A IFNL3,19-39738787-C-T,19-39248147-C-T,rs12979860,19,39738787,39248147,C,C,T,N/A,N/A,N/A IFNL3,19-39743165-T-G,19-39252525-T-G,rs8099917,19,39743165,39252525,T,T,G,N/A,N/A,N/A +IFNL4,19-39738787-C-T,19-39248147-C-T,rs12979860,19,39738787,39248147,C,C,T,N/A,N/A,N/A +ITGB3,17-45360730-T-C,17-47283364-T-C,rs5918,17,45360730,47283364,T,T,C,N/A,N/A,N/A +ITPA,20-3193842-C-A,20-3213196-C-A,rs1127354,20,3193842,3213196,C,C,A,N/A,N/A,N/A +ITPA,20-3193893-A-C,20-3213247-A-C,rs7270101,20,3193893,3213247,A,A,C,N/A,N/A,N/A MTHFR,1-11847449-G-A,1-11787392-G-A,rs3737967,1,11847449,11787392,G,G,A,N/A,N/A,N/A MTHFR,1-11850927-C-T,1-11790870-C-T,rs2274976,1,11850927,11790870,C,C,T,N/A,N/A,N/A MTHFR,1-11852300-C-T,1-11792243-C-T,rs1476413,1,11852300,11792243,C,C,T,N/A,N/A,N/A @@ -956,6 +979,8 @@ NUDT15,13-48619826-C-G,13-48045690-C-G,rs768324690,13,48619826,48045690,C,C,G,P1 NUDT15,13-48619855-C-T,13-48045719-C-T,rs116855232,13,48619855,48045719,C,C,T,R139C,N/A,N/A NUDT15,13-48619856-G-A,13-48045720-G-A,rs147390019,13,48619856,48045720,G,G,A,R139H,N/A,N/A NUDT15,13-48619907-T-A,13-48045771-T-A,rs139551410,13,48619907,48045771,T,T,A,L156Q,N/A,N/A +OPRK1,8-54152982-T-C,8-53240422-T-C,rs6473797,8,54152982,53240422,T,T,C,N/A,N/A,N/A +OPRM1,6-154360797-A-G,6-154039662-A-G,rs1799971,6,154360797,154039662,A,A,G,N40D,N/A,N/A POR,7-75583452-AG-A,7-75954134-AG-A,N/A,7,75583452,75954134,AG,AG,A,R48fs,N/A,N/A POR,7-75583457-G-C,7-75954139-G-C,rs56355228,7,75583457,75954139,G,G,C,K49N,N/A,N/A POR,7-75608835-T-C,7-75979517-T-C,rs782804219,7,75608835,75979517,T,T,C,S102P,N/A,N/A @@ -1011,6 +1036,7 @@ PTGIS,20-48184654-C-CGCGGGGCTG,20-49568117-C-CGCGGGGCTG,rs773006734,20,48184654, PTGIS,20-48184654-C-CGCGGGGCTGGCGGGGCTG,20-49568117-C-CGCGGGGCTGGCGGGGCTG,rs773006734,20,48184654,49568117,C,C,CGCGGGGCTGGCGGGGCTG,Promoter Defect,N/A,N/A PTGIS,20-48184654-C-CGCGGGGCTGGCGGGGCTGGCGGGGCTG,20-49568117-C-CGCGGGGCTGGCGGGGCTGGCGGGGCTG,rs773006734,20,48184654,49568117,C,C,CGCGGGGCTGGCGGGGCTGGCGGGGCTG,Promoter Defect,N/A,N/A PTGIS,20-48184654-C-CGCGGGGCTGGCGGGGCTGGCGGGGCTGGCGGGGCTG,20-49568117-C-CGCGGGGCTGGCGGGGCTGGCGGGGCTGGCGGGGCTG,rs773006734,20,48184654,49568117,C,C,CGCGGGGCTGGCGGGGCTGGCGGGGCTGGCGGGGCTG,Promoter Defect,N/A,N/A +RARG,12-53605545-G-A,12-53211761-G-A,rs2229774,12,53605545,53211761,G,G,A,S427L,N/A,N/A RYR1,19-38931442-T-C,19-38440802-T-C,rs193922747,19,38931442,38440802,T,T,C,C35R,N/A,N/A RYR1,19-38931469-C-T,19-38440829-C-T,rs193922748,19,38931469,38440829,C,C,T,R44C,N/A,N/A RYR1,19-38934851-C-T,19-38444211-C-T,rs118192161,19,38934851,38444211,C,C,T,R163C,N/A,N/A @@ -1059,6 +1085,7 @@ RYR1,19-39071010-C-G,19-38580370-C-G,rs193922878,19,39071010,38580370,C,C,G,L483 RYR1,19-39071043-G-A,19-38580403-G-A,rs118192168,19,39071043,38580403,G,G,A,V4849I,N/A,N/A RYR1,19-39071080-G-A,19-38580440-G-A,rs63749869,19,39071080,38580440,G,G,A,R4861H,N/A,N/A RYR1,19-39075629-T-C,19-38584989-T-C,rs118192170,19,39075629,38584989,T,T,C,I4898T,N/A,N/A +SLC6A4,17-28564346-T-C,17-30237328-T-C,rs25531,17,28564346,30237328,T,T,C,N/A,N/A,N/A SLC15A2,3-121643804-C-T,3-121924957-C-T,rs2257212,3,121643804,121924957,C,C,T,L350F,N/A,N/A SLC15A2,3-121647286-C-T,3-121928439-C-T,rs1143671,3,121647286,121928439,C,C,T,P409S,N/A,N/A SLC15A2,3-121648168-G-A,3-121929321-G-A,rs1143672,3,121648168,121929321,G,G,A,R509K,N/A,N/A @@ -1070,6 +1097,8 @@ SLC22A2,6-160670282-A-C,6-160249250-A-C,rs316019,6,160670282,160249250,A,A,C,A27 SLC22A2,6-160671584-G-A,6-160250552-G-A,rs8177510,6,160671584,160250552,G,G,A,N/A,N/A,N/A SLC22A2,6-160677683-A-G,6-160256651-A-G,rs8177509,6,160677683,160256651,A,A,G,F161L,N/A,N/A SLC22A2,6-160679400-C-A,6-160258368-C-A,rs624249,6,160679400,160258368,C,C,A,N/A,N/A,N/A +SLC28A3,9-86900926-G-A,9-84286011-G-A,rs7853758,9,86900926,84286011,G,G,A,L461L,N/A,N/A +SLC47A2,17-19619998-G-A,17-19716685-G-A,rs12943590,17,19619998,19716685,G,G,A,N/A,N/A,N/A SLCO1B1,12-21325668-C-T,12-21172734-C-T,rs139257324,12,21325668,21172734,C,C,T,R57W,N/A,N/A SLCO1B1,12-21325710-G-A,12-21172776-G-A,rs373327528,12,21325710,21172776,G,G,A,G71R,N/A,N/A SLCO1B1,12-21325716-T-C,12-21172782-T-C,rs56101265,12,21325716,21172782,T,T,C,F73L,N/A,N/A @@ -1183,6 +1212,7 @@ UGT1A4,2-234627914-T-C,2-233719268-T-C,rs12468274,2,234627914,233719268,T,T,C,N/ UGT1A4,2-234628270-G-A,2-233719624-G-A,rs3732217,2,234628270,233719624,G,G,A,N/A,N/A,N/A UGT1A4,2-234628334-G-T,2-233719688-G-T,rs562977700,2,234628334,233719688,G,G,T,Splice Defect,N/A,N/A UGT1A4,2-234628376-C-T,2-233719730-C-T,rs2011219,2,234628376,233719730,C,C,T,N/A,N/A,N/A +UGT1A6,2-234602277-G-T,2-233693631-G-T,rs17863783,2,234602277,233693631,G,G,T,V209V,N/A,N/A UGT2B7,4-69962449-G-T,4-69096731-G-T,rs12233719,4,69962449,69096731,G,G,T,A71S,N/A,N/A UGT2B7,4-69964338-T-C,4-69098620-T-C,rs7439366,4,69964338,69098620,T,T,C,H268Y,N/A,N/A UGT2B7,4-69973922-G-A,4-69108204-G-A,rs776991562,4,69973922,69108204,G,G,A,D398N,N/A,N/A diff --git a/pypgx/version.py b/pypgx/version.py index f8ab8c2..8c308d7 100644 --- a/pypgx/version.py +++ b/pypgx/version.py @@ -1 +1 @@ -__version__ = '0.24.0' +__version__ = '0.25.0'