title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2 Alleles.
abstract: CYP2C19 rs12769205 alters an intron 2 branch point adenine leading to an alternative mRNA in human liver with complete inclusion of intron 2 (exon 2B). rs12769205 changes the mRNA reading frame, introduces 87 amino acids, and leads to a premature stop codon. The 1000 Genomes project (http://browser.1000genomes.org/index.html) indicated rs12769205 is in linkage disequilibrium with rs4244285 on CYP2C19*2, but found alone on CYP2C19*35 in Blacks. Minigenes containing rs12769205 transfected into HepG2 cells demonstrated this single nucleotide polymorphism (SNP) alone leads to exon 2B and decreases CYP2C19 canonical mRNA. A residual amount of CYP2C19 protein was detectable by quantitative proteomics with tandem mass spectrometry in CYP2C19*2/*2 and *1/*35 liver microsomes with an exon 2 probe. However, an exon 4 probe, downstream from rs12769205, but upstream of rs4244285, failed to detect CYP2C19 protein in livers homozygous for rs12769205, demonstrating rs12769205 alone can lead to complete loss of CYP2C19 protein. CYP2C19 genotypes and mephenytoin phenotype were compared in 104 Ethiopians. Poor metabolism of mephenytoin was seen in persons homozygous for both rs12769205 and rs4244285 (CYP2C19*2/*2), but with little effect on mephenytoin disposition of CYP2C19*1/*2, CYP2C19*1/*3, or CYP2C19*1/*35 heterozygous alleles. Extended haplotype homozygosity tests of the HapMap Yorubans (YRI) showed both haplotypes carrying rs12769205 (CYP2C19*35 and CYP2C19*2) are under significant natural selection, with CYP2C19*35 having a higher relative extended haplotype homozygosity score. The phylogenetic tree of the YRI CYP2C19 haplotypes revealed rs12769205 arose first on CYP2C19*35 and that rs4244285 was added later, creating CYP2C19*2. In conclusion, rs12769205 is the ancestral polymorphism leading to aberrant splicing of CYP2C19*35 and CYP2C19*2 alleles in liver.
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Amarjit S
authors.initials: AS
authors.lastname: Chaudhry
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Bhagwat
authors.initials: B
authors.lastname: Prasad
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Shirasaka
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Alison
authors.initials: A
authors.lastname: Fohner
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: David
authors.initials: D
authors.lastname: Finkelstein
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Yiping
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Shuoguo
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Gang
authors.initials: G
authors.lastname: Wu
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Eleni
authors.initials: E
authors.lastname: Aklillu
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Sarah C
authors.initials: SC
authors.lastname: Sim
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.).
authors.forename: Kenneth E
authors.initials: KE
authors.lastname: Thummel
authors.affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.) erin.schuetz@stjude.org.
authors.forename: Erin G
authors.initials: EG
authors.lastname: Schuetz
mesh_terms: D000107:Acetylation; D000328:Adult; D000483:Alleles; D065731:Cytochrome P-450 CYP2C19 / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000096:biosynthesis / Q000235:genetics; D005002:Ethiopia / Q000453:epidemiology; D005091:Exons; D005260:Female; D005787:Gene Frequency; D006239:Haplotypes; D006801:Humans; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008099:Liver / Q000201:enzymology*; D008297:Male; D008617:Mephenytoin / Q000493:pharmacokinetics; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing; D053719:Tandem Mass Spectrometry
chemical_list: D018076:DNA, Complementary; D007527:Isoenzymes; C045793:CYP2C19 protein, human; D065731:Cytochrome P-450 CYP2C19; D008617:Mephenytoin