Mast cell tryptases have proposed roles in allergic inflammation and host defense against infection. Tryptase gene loci TPSAB1 and TPSB2 are known to be polymorphic, but the nature and extent of diversity at these loci have not been fully explored.

We sought to compare functional and nonfunctional tryptase allele frequencies and establish haplotypes in human populations.

Tryptase allele frequencies were determined by means of direct sequencing in 270 individuals from HapMap populations of European, African, Chinese, and Japanese ancestry. Haplotypes were predicted, validated in parent-child trios, and compared between populations.

We identify a new frame-shifted tryptase allele (βIII^FS) carried by 23% and 19% of individuals of European and African ancestry but 0% of Asian subjects. Homology models predict that βIII^FS is functionless. Our genotyping assay shows that allele and haplotype distributions in each population are unique. Strong linkage disequilibrium between TPSAB1 and TPSB2 (r²=0.83, D′=0.85) yields 2 major and 5 minor tryptase haplotypes.

Tryptase deficiency alleles (⍺ and the newly discovered βIII^FS) are common, causing the number of inherited active genes to range from a minimum of 2 to a maximum of 4, with major differences between populations in the proportion of individuals inheriting 2 versus 4 active alleles. African and Asian populations are especially enriched in genes encoding functional and nonfunctional tryptases, respectively. Strong linkage of TPSAB1 and TPSB2 and pairing of deficiency alleles with functional alleles in observed haplotypes protect human subjects from “knockout” genomes and indeed from inheritance of fewer than 2 active alleles.