PharmVar GeneFocus: CYP2C19

Abstract

The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Figure 1. Overview of the gene locus and allelic variation

Panel A provides a graphical overview of the CYP2C gene locus containing CYP2C18, CYP2C19, CYP2C9, and CYP2C8. The latter is encoded on the reverse strand (arrow) while the other three genes are encoded on the forward strand. CYP2C19 is composed of nine exons, covering 92.9 kb. Rare whole and partial gene deletion events that include at least exon 1 of the CYP2C19 gene have been designated by PharmVar as CYP2C19*36 and *37, respectively. Whole gene deletions may include the neighboring CYP2C gene(s) and even extend beyond the CYP2C gene locus. Partial deletions affect different regions of CYP2C19 and may affect CYP2C18 and/or 2C9 as well. Panel B summarizes the core sequence variations defining CYP2C19*2 through*10 and *17.

Figure 2. Allele default assignment strategy used by many testing platforms

Many pharmacogenetic test platforms only comprise the more commonly observed SNVs and do not include all known SNVs, or star (*) alleles that are defined by PharmVar. Consequently, some alleles may not be identified or receive an assignment by ‘default’. It is therefore important to know which SNVs are tested in order to fully understand how alleles were called and translated into phenotype, as well as to appreciate a test’s limitations. Panel A visualizes the two known CYP2C19*4 subvariants which are nonfunctional due to c.1A>G (p.M1V). The CYP2C19*4.002 subvariant also carries c.−806C>T which is the core SNV defining the increased function *17 allele. Thus, if testing only includes c.−806C>T and not c.1A>G, a CYP2C19*4 allele will be called *17 potentially leading to an incorrect phenotype assignment. Panel B illustrates that g.12662A>G (c.332-23A>G), which causes aberrant splicing, occurs on both, CYP2C19*2 and *35. If not tested, the latter will be defaulted to a CYP2C19*1 assignment that may also lead to an incorrect phenotype assignment. Panel C shows the comparison of CYP2C19*2, *4, *17 and *35, created with the PharmVar CAVE tool. Blue boxes indicate the presence of a core SNV on all suballeles, while the gray box indicates that the core SNV is not present on all suballeles. The function ()symbol indicates that a core SNV alters function and the PharmVar () symbol highlights that a core SNV is unique to a star allele. SNV positions refer to genomic coordinates on the NG_008384.3 reference sequence (with the ATG start codon being +1).

Figure 3. Overview of core alleles, suballeles, and the graphical Core Allele ViewEr (CAVE)

Panel A shows the CYP2C19*2 core allele definition (gray bar). Core SNVs, PharmVar ID (PVID), and evidence level is shown for each allele. All currently defined suballeles are displayed. Legacy allele designations are cross-referenced (e.g., *2.001 corresponds to *2A). Note that g.12662A>G (c.332-23A>G) was added to all suballeles, when the gene was transferred to PharmVar (Table 3). Panel B is a graphical representation of the CYP2C19*2 and *11 core alleles and their core SNVs. c.991A>G (p.I331V) is present on both alleles, while c.332-23A>G and c.681G>A (splice defects) are the CYP2C19*2 core SNVs and c.449G>A (p.R150H) is the core SNV defining CYP2C19*11. Core SNVs are shown by red lines; gray boxes represent the nine exons (scale is approximated). Panel C shows three of the ten CYP2C19*2 suballeles defined to date and the only CYP2C19*11 haplotype. Of note, the core SNV of the latter (c.449G>A (p.R150H)) is also present on the CYP2C19*2.010 suballele. Core SNVs (causing an amino acid change or aberrant splicing) are shown in red, all other SNVs are highlighted in blue (c.449G>A (p.R150H)) is not a *2 core SNP because it is not found on all suballeles.

Figure 4. Experimental approaches for phasing SNVs to establish haplotype

Panels A and B depict a subject who is heterozygous for three SNVs of which two designate the CYP2C19*2 allele. Whether the novel SNV is in cis or trans with the CYP2C19*2 SNVs can be informed by e.g., inheritance (panel A), or experimentally determined using e.g., allele-specific (long-range) PCR, followed by sequencing (panel B), given that the distance among the novel SNV is not exceeding PCR amplification limitations. Panel C provides an example of a subject who is heterozygous for two SNPs, one of which designates the CYP2C19*17 allele. In this instance, the phase of the novel SNV may be inferred by inheritance (not shown) or experimentally determined by single molecule sequencing or utilizing ddPCR-based SNP-linkage analysis. Panel D details a submission for the CYP2C19*35 allele. The haplotype of the CYP2C19*35 suballele was determined from whole genome sequence data of each member of the trio. This data revealed an additional SNV on the CYP2C19*35 haplotype, as well as provided evidence to support changing the allele’s evidence level to ‘Def’.