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Evidence for natural selection in the HAVCR1 gene: high degree of amino-acid variability in the mucin domain of human HAVCR1 protein

Genes & Immunity volume 6, pages 398–406 (2005)Cite this article

Abstract

The family of genes encoding T-cell immunoglobulin and mucin-domain containing proteins (Tim), which are cell-surface molecules expressed in CD4+ T helper cells, has important roles in the immune system. Here, we report three unusual patterns of genetic variation in the human hepatitis A virus cellular receptor 1 gene (HAVCR1) that are similar to patterns observed in major histocompatibility complex loci. First, levels of polymorphism in exon 4 of HAVCR1 were exceptionally high in humans (nucleotide diversity (π)=45.45 × 10−4). Second, nonsynonymous substitutions and insertion/deletion variants were more frequent than synonymous substitutions in that exon (10 out of 12 variants). The rate of the mean number of nucleotide substitutions at nonsynonymous sites to synonymous sites at HAVCR1-exon 4 is >1 (PA/PS=1.92 and πA/πS=2.23). Third, levels of divergence among human, chimp, and gorilla sequences were unusually high in HAVCR1-exon 4 sequences. These features suggest that patterns of variation in HAVCR1 have been shaped by both positive and balancing natural selection in the course of primate evolution. Evidence that the effects of natural selection are largely restricted to the mucin domain of HAVCR1 suggests that this region may be of particular evolutionary and epidemiological interest.

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Acknowledgements

We thank Yoshiko Miwa for technical assistance. This work was supported by a Future Program Grant of The Japan Society for the Promotion of Science (II, ME); by a grant from the Japanese Ministry of Public Health and Welfare for Research on the Human Genome; by a Grant-in-Aid for Scientific Research on Medical Genome Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan; and by NIH Grants GM 59290 and HL070048.

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Authors and Affiliations

  1. Division of Genetic Diagnosis, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan

    T Nakajima, N Jinnai, S Goto & I Inoue

  2. Department of Molecular Biology, Institute of Gerontology, Nippon Medical School, Kawasaki, Japan

    T Nakajima & M Emi

  3. Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT, USA

    S Wooding & L B Jorde

  4. Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, Japan

    Y Satta

  5. Kumamoto Primates Park, Sanwa Kagaku Kenkyusho Co. Ltd, Kumamoto, Japan

    I Hayasaka

  6. Division of Population Genetics, National Institute of Genetics, Mishima, Japan

    N Saitou

  7. Red Cross Blood Center of Harbin, Harbin, China

    J Guan-jun

  8. Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan

    K Tokunaga

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  1. T Nakajima
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Correspondence to T Nakajima.

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Nakajima, T., Wooding, S., Satta, Y. et al. Evidence for natural selection in the HAVCR1 gene: high degree of amino-acid variability in the mucin domain of human HAVCR1 protein. Genes Immun 6, 398–406 (2005). https://doi.org/10.1038/sj.gene.6364215

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