Allele Submission

PharmVar is accepting submissions for CYP allele designations. While we are working on the online submission portal, please use the submission form and email to pharmvar@cmh.edu with the gene name in the subject line.

Important information for submissions

A standardized submission form has been developed to collect complete sets of high-quality data across all genes. To that end, all submissions MUST be provided in reference to the gene's RefSeqGene sequence (RefSeq IDs are provided on the RefSeq tab of the submission form).

Only complete submissions will be accepted and reviewed by the gene expert panels.

The requested information is detailed in each tab and an example is provided; please check out all tabs for a range of examples.

For each gene a minimum of 500 bp of the 5' untranslated and 250 bp of the 3' untranslated regions must be sequenced. Submitters are strongly encouraged to extend the sequenced untranslated regions if they harbor key SNVs defining star (*) alleles. For example, for CYP2C19 there are two SNPs at positions -806 and -1041 that are key to define *17 and *27, respectively.

To facilitate allele/haplotype definitions, genes under 10 kb in length (defined as exon 1 through exon 9) MUST be entirely sequenced. See RefSeq tab on submission form whether gene of interest falls into this category.

For genes over 10 kb in length (defined as exon 1 through exon 9), all exons and 50 bp of flanking introns must be sequenced. See RefSeq tab on submission form whether gene of interest falls into this category. Submitters are strongly encouraged to also cover intronic regions that harbor key SNVs defining star (*) alleles. Examples are CYP2C19 12662A>G in intron 2 defining the *35 allele and CYP3A5 6986A>G in intron 3 defining the *3 allele.

To adequately capture structural and copy number variation, there are separate tabs for CYP2A6 and CYP2D6. For CYP2A6 submissions covering the entire gene are encouraged although submissions fulfilling the requirements for exon and flanking regions are also accepted. For CYP2D6 the entire gene must be sequenced; submitters are also strongly encouraged to cover the untranslated region to include the SNP at position -1584 as this SNP is part of many haplotype definitions.

Novel sequence variations detected by Next Gen Sequencing must be confirmed by orthogonal methods.