The PRDM9 Variant Database

The PRDM9 fandom is a bit of a mess:

• There is inconsistency in how alleles are named
• Different alleles have the same name
• The same name is used for different alleles
• Publications are claiming to have identified novel alleles that have actually been previously described
• Publications and NCBI Nucleotide entries have typos
• There is no database for all of the alleles uncovered to date

This is a collection of all known/described PRDM9 allele and zinc finger variants. In addition, they have been renamed in a standardized manner: alleles are P### and zinc finger repeats are Z###. The allele zinc finger content and zinc finger sequence files contain a "map" to connect the standardized names to original names.

Standardized lists

Variants observed in the population:

• Allele sequences
• Zinc finger content of alleles
• Zinc finger sequences

Above lists plus variants observed only in sperm or as somatic mutations in blood (see Jeffreys et al.)

• Allele sequences blood/sperm
• Zinc finger content of alleles blood/sperm
• Zinc finger sequences blood/sperm

Process

• Step 1: Collect known PRDM9 alleles and associated zinc fingers from publications
• Steps 2-4: Compile the publication variants
• Step 5-8: Collect known PRDM9 allele DNA sequences from NCBI
• Step 9: Infer allele sequencess mentioned in publications but not explicitly defined
• Steps 10-11: Finalize lists of PRDM9 alleles and zinc finger repeats

TODO

• Add ref https://onlinelibrary.wiley.com/doi/10.1002/mgg3.56 for Genbank alleles L39-L46
• Add ref https://www.nature.com/articles/srep40031 for undefined allele L50
• Add note re: Alleva using allele N for Jeffreys Av:s:0053:M1S:A-A
• Add novel variants from thesis