Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk


The identification of common variants that contribute to the genesis of human inherited disorders remains a significant challenge. Hirschsprung disease (HSCR) is a multifactorial, non-mendelian disorder in which rare high-penetrance coding sequence mutations in the receptor tyrosine kinase RET contribute to risk in combination with mutations at other genes. We have used family-based association studies to identify a disease interval, and integrated this with comparative and functional genomic analysis to prioritize conserved and functional elements within which mutations can be sought. We now show that a common non-coding RET variant within a conserved enhancer-like sequence in intron 1 is significantly associated with HSCR susceptibility and makes a 20-fold greater contribution to risk than rare alleles do. This mutation reduces in vitro enhancer activity markedly, has low penetrance, has different genetic effects in males and females, and explains several features of the complex inheritance pattern of HSCR. Thus, common low-penetrance variants, identified by association studies, can underlie both common and rare diseases.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Transmission disequilibrium tests.
Figure 2: Identification and characterization of conserved sequence elements within 350 kb encompassing RET.
Figure 3: Identification and functional characterization of RET MCS + 9.7.
Figure 4: Worldwide allele frequencies of RET + 3.

Similar content being viewed by others


  1. Bolk, S. et al. A human model for multigenic inheritance: phenotypic expression in Hirschsprung disease requires both the RET gene and a new 9q31 locus. Proc. Natl Acad. Sci. USA 97, 268–273 (2000)

    Article  ADS  CAS  Google Scholar 

  2. Gabriel, S. B. et al. Segregation at three loci explains familial and population risk in Hirschsprung disease. Nature Genet. 31, 89–93 (2002)

    Article  CAS  Google Scholar 

  3. Chakravarti, A. & Lyonnet, S. in The Metabolic and Molecular Bases of Inherited Disease 8th edn (eds Scriver, C. R., Beaudet, A. R., Sly, W. & Valle, D.) Ch. 251, 6231–6255 (McGraw-Hill, New York, 2001)

    Google Scholar 

  4. Carrasquillo, M. M. et al. Genome-wide association study and mouse model identify interaction between RET and EDNRB pathways in Hirschsprung disease. Nature Genet. 32, 237–244 (2002)

    Article  CAS  Google Scholar 

  5. Borrego, S. et al. RET genotypes comprising specific haplotypes of polymorphic variants predispose to isolated Hirschsprung disease. J. Med. Genet. 37, 572–578 (2000)

    Article  CAS  Google Scholar 

  6. Garcia-Barcelo, M. M. et al. Chinese patients with sporadic Hirschsprung's disease are predominantly represented by a single RET haplotype. J. Med. Genet. 40, e122 (2003)

    Article  Google Scholar 

  7. Sancandi, M. et al. Single nucleotide polymorphic alleles in the 5′ region of the RET proto-oncogene define a risk haplotype in Hirschsprung's disease. J. Med. Genet. 40, 714–718 (2003)

    Article  CAS  Google Scholar 

  8. McCallion, A. S. et al. Genomic variation in multigenic traits: Hirschsprung disease. Cold Spring Harb. Symp. Quant. Biol. 68, 373–381 (2003)

    Article  CAS  Google Scholar 

  9. Uyama, T. et al. Molecular cloning and expression of a second chondroitin N-acetylgalactosaminyltransferase involved in the initiation and elongation of chondroitin/dermatan sulfate. J. Biol. Chem. 278, 3072–3078 (2003)

    Article  CAS  Google Scholar 

  10. Sato, T. et al. Molecular cloning and characterization of a novel human β1,4-N-acetylgalactosaminyltransferase, β4GalNAc-T3, responsible for the synthesis of N,N′-diacetyllactosediamine, galNAc β1-4GlcNAc. J. Biol. Chem. 278, 47534–47544 (2003)

    Article  CAS  Google Scholar 

  11. Spielman, R. S., McGinnis, R. E. & Ewens, W. J. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52, 506–516 (1993)

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Lin, S., Chakravarti, A. & Cutler, D. J. Haplotype and missing data inference in nuclear families. Genome Res. 14, 1624–1632 (2004)

    Article  CAS  Google Scholar 

  13. Lin, S., Chakravarti, A. & Cutler, D. J. Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. Nature Genet. 36, 1181–1188 (2004)

    Article  CAS  Google Scholar 

  14. Loots, G. G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136–140 (2000)

    Article  ADS  CAS  Google Scholar 

  15. Thomas, J. W. et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788–793 (2003)

    Article  ADS  CAS  Google Scholar 

  16. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003)

    Article  ADS  CAS  Google Scholar 

  17. Nobrega, M. & Pennacchio, L. A. Comparative genomic analysis as a tool for biological discovery. J. Physiol. 554, 31–39 (2003)

    Article  Google Scholar 

  18. Bray, N., Dubchak, I. & Pachter, L. AVID: A global alignment program. Genome Res. 13, 97–102 (2003)

    Article  CAS  Google Scholar 

  19. Margulies, E. H., Blanchette, M., Haussler, D. & Green, E. D. Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507–2518 (2003)

    Article  CAS  Google Scholar 

  20. Shepherd, I. T., Pietsch, J., Elworthy, S., Kelsh, R. N. & Raible, D. W. Roles for GFRalpha1 receptors in zebrafish enteric nervous system development. Development 131, 241–249 (2004)

    Article  CAS  Google Scholar 

  21. Shepherd, I. T., Beattie, C. E. & Raible, D. W. Functional analysis of zebrafish GDNF. Dev. Biol. 231, 420–435 (2001)

    Article  CAS  Google Scholar 

  22. Rivas, E. & Eddy, S. R. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2, 8 (2001)

    Article  CAS  Google Scholar 

  23. Shoba, T., Dheen, S. T. & Tay, S. S. Retinoic acid influences the expression of the neuronal regulatory genes Mash-1 and c-ret in the developing rat heart. Neurosci. Lett. 318, 129–132 (2002)

    Article  CAS  Google Scholar 

  24. Batourina, E. et al. Vitamin A controls epithelial/mesenchymal interactions through Ret expression. Nature Genet. 27, 74–78 (2001)

    Article  CAS  Google Scholar 

  25. Pitera, J. E., Smith, V. V., Woolf, A. S. & Milla, P. J. Embryonic gut anomalies in a mouse model of retinoic Acid-induced caudal regression syndrome: delayed gut looping, rudimentary cecum, and anorectal anomalies. Am. J. Pathol. 159, 2321–2329 (2001)

    Article  CAS  Google Scholar 

  26. ENCODE Project Consortium . The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636–640 (2004)

    Article  ADS  Google Scholar 

  27. Haldane, J. B. S. The rate of mutation of human genes. Hereditas 35 (suppl.), 267–273 (1948)

    MathSciNet  Google Scholar 

  28. Allison, A. C. G-6-PD deficiency in red blood cells of East Africans. Nature 186, 531–532 (1960)

    Article  ADS  CAS  Google Scholar 

  29. Allison, A. C. & Clyde, D. F. Malaria in African children with deficient erythrocyte glucose-6-phosphate dehydrogenase. Br. Med. J. 5236, 1346–1349 (1961)

    Article  Google Scholar 

  30. Motulsky, A. Metabolic polymorphisms and the role of infectious disease in human evolution. Hum. Biol. 32, 28–62 (1960)

    CAS  PubMed  Google Scholar 

  31. Hill, A. V. et al. Common west African HLA antigens are associated with protection from severe malaria. Nature 352, 595–600 (1991)

    Article  ADS  CAS  Google Scholar 

  32. Miller, L. H., Mason, S. J., Clyde, D. F. & McGinniss, M. H. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N. Engl. J. Med. 295, 302–304 (1976)

    Article  CAS  Google Scholar 

  33. Samson, M. et al. Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722–725 (1996)

    Article  ADS  CAS  Google Scholar 

  34. Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273, 1856–1862 (1996)

    Article  ADS  CAS  Google Scholar 

  35. Huang, Y. et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nature Med. 2, 1240–1243 (1996)

    Article  CAS  Google Scholar 

  36. Collins, F. S. et al. New goals for the U.S. Human Genome Project: 1998–2003. Science 282, 682–689 (1998)

    Article  ADS  CAS  Google Scholar 

  37. Lander, E. S. The new genomics: global views of biology. Science 274, 536–539 (1996)

    Article  ADS  CAS  Google Scholar 

  38. Falconer, D. S. The inheritance of liability to diseases with variable age of onset, with particular reference to diabetes mellitus. Ann. Hum. Genet. 31, 1–20 (1967)

    Article  CAS  Google Scholar 

  39. Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)

    Article  ADS  CAS  Google Scholar 

  40. Cann, H. M. et al. A human genome diversity cell line panel. Science 296, 261–262 (2002)

    Article  CAS  Google Scholar 

  41. Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978–989 (2001)

    Article  CAS  Google Scholar 

  42. Cutler, D. J. et al. High-throughput variation detection and genotyping using microarrays. Genome Res. 11, 1913–1925 (2001)

    Article  CAS  Google Scholar 

Download references


We thank members of the Chakravarti laboratory for their discussions on this manuscript, M. Kenton for assistance with family recruitment, and E. Margulies and M. Blanchette for help with multi-species sequence analysis. We thank the NISC Comparative Sequencing Program for generating the multi-species sequence data. We also acknowledge the many participants of the NISC Comparative Sequencing Program, especially the leadership provided by G. Bouffard and B. Blakesley. We also acknowledge the many participants of the NISC Comparative Sequencing Program, especially the leadership provided by G. Bouffard and B. Blakesley. This work was supported by grants from the US National Institute of Child Health and Development.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Aravinda Chakravarti.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Table S1

Positions of all identified MCSs. Nucleotide positions are given on human chromosome 10 relative to build 34 (July 2003) of the genome. (XLS 22 kb)

Supplementary Table S2

Predicted transcription factor binding sites in MCS+9.7. TRANSFAC predictions of putative transcription factor binding sites given with reference to build 34 of the human genome. (XLS 28 kb)

Supplementary Table S3

Haplotype frequencies in Africa, Asia, Europe and HSCR cases. PHASE was used to reconstruct haplotypes in the 5′ region of RET. (XLS 20 kb)

Supplementary Figure S1

Multi-species alignment showing the position of RET+3 within the context of MCS+9.7. (PDF 20 kb)

Supplementary Methods

Additional methodological details are provided in this file. (DOC 44 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Emison, E., McCallion, A., Kashuk, C. et al. A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk. Nature 434, 857–863 (2005).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing