PharmVar GeneFocus: CYP3A5

Abstract

The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP3A5 gene. Genetic variation within the CYP3A5 gene locus impacts the metabolism of several clinically important drugs, including the immunosuppressants tacrolimus, sirolimus, cyclosporine, and the benzodiazepine midazolam. Variable CYP3A5 activity is of clinical importance regarding tacrolimus metabolism. This GeneFocus provides a CYP3A5 gene summary with a focus on aspects regarding standardized nomenclature. In addition, this review also summarizes recent changes and updates, including the retirement of several allelic variants and provides an overview of how PharmVar CYP3A5 star allele nomenclature is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Figure 1. Overview of the gene locus and allelic variation

The top panel provides a graphical overview of the CYP3A gene locus containing the CYP3A5, CYP3A7, CYP3A4 and CYP3A43 genes and their approximate length in kilobase pairs (kb). CYP3A43 is encoded on the forward strand, while the other three genes are encoded on the minus strand as indicated by the white arrows. The bottom panel shows the CYP3A5 gene in the forward orientation (5’ to 3’). CYP3A5 comprises 13 exons as indicated by the green boxes; 5’ and 3’ untranslated regions (UTRs) are highlighted in light green. The core variants defining the CYP3A5*3, *6, *7, *8 and *9 alleles are as shown.

Figure 2. Overview of core allele and suballele categorization

Panel (a) is an excerpt of the CYP3A5 gene page showing *3, *6 and *7 allele definitions with NM_000777.5 as the reference sequence; their respective core allele definitions are depicted by gray bars. Core variants, PharmVar ID (PVID), and haplotype evidence levels are shown for each allele. Selected CYP3A5*3 suballeles are displayed underneath the core allele bar; currently, CYP3A5*6 and *7 have only one suballele. Legacy allele designations are cross-referenced (e.g., CYP3A5*3.001 corresponds to *3A and *3.003 corresponds *3D). Panel (b) is a graphical representation of the CYP3A5*3 suballeles containing the variants that previously defined the CYP3A5*2, *4 and *5 alleles; these are now cataloged as CYP3A5*3 suballeles due to having the intron 3 c.219–237A>G splice variant (highlighted in red). Green boxes represent exons; the 5’ and 3’ untranslated regions are shown in light green. Panel (c) represents the graphical output of the Comparative Allele ViewEr (CAVE) when comparing the five currently existing star alleles. The PharmVar symbols indicate that the variant is unique to the allele and the function symbol signifies that the variant alters function.

Figure 3. Methods and approaches to characterize CYP3A5 allelic variants

Panels (a-c) provide examples of alleles submitted to PharmVar to name or confirm existing allele definitions. Red lines highlight variants found on the submitted alleles. Haplotypes shown in panels a and b utilized WGS data either confirmed by WES or targeted NGS-based sequencing panels; haplotypes in panel c represent two subjects of the Simons Genome Diversity Project (93) who underwent WGS. Haplotypes are inferred; variants were not independently confirmed. Panel (a) provides examples of haplotypes that can unequivocally be deduced as only a single variant is heterozygous. These include selected submissions supporting the reclassification of CYP3A5*2, *4 and *5 as CYP3A5*3 suballeles as shown. Each subject was homozygous for the CYP3A5*3 splice variant c.219–237A>G and heterozygous for c.1193C>A, c.599A>G or c.432+2T>C. Thus, the latter variants are part of CYP3A5*3 haplotypes and do not occur independently. Panel (b) shows a subject whose three heterozygous variants were placed on the same chromosome because c.88C>T and c.92_93insG were found on the same short reads. Thus, variants in close proximity may be deduced directly from short-read data. Panel (c) illustrates two samples with the CYP3A5*8 core variant c.82C>T. Although the phase of their respective haplotypes could not be inferred with certainty, the data support that c.82C>T is not on a CYP3A5*3 haplotype.