GM17280
LCL from B-Lymphocyte
Description:
HUMAN VARIATION PANEL - WHITE PANEL OF 100 (SET 1)
HUMAN VARIATION PANEL - WHITE PANEL OF 200
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
CYTOCHROME P450, SUBFAMILY IID, POLYPEPTIDE 6; CYP2D6
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Repository
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NIGMS Human Genetic Cell Repository
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| Subcollection |
Human Variation
Pharmacogenetics
GeT-RM Samples
dbGaP |
| Alternate IDs |
GM08036 [HUMAN VARIATION PANEL - WHITE PANEL OF 100 (SET 1)] |
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Biopsy Source
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Peripheral vein
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Cell Type
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B-Lymphocyte
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Tissue Type
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Blood
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Transformant
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Epstein-Barr Virus
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Sample Source
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LCL from B-Lymphocyte
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Species
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Homo sapiens
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Common Name
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Human
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Remarks
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| Pharmacogenomics Panel |
For pharmacogenetic variants please click here: GeT-RM PGx Search |
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| IDENTIFICATION OF SPECIES OF ORIGIN |
Species of Origin Confirmed by LINE assay |
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| Gene |
CYP2C19 |
| Chromosomal Location |
10q23.33 |
| Allelic Variant 1 |
W120R; MEPHENYTOIN 4-HYDROXYLASE POOR METABOLIZER |
| Identified Mutation |
TRP120ARG |
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| Gene |
CYP2D6 |
| Chromosomal Location |
22q13.1 |
| Allelic Variant 1 |
124030.0006; DEBRISOQUINE, POOR METABOLISM OF |
| Identified Mutation |
1-BP DEL, 2549A; This allelic variant is also known as CYP2D6*3 or CYP2D6(A). Marez et al. (Pharmacogenetics 7: 193-202, 1997) identified a 1-bp deletion (2637A) in exon 5 of the CYP2D6 gene in a group of individuals with the poor metabolizer phenotype (608902). |
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| Gene |
CYP2D6 |
| Chromosomal Location |
22q13.1 |
| Allelic Variant 2 |
124030.0007; DEBRISOQUINE, ULTRARAPID METABOLISM OF |
| Identified Mutation |
ARG296CYS AND SER486THR; This allelic variant is also known as CYP2D6*2 or CYP2D6L. In a family in which 2 sibs and their father had MRs of less that 0.02 (ultrarapid phenotype, see 608902), Johansson et al. (Proc Nat Acad Sci 90:11825-11829, 1993) found 12 extra copies of the CYP2D6 gene inherited in an autosomal dominant pattern; in a second family in which 2 sibs had MRs of less than 0.1, the authors found 2 extra copies of the CYP2D6 gene. All affected individuals had a variant CYP2D6 gene, termed CYP2D6L, which contained 2 amino acid substitutions: a 2938C-T transition in exon 6, resulting in an arg296-to-cys (R296C), and a 4268G-to-C transversion in exon 9, resulting in a resulting in a ser486-to-thr (S486T) substitution. The MR of individuals with 1 copy of the CYP2D6L gene did not differ from those with the wildtype gene, but there was a correlation between decreased MR and increased copies of the CYP2D6L gene. |
| Remarks |
Donor subject is heterozygous for a T>C change at nucleotide 358 (358T>C) in exon 3 of the CYP2C19 gene (CYP2C19*8) which results in a substitution of an arginine for tryptophan at codon 120 [Trp120Arg (W120R)] and donor subject is also a compound heterozygote with respect to CYP2D6: one allele has a variant CYP2D6 gene (CYP2D6*2) which contains two amino acid substitutions: a C>T transition at nucleotide 2938 in exon 6 resulting in an arg296-to-cys [Arg296Cys (R296C)] and a G>C transversion at nucleotide 4268 in exon 9 resulting in a ser486-to-thr [Ser486Thr (S486T)]; a second allele has a 1 bp deletion at nucleotide 2637 (2637delA) in exon 5 (CYP2D6*3) |
| Charnaud S, Munro JE, Semenec L, Mazhari R, Brewster J, Bourke C, Ruybal-Pesántez S, James R, Lautu-Gumal D, Karunajeewa H, Mueller I, Bahlo M, PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus Communications biology5:168 2021 |
| PubMed ID: 35217695 |
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| Moon MH, Hong SR, Shin KJ, Sequence Variations of 31 ?-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three US Population Groups and Korean Population Journal of Korean medical science37:e40 2021 |
| PubMed ID: 35166077 |
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| Pratt VM, Turner A, Broeckel U, Dawson DB, Gaedigk A, Lynnes TC, Medeiros EB, Moyer AM, Requesens D, Ventrini F, Kalman LV, Characterization of Reference Materials for CYP2C9, CYP2C19, VKORC1, CYP2C Cluster Variant, GGCX, and Other Pharmacogenetic Alleles with an Association for Molecular Pathology (AMP) Pharmacogenetics Working Group Tier 2 Status - A GeT-RM Collaborative Project The Journal of molecular diagnostics : JMD37:e40 2021 |
| PubMed ID: 34020041 |
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| Botton MR, Yang Y, Scott ER, Desnick RJ, Scott SA, Phased Haplotype Resolution of the Genes11:e40 2020 |
| PubMed ID: 33198140 |
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| Kwon YL, Kim BM, Lee EY, Shin KJ, Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications Scientific reports11:4701 2020 |
| PubMed ID: 33633141 |
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| Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L, Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection Clinical and translational science14:204-213 2020 |
| PubMed ID: 32931151 |
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| Swart M, Stansberry WM, Pratt VM, Medeiros EB, Kiel PJ, Shen F, Schneider BP, Skaar TC, Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology The Journal of molecular diagnostics : JMD21:491-502 2018 |
| PubMed ID: 30794985 |
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| Yousaf R, Ahmed ZM, Giese AP, Morell RJ, Lagziel A, Dabdoub A, Wilcox ER, Riazuddin S, Friedman TB, Riazuddin S, Modifier variant of METTL13 suppresses human GAB1-associated profound deafness The Journal of clinical investigation21:491-502 2018 |
| PubMed ID: 29408807 |
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| Lee CC, McMillin GA, Babic N, Melis R, Yeo KT, Evaluation of a CYP2C19 genotype panel on the GenMark eSensor® platform and the comparison to the Autogenomics Infiniti™ and Luminex CYP2C19 panels Clinica chimica acta; international journal of clinical chemistry412(11-12):133-7 2010 |
| PubMed ID: 21385571 |
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| Pratt VM, Zehnbauer B, Wilson JA, Baak R, Babic N, Bettinotti M, Buller A, Butz K, Campbell M, Civalier C, El-Badry A, Farkas DH, Lyon E, Mandal S, McKinney J, Muralidharan K, Noll L, Sander T, Shabbeer J, Smith C, Telatar M, Toji L, Vairavan A, Vance C, Weck KE, Wu AH, Yeo KT, Zeller M, and Kalman L., Characterization of 107 Genomic DNA Reference Materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1 J Mol Diagn12(6):835-46 2010 |
| PubMed ID: 20889555 |
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| Marini NJ, Gin J, Ziegle J, Keho KH, Ginzinger D, Gilbert DA, Rine J, The prevalence of folate-remedial MTHFR enzyme variants in humans Proceedings of the National Academy of Sciences of the United States of America12(6):835-46 2008 |
| PubMed ID: 18523009 |
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| Mohler PJ, Le Scouarnec S, Denjoy I, Lowe JS, Guicheney P, Caron L, Driskell IM, Schott JJ, Norris K, Leenhardt A, Kim RB, Escande D, Roden DM, Defining the cellular phenotype of "ankyrin-B syndrome" variants: human ANK2 variants associated with clinical phenotypes display a spectrum of activities in cardiomyocytes Circulation115:432-41 2007 |
| PubMed ID: 17242276 |
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| Melis, R., Lyon, E., and McMillin, G.A., Determination of CYP2D6, CYP2C9 and CYP2C19 genotypes with Tag-It mutation detection assays Expert Rev Mol Diagn6(6):811-20 2006 |
| PubMed ID: 17140368 |
| dbSNP |
dbSNP ID: 12536 |
| Gene Cards |
CYP2C19 |
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CYP2D6 |
| Gene Ontology |
GO:0004497 monooxygenase activity |
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GO:0005783 endoplasmic reticulum |
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GO:0005792 microsome |
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GO:0006118 electron transport |
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GO:0016020 membrane |
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GO:0016712 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen |
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GO:0018676 (S)-limonene 7-monooxygenase activity |
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GO:0019825 oxygen binding |
| GEO |
GEO Accession No: GSM569757 |
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GEO Accession No: GSM924882 |
| NCBI Gene |
Gene ID:1557 |
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Gene ID:1565 |
| NCBI GTR |
124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19 |
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124030 CYTOCHROME P450, SUBFAMILY IID, POLYPEPTIDE 6; CYP2D6 |
| OMIM |
124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19 |
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124030 CYTOCHROME P450, SUBFAMILY IID, POLYPEPTIDE 6; CYP2D6 |
| PharmGKB |
Pharmgkb ID (requires login): PA126721746 |
| Split Ratio |
1:2 |
| Temperature |
37 C |
| Percent CO2 |
5% |
| Percent O2 |
AMBIENT |
| Medium |
Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent |
| Serum |
15% fetal bovine serum Not Inactivated |
| Substrate |
None specified |
| Subcultivation Method |
dilution - add fresh medium |
| Supplement |
- |
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