Friday, July 29, 2022

PharmVar GeneFocus paper for SLCO1B1 is published

The PharmVar GeneFocus: SLCO1B1 paper has just been published by Clinical Pharmacology & Therapeutics.


This review provides a general overview of SLCO1B1 as well as a deeper dive into its nomenclature. This GeneFocus covers genetic variability, functional impact, clinical relevance, gene nomenclature before and after PharmVar updates, methods for allele characterization and how the new nomenclature impacts pharmacogenetic testing and interpretationSpecific details of changes to allele definitions can be found on the PharmVar SLCO1B1 page and on the Change Log tab of the SLCO1B1 Allele Definition Table available from PharmGKB. This new nomenclature has been used in the recently published CPIC guideline on statin-associated musculoskeletal symptoms.


For more details, please see:

PharmVar GeneFocus: SLCO1B1

Clin Pharmacol Ther. 2022 Jul 7. doi: 10.1002/cpt.2705. 

Laura B. Ramsey, Li Gong, Seung-been Lee, Jonathan B. Wagner, Xujia Zhou, Katrin Sangkuhl, Solomon M. Adams, Robert J. Straka, Philip E. Empey, Erin C. Boone, Teri E. Klein, Mikko Niemi, Andrea Gaedigk.

PMID: 35797228

Friday, July 22, 2022

CYP2A6 now released on PharmVar

PharmVar and PharmGKB are excited to share that CYP2A6 has been transitioned into the PharmVar database. CYP2A6 metabolizes several substates including coumarin, nicotine, aflatoxin B1, nitrosamines, and some pharmaceuticals. Owing to its highly polymorphic nature, CYP2A6 activity varies considerably between individuals. Due to the complex nature of the CYP2A gene locus that contains not only CYP2A6, but also the highly similar CYP2A7 and CYP2A13 genes, CYP2A6 genotype analysis and characterization of allelic variants is not trivial. It is therefore of utmost importance to have up-to-date information regarding sequence variation and star allele (haplotype) definitions to facilitate accurate genetic testing, data interpretation and phenotype prediction in the research and clinical settings.  

The PharmVar CYP2A6 gene experts have systematically reviewed and curated all star allele definitions that were previously issued by the CYP450 Nomenclature databases (these were last updated in 2014 and can be accessed through the archive). Some notable changes include:

  • Variants and star alleles are now defined using the most current genomic reference sequence
  • Several alleles have been merged, revised and/or redesignated (legacy allele designations are cross-referenced)
  • Regions used for allele definitions have been updated
  • Structural variants including a common conversion at the 3’UTR have been updated to current knowledge and are detailed in the ‘Structural Variation’ document.

Changes made are detailed in the ‘Change Log’ document and other important information about CYP2A6 and the information displayed by PharmVar can be found in the ‘Read Me’ document. All accompanying documents can be accessed at the PharmVar CYP2A6 page at 


Since there are no CPIC guidelines for CYP2A6, the PharmVar CYP2A6 page does not provide information for ‘CPIC clinical function’. The expert panel has, however, compiled a table in the ‘Read Me’ document summarizing function information for selected star alleles.  


Lastly, we would like to thank the PharmVar CYP2A6 experts Rachel Tyndale, Alec Langlois, Meghan Chenoweth, Giada Scantamburlo, Charity Nofziger, David Twesigmwe, Rachel Huddart and Andrea Gaedigk for their tireless efforts that made this massive update possible.