Low bone mineral density (BMD) is used as a parameter of osteoporosis. Genome-wide association studies of BMD have hitherto focused on BMD as a quantitative trait, yielding common variants of small effects that contribute to the population diversity in BMD1,2,3,4,5,6,7. Here we use BMD as a dichotomous trait, searching for variants that may have a direct effect on the risk of pathologically low BMD rather than on the regulation of BMD in the healthy population. Through whole-genome sequencing of Icelandic individuals, we found a rare nonsense mutation within the leucine-rich-repeat-containing G-protein-coupled receptor 4 (LGR4) gene (c.376C>T) that is strongly associated with low BMD, and with osteoporotic fractures. This mutation leads to termination of LGR4 at position 126 and fully disrupts its function. The c.376C>T mutation is also associated with electrolyte imbalance, late onset of menarche and reduced testosterone levels, as well as an increased risk of squamous cell carcinoma of the skin and biliary tract cancer. Interestingly, the phenotype of carriers of the c.376C>T mutation overlaps that of Lgr4 mutant mice.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    et al. Multiple genetic loci for bone mineral density and fractures. N. Engl. J. Med. 358, 2355–2365 (2008)

  2. 2.

    et al. Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. Lancet 371, 1505–1512 (2008)

  3. 3.

    et al. New sequence variants associated with bone mineral density. Nature Genet. 41, 15–17 (2009)

  4. 4.

    et al. Association of JAG1 with bone mineral density and osteoporotic fractures: a genome-wide association study and follow-up replication studies. Am. J. Hum. Genet. 86, 229–239 (2010)

  5. 5.

    et al. Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. PLoS Genet. 7, e1001372 (2011)

  6. 6.

    et al. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nature Genet. 41, 1199–1206 (2009)

  7. 7.

    et al. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nature Genet. 44, 491 (2012)

  8. 8.

    et al. A reference standard for the description of osteoporosis. Bone 42, 467–475 (2008)

  9. 9.

    , , , & R-spondins function as ligands of the orphan receptors LGR4 and LGR5 to regulate Wnt/β-catenin signaling. Proc. Natl Acad. Sci. USA 108, 11452–11457 (2011)

  10. 10.

    et al. Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature 476, 293–297 (2011)

  11. 11.

    et al. LGR4 and LGR5 are R-spondin receptors mediating Wnt/β-catenin and Wnt/PCP signalling. EMBO Rep. 12, 1055–1061 (2012)

  12. 12.

    & Cellular signaling and biological functions of R-spondins. Cell. Signal. 24, 369–377 (2012)

  13. 13.

    & Genetics of osteoporosis. Endocr. Rev. 31, 629–662 (2010)

  14. 14.

    , & Genetics of osteoporosis from genome-wide association studies: advances and challenges. Nature Rev. Genet. 13, 576–588 (2012)

  15. 15.

    Building strong bones: molecular regulation of the osteoblast lineage. Nature Rev. Mol. Cell Biol. 13, 27 (2012)

  16. 16.

    et al. Regulation of bone formation and remodeling by G-protein-coupled receptor 48. Development 136, 2747–2756 (2009)

  17. 17.

    et al. Gene inactivation and its implications for annotation in the era of personal genomics. Genes Dev. 25, 1–10 (2011)

  18. 18.

    NHLBI. Exome Sequencing Project. Exome Variant Server v.0.0.17 (NHLBI, Seattle, Washington, 2012)

  19. 19.

    et al. Links between cardiovascular disease and osteoporosis in postmenopausal women: serum lipids or atherosclerosis per se? Osteoporos. Int. 18, 505–512 (2007)

  20. 20.

    , & Sources of variability in bone mineral density measurements: implications for study design and analysis of bone loss. J. Bone Miner. Res. 12, 124–135 (1997)

  21. 21.

    et al. Defective postnatal development of the male reproductive tract in LGR4 knockout mice. Dev. Biol. 290, 421–434 (2006)

  22. 22.

    et al. Leucine-rich repeat-containing G protein-coupled receptor-4 (LGR4, Gpr48) is essential for renal development in mice. Nephron, Exp. Nephrol. 104, e63–e75 (2006)

  23. 23.

    et al. Defective development of the gall bladder and cystic duct in Lgr4- hypomorphic mice. Dev. Dyn. 238, 993–1000 (2009)

  24. 24.

    , , , & Conditional knockout of Lgr4 leads to impaired ductal elongation and branching morphogenesis in mouse mammary glands. Sex Dev. 5, 205–212 (2011)

  25. 25.

    et al. GPR48 increases mineralocorticoid receptor gene expression. J. Am. Soc. Nephrol. 23, 281–293 (2012)

  26. 26.

    et al. Leucine-rich repeat-containing, G protein-coupled receptor 4 null mice exhibit intrauterine growth retardation associated with embryonic and perinatal lethality. Mol. Endocrinol. 18, 2241–2254 (2004)

  27. 27.

    et al. GPR48 regulates epithelial cell proliferation and migration by activating EGFR during eyelid development. Invest. Ophthalmol. Vis. Sci. 49, 4245–4253 (2008)

  28. 28.

    et al. Deletion of G protein-coupled receptor 48 leads to ocular anterior segment dysgenesis (ASD) through down-regulation of Pitx2. Proc. Natl Acad. Sci. USA 105, 6081–6086 (2008)

  29. 29.

    et al. R-spondin1 is essential in sex determination, skin differentiation and malignancy. Nature Genet. 38, 1304 (2006)

Download references


We thank the subjects of the Icelandic deCODE study, the Danish PERF study and the Australian DOES study for their participation. We also thank the staff at deCODE Genetics core facilities and all our colleagues for their important contribution to this work. The authors would like to thank the NHLBI GO Exome Sequencing Project and its continuing studies, which produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923); the WHI Sequencing Project (HL-102924); the Broad GO Sequencing Project (HL-102925); the Seattle GO Sequencing Project (HL-102926); and the Heart GO Sequencing Project (HL-103010). This work was supported in part by the European Commission (HEALTH-F2-2008-201865-GEFOS).

Author information


  1. deCODE Genetics/Amgen, 101 Reykjavik, Iceland

    • Unnur Styrkarsdottir
    • , Gudmar Thorleifsson
    • , Patrick Sulem
    • , Daniel F. Gudbjartsson
    • , Asgeir Sigurdsson
    • , Aslaug Jonasdottir
    • , Adalbjorg Jonasdottir
    • , Asmundur Oddsson
    • , Agnar Helgason
    • , Olafur T. Magnusson
    • , G. Bragi Walters
    • , Michael L. Frigge
    • , Hafdis T. Helgadottir
    • , Hrefna Johannsdottir
    • , Thorunn Rafnar
    • , Augustine Kong
    • , Gisli Masson
    • , Unnur Thorsteinsdottir
    •  & Kari Stefansson
  2. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden

    • Asmundur Oddsson
  3. Department of Biochemistry and Molecular Biology, University of Iceland, Biomedical Center, Faculty of Medicine, 101 Reykjavik, Iceland

    • Kristin Bergsteinsdottir
    • , Margret H. Ogmundsdottir
    •  & Erikur Steingrimsson
  4. Garvan Institute of Medical Research, 2010 Sydney, Australia

    • Jacqueline R. Center
    • , Tuan V. Nguyen
    •  & John A. Eisman
  5. St Vincent’s Hospital, 2010 Sydney, Australia

    • Jacqueline R. Center
    •  & John A. Eisman
  6. University of New South Wales (UNSW), 2010 Sydney, Australia

    • Jacqueline R. Center
    • , Tuan V. Nguyen
    •  & John A. Eisman
  7. University of Notre Dame Australia (UNDA), 2010 Sydney, Australia

    • John A. Eisman
  8. Center for Clinical and Basic Research (CCBR), 2750 Ballerup, Denmark

    • Claus Christiansen
  9. Department of Pathology, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland

    • Jon G. Jonasson
  10. Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland

    • Jon G. Jonasson
    • , Laufey Tryggvadottir
    • , Thorvaldur Jonsson
    • , Gunnar Sigurdsson
    • , Unnur Thorsteinsdottir
    •  & Kari Stefansson
  11. Icelandic Cancer Registry, 105 Reykjavik, Iceland

    • Jon G. Jonasson
    •  & Laufey Tryggvadottir
  12. Laboratory in Mjodd (RAM), Icelandic Medical Center (Laeknasetrid), 109 Reykjavik, Iceland

    • Gudmundur I. Eyjolfsson
  13. Department of Gastroenterology, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland

    • Asgeir Theodors
  14. Department of Surgery, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland

    • Thorvaldur Jonsson
  15. Department of Orthopedic Surgery, Akureyri Hospital, 600 Akureyri, Iceland

    • Thorvaldur Ingvarsson
  16. Institution of Health Science, University of Akureyri, 600 Akureyri, Iceland

    • Thorvaldur Ingvarsson
  17. Department of Clinical Biochemistry, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland

    • Isleifur Olafsson
  18. Department of Endocrinology and Metabolism, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland

    • Gunnar Sigurdsson


  1. Search for Unnur Styrkarsdottir in:

  2. Search for Gudmar Thorleifsson in:

  3. Search for Patrick Sulem in:

  4. Search for Daniel F. Gudbjartsson in:

  5. Search for Asgeir Sigurdsson in:

  6. Search for Aslaug Jonasdottir in:

  7. Search for Adalbjorg Jonasdottir in:

  8. Search for Asmundur Oddsson in:

  9. Search for Agnar Helgason in:

  10. Search for Olafur T. Magnusson in:

  11. Search for G. Bragi Walters in:

  12. Search for Michael L. Frigge in:

  13. Search for Hafdis T. Helgadottir in:

  14. Search for Hrefna Johannsdottir in:

  15. Search for Kristin Bergsteinsdottir in:

  16. Search for Margret H. Ogmundsdottir in:

  17. Search for Jacqueline R. Center in:

  18. Search for Tuan V. Nguyen in:

  19. Search for John A. Eisman in:

  20. Search for Claus Christiansen in:

  21. Search for Erikur Steingrimsson in:

  22. Search for Jon G. Jonasson in:

  23. Search for Laufey Tryggvadottir in:

  24. Search for Gudmundur I. Eyjolfsson in:

  25. Search for Asgeir Theodors in:

  26. Search for Thorvaldur Jonsson in:

  27. Search for Thorvaldur Ingvarsson in:

  28. Search for Isleifur Olafsson in:

  29. Search for Thorunn Rafnar in:

  30. Search for Augustine Kong in:

  31. Search for Gunnar Sigurdsson in:

  32. Search for Gisli Masson in:

  33. Search for Unnur Thorsteinsdottir in:

  34. Search for Kari Stefansson in:


The study was designed and results were interpreted by U.S., G.T., D.F.G., P.S., A.K., U.T. and K.S. Sequence data analysis, imputation and association analysis was carried out by G.T., P.S., D.F.G., O.T.M., M.L.F., A.K. and G.M. Subject recruitment, phenotype analysis and biological material collection was organized and carried out by G.B.W., J.R.C., T.V.N., J.A.E., C.C., J.G.J., L.T., G.I.E., A.T., T.J., T.I., I.O., T.R. and G.S. Sequencing and genotyping were supervised by O.T.M. and U.T. Sanger sequencing and Centaurus genotyping was carried out and analysed by H.T.H. and H.J. Expression experiments were carried out and analysed by G.T., A.S., Aslaug J., Adalbjorg J., K.B., M.H.O. and E.S. Multiple alignment and topology analysis of LGR4 was performed by A.O. The age of the LGR4 mutation in the population gene pool was estimated by A.H. The paper was drafted by U.S., G.T., U.T. and K.S. All authors contributed to the final version of the paper.

Competing interests

U.S., G.T., P.S., A.S., Aslaug J., Adalbjorg J., A.O., D.F.G., A.H., O.T.M., G.B.W., M.L.F., H.T.H., H.J., T.R., A.K., G.M., U.T. and K.S. are employees of deCODE Genetics/Amgen.

Corresponding authors

Correspondence to Unnur Thorsteinsdottir or Kari Stefansson.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Text and Data, Supplementary Tables 1-7, Supplementary Figures 1-6 and Supplementary References.

About this article

Publication history






Further reading


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.

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