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GM17201 LCL from B-Lymphocyte

Description:

HUMAN VARIATION PANEL - WHITE PANEL OF 50
HUMAN VARIATION PANEL - WHITE PANEL OF 100 (SET 1)
HUMAN VARIATION PANEL - WHITE PANEL OF 200
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 24
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19

Affected:

No

Sex:

Male

Age:

25 YR (At Sampling)

  • Overview
  • Characterizations
  • Phenotypic Data
  • Publications
  • External Links
  • Culture Protocols

Overview

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Repository NIGMS Human Genetic Cell Repository
Subcollection Human Variation
Pharmacogenetics
GeT-RM Samples
dbGaP
Alternate IDs GM00130 [HUMAN VARIATION PANEL - WHITE PANEL OF 50]
Biopsy Source Peripheral vein
Cell Type B-Lymphocyte
Tissue Type Blood
Transformant Epstein-Barr Virus
Sample Source LCL from B-Lymphocyte
Species Homo sapiens
Common Name Human
Remarks Donor subject has a single bp (G-to-A) mutation in exon 5 of the CYP2C19 gene (CYP2C19*2) which creates an aberrant splice site. The change altered the reading frame of the mRNA starting with amino acid 215 and produced a premature stop codon 20 amino acids downstream, resulting in a truncated, nonfunctional protein. Because of the aberrant splice site, a 40-bp deletion occurred at the beginning of exon 5 (from bp 643 to bp 682), resulting in deletion of amino acids 215 to 227. The truncated protein had 234 amino acids and would be catalytically inactive because it lacked the heme-binding region.

Characterizations

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IDENTIFICATION OF SPECIES OF ORIGIN Species of Origin Confirmed by Nucleoside Phosphorylase,Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis
 
Pharmacogenomics Panel For pharmacogenetic variants please click here: GeT-RM PGx Search
 
Gene CYP2C19
Chromosomal Location 10q23.33
Allelic Variant 1 124020.0001; MEPHENYTOIN 4-HYDROXYLASE POOR METABOLIZER
Identified Mutation 21158G>A ; The principal defect in CYP2C19 responsible for the S-mephenytoin poor metabolizer phenotype was found by de Morais et al. (1994) to be a single bp (G-to-A) mutation in exon 5 which creates an aberrant splice site. The change altered the reading frame of the mRNA starting with amino acid 215 and produced a premature stop codon 20 amino acids downstream, resulting in a truncated, nonfunctional protein. De Morais et al. (1994) demonstrated that 7/10 Caucasian and 10/17 Japanese poor metabolizers were homozygous for this defect. The inheritance of the deficient allele was found to be concordant with that of the PM trait. To determine the nature of the defect, since the genomic sequence of CYP2C19 was not yet known, de Morais et al. (1994) developed primers for the intron 4/exon 5 junction empirically. This involved the use of multiple primers for intron 4 based on the sequence of this region in CYP2C9, a closely related gene that shows 95% similarity to CYP2C19 in the upstream region and several exons, and a specific reverse primer for exon 5 of CYP2C19. Because of the aberrant splice site, a 40-bp deletion occurred at the beginning of exon 5 (from bp 643 to bp 682), resulting in deletion of amino acids 215 to 227. The truncated protein had 234 amino acids and would be catalytically inactive because it lacked the heme-binding region. De Morais et al. (1994) developed a simple PCR-based test for the defective CYP2C19 allele.

Phenotypic Data

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Remarks Donor subject has a single bp (G-to-A) mutation in exon 5 of the CYP2C19 gene (CYP2C19*2) which creates an aberrant splice site. The change altered the reading frame of the mRNA starting with amino acid 215 and produced a premature stop codon 20 amino acids downstream, resulting in a truncated, nonfunctional protein. Because of the aberrant splice site, a 40-bp deletion occurred at the beginning of exon 5 (from bp 643 to bp 682), resulting in deletion of amino acids 215 to 227. The truncated protein had 234 amino acids and would be catalytically inactive because it lacked the heme-binding region.

Publications

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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
 
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
 
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
 
Ruiz-Deya G, Matta J, Encarnación-Medina J, Ortiz-Sanchéz C, Dutil J, Putney R, Berglund A, Dhillon J, Kim Y, Park JY, Differential DNA Methylation in Prostate Tumors from Puerto Rican Men International journal of molecular sciences22:4701 2020
PubMed ID: 33450964
 
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
 
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
 
Lambert CA, Connelly CF, Madeoy J, Qiu R, Olson MV, Akey JM, Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history American journal of human genetics86:34-44 2009
PubMed ID: 20085712
 
Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L, Gemcitabine and Cytosine Arabinoside Cytotoxicity: Association with Lymphoblastoid Cell Expression Cancer research68:7050-7058 2008
PubMed ID: 18757419
 
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 America68:7050-7058 2008
PubMed ID: 18523009
 
Atwal GS, Bond GL, Metsuyanim S, Papa M, Friedman E, Distelman-Menachem T, Ben Asher E, Lancet D, Ross DA, Sninsky J, White TJ, Levine AJ, Yarden R, Haplotype structure and selection of the MDM2 oncogene in humans Proceedings of the National Academy of Sciences of the United States of America104:4524-9 2007
PubMed ID: 17360557
 
Gonzalez-Covarrubias V, Ghosh D, Lakhman SS, Pendyala L, Blanco JG, A functional genetic polymorphism on human carbonyl reductase 1 (CBR1 V88I) impacts on catalytic activity and NADPH binding affinity Drug metabolism and disposition: the biological fate of chemicals35:973-80 2007
PubMed ID: 17344335
 
Bubb KL, Bovee D, Buckley D, Haugen E, Kibukawa M, Paddock M, Palmieri A, Subramanian S, Zhou Y, Kaul R, Green P, Olson MV, Scan of human genome reveals no new Loci under ancient balancing selection Genetics173:2165-77 2006
PubMed ID: 16751668
 
Mukherjee B, Salavaggione OE, Pelleymounter LL, Moon I, Eckloff BW, Schaid DJ, Wieben ED, Weinshilboum RM, Glutathione S-transferase omega 1 and omega 2 pharmacogenomics Drug metabolism and disposition: the biological fate of chemicals34:1237-46 2006
PubMed ID: 16638819
 
Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu PP, Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De La Vega FM, Rhodes MD, Hennessy KM, Wenz HM, The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping Journal of biomolecular techniques : JBT16:398-406 2006
PubMed ID: 16522862
 
Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA, Genomic regions exhibiting positive selection identified from dense genotype data Genome research15:1553-65 2005
PubMed ID: 16251465
 
Chen HJ, Tian H, Edenberg HJ, Natural haplotypes in the regulatory sequences affect human alcohol dehydrogenase 1C (ADH1C) gene expression Human mutation25:150-5 2005
PubMed ID: 15643610
 
De La Vega FM, Isaac H, Collins A, Scafe CR, Halldorsson BV, Su X, Lippert RA, Wang Y, Laig-Webster M, Koehler RT, Ziegle JS, Wogan LT, Stevens JF, Leinen KM, Olson SJ, Guegler KJ, You X, Xu LH, Hemken HG, Kalush F, Itakura M, Zheng Y, de The G, O'Brien SJ, Clark AG, Istrail S, Hunkapiller MW, Spier EG, Gilbert DA, The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res15(4):454-62 2005
PubMed ID: 15781572
 
Dib-Hajj SD, Rush AM, Cummins TR, Hisama FM, Novella S, Tyrrell L, Marshall L, Waxman SG, Gain-of-function mutation in Nav17 in familial erythromelalgia induces bursting of sensory neurons Brain : a journal of neurology128:1847-54 2005
PubMed ID: 15958509
 
Dick DM, Edenberg HJ, Xuei X, Goate A, Hesselbrock V, Schuckit M, Crowe R, Foroud T, No association of the GABAA receptor genes on chromosome 5 with alcoholism in the collaborative study on the genetics of alcoholism sample American journal of medical genetics Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics132:24-8 2005
PubMed ID: 15690551
 
Harris SL, Gil G, Robins H, Hu W, Hirshfield K, Bond E, Bond G, Levine AJ, Detection of functional single-nucleotide polymorphisms that affect apoptosis Proceedings of the National Academy of Sciences of the United States of America102:16297-302 2005
PubMed ID: 16260726
 
Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR, Whole-genome patterns of common DNA variation in three human populations. Science307(5712):1072-9 2005
PubMed ID: 15718463
 
Slater HR, Bailey DK, Ren H, Cao M, Bell K, Nasioulas S, Henke R, Choo KH, Kennedy GC, High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs American journal of human genetics77:709-26 2005
PubMed ID: 16252233
 
Ulrich CM, Carlson CS, Sibert J, Poole EM, Yu JH, Wang LH, Sparks R, Potter JD, Bigler J, Thromboxane synthase (TBXAS1) polymorphisms in African-American and Caucasian populations: evidence for selective pressure Human mutation26:394-5 2005
PubMed ID: 16134166
 
Hu X, Schrodi SJ, Ross DA, Cargill M, Selecting tagging SNPs for association studies using power calculations from genotype data Human heredity57:156-70 2004
PubMed ID: 15297809
 
Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SP, Mei R, Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods1(2):109-11 2004
PubMed ID: 15782172

External Links

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dbSNP dbSNP ID: 896
Gene Cards CYP2C19
Gene Ontology GO:0004497 monooxygenase activity
GO:0005783 endoplasmic reticulum
GO:0005792 microsome
GO:0006118 electron transport
GO:0016020 membrane
GO:0018676 (S)-limonene 7-monooxygenase activity
GO:0019825 oxygen binding
GEO GEO Accession No: GSM569492
GEO Accession No: GSM924803
NCBI Gene Gene ID:1557
NCBI GTR 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
OMIM 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
PharmGKB Pharmgkb ID (requires login): PA126721667

Culture Protocols

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Split Ratio 1:4
Temperature 37 C
Percent CO2 5%
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 -
Pricing
Commercial/For-profit:
$373.00USD
Academic/Non-profit/Government:
$216.00USD
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