Cited by 610Genetic Associations and EpidemiologyGenetics and Physical PerformanceGrowth Hormone and Insulin-like Growth Factors

Rare and low-frequency coding variants alter human adult height

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Marouli, Eirini, Graff, Mariaelisa, Medina-Gomez, Carolina, Lo, Ken Sin, Wood, Andrew R., Kjaer, Troels R., Fine, Rebecca S., Lu, Yingchang +372 more·2017·Nature

Abstract

Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height-increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.

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  • Rare variants can have a continuum of risk, and a fraction of common variants have large effects, such as APOE in Alzheimer's disease.

    “This is not an invariant rule, as rare variants may have a continuum of risk (Marouli et al., 2017), and a fraction of common variants have large effects (e.g., APOE and Alzheimer’s disease).”

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Marouli, E., Graff, M., Medina-Gomez, C., Lo, K. S., Wood, A. R., Kjaer, T. R., Fine, R. S., Lu, Y., Schurmann, C., Highland, H. M., Rüeger, S., Thorleifsson, G., Justice, A. E., Lamparter, D., Stirrups, K. E., Turcot, V., Young, K. L., Winkler, T. W., Esko, T., Karaderi, T., Locke, A. E., Masca, N. G. D., Ng, M. C. Y., Mudgal, P., Rivas, M. A., Vedantam, S., Mahajan, A., Guo, X., Abecasis, G., Aben, K. K., Adair, L. S., Alam, D. S., Albrecht, E., Allin, K. H., Allison, M., Amouyel, P., Appel, E. V., Arveiler, D., Asselbergs, F. W., Auer, P. L., Balkau, B., Banas, B., Bang, L. E., Benn, M., Bergmann, S., Bielak, L. F., Blüher, M., Boeing, H., Boerwinkle, E., Böger, C. A., Bonnycastle, L. L., Bork-Jensen, J., Bots, M. L., Bottinger, E. P., Bowden, D. W., Brandslund, I., Breen, G., Brilliant, M. H., Broer, L., Burt, A. A., Butterworth, A. S., Carey, D. J., Caulfield, M. J., Chambers, J. C., Chasman, D. I., Chen, Y.-D. I., Chowdhury, R., Christensen, C., Chu, A. Y., Cocca, M., Collins, F. S., Cook, J. P., Corley, J., Galbany, J. C., Cox, A. J., Cuellar-Partida, G., Danesh, J., Davies, G., de Bakker, P. I. W., de Borst, G. J., de Denus, S., de Groot, M. C. H., de Mutsert, R., Deary, I. J., Dedoussis, G., Demerath, E. W., den Hollander, A. I., Dennis, J. G., Di Angelantonio, E., Drenos, F., Du, M., Dunning, A. M., Easton, D. F., Ebeling, T., Edwards, T. L., Ellinor, P. T., Elliott, P., Evangelou, E., Farmaki, A.-E., Faul, J. D., Feitosa, M. F., Feng, S., Ferrannini, E., Ferrario, M. M., Ferrieres, J., Florez, J. C., Ford, I., Fornage, M., Franks, P. W., Frikke-Schmidt, R., Galesloot, T. E., Gan, W., Gandin, I., Gasparini, P., Giedraitis, V., Giri, A., Girotto, G., Gordon, S. D., Gordon-Larsen, P., Gorski, M., Grarup, N., Grove, M. L., Gudnason, V., Gustafsson, S., Hansen, T., Harris, K. M., Harris, T. B., Hattersley, A. T., Hayward, C., He, L., Heid, I. M., Heikkilä, K., Helgeland, Ø., Hernesniemi, J., Hewitt, A. W., Hocking, L. J., Hollensted, M., Holmen, O. L., Hovingh, G. K., Howson, J. M. M., Hoyng, C. B., Huang, P. L., Hveem, K., Ikram, M. A., Ingelsson, E., Jackson, A. U., Jansson, J.-H., Jarvik, G. P., Jensen, G. B., Jhun, M. A., Jia, Y., Jiang, X., Johansson, S., Jørgensen, M. E., Jørgensen, T., Jousilahti, P., Jukema, J. W., Kahali, B., Kahn, R. S., Kähönen, M., Kamstrup, P. R., Kanoni, S., Kaprio, J., Karaleftheri, M., Kardia, S. L. R., Karpe, F., Kee, F., Keeman, R., Kiemeney, L. A., Kitajima, H., Kluivers, K. B., Kocher, T., Komulainen, P., Kontto, J., Kooner, J. S., Kooperberg, C., Kovacs, P., Kriebel, J., Kuivaniemi, H., Küry, S., Kuusisto, J., La Bianca, M., Laakso, M., Lakka, T. A., Lange, E. M., Lange, L. A., Langefeld, C. D., Langenberg, C., Larson, E. B., Lee, I.-T., Lehtimäki, T., Lewis, C. E., Li, H., Li, J., Li-Gao, R., Lin, H., Lin, L.-A., Lin, X., Lind, L., Lindström, J., Linneberg, A., Liu, Y., Liu, Y., Lophatananon, A., Luan, J., Lubitz, S. A., Lyytikäinen, L.-P., Mackey, D. A., Madden, P. A. F., Manning, A. K., Männistö, S., Marenne, G., Marten, J., Martin, N. G., Mazul, A. L., Meidtner, K., Metspalu, A., Mitchell, P., Mohlke, K. L., Mook-Kanamori, D. O., Morgan, A., Morris, A. D., Morris, A. P., Müller-Nurasyid, M., Munroe, P. B., Nalls, M. A., Nauck, M., Nelson, C. P., Neville, M., Nielsen, S. F., Nikus, K., Njølstad, P. R., Nordestgaard, B. G., Ntalla, I., O'Connel, J. R., Oksa, H., Loohuis, L. M. O., Ophoff, R. A., Owen, K. R., Packard, C. J., Padmanabhan, S., Palmer, C. N. A., Pasterkamp, G., Patel, A. P., Pattie, A., Pedersen, O., Peissig, P. L., Peloso, G. M., Pennell, C. E., Perola, M., Perry, J. A., Perry, J. R. B., Person, T. N., Pirie, A., Polasek, O., Posthuma, D., Raitakari, O. T., Rasheed, A., Rauramaa, R., Reilly, D. F., Reiner, A. P., Renström, F., Ridker, P. M., Rioux, J. D., Robertson, N., Robino, A., Rolandsson, O., Rudan, I., Ruth, K. S., Saleheen, D., Salomaa, V., Samani, N. J., Sandow, K., Sapkota, Y., Sattar, N., Schmidt, M. K., Schreiner, P. J., Schulze, M. B., Scott, R. A., Segura-Lepe, M. P., Shah, S., Sim, X., Sivapalaratnam, S., Small, K. S., Smith, A. V., Smith, J. A., Southam, L., Spector, T. D., Speliotes, E. K., Starr, J. M., Steinthorsdottir, V., Stringham, H. M., Stumvoll, M., Surendran, P., ‘t Hart, L. M., Tansey, K. E., Tardif, J.-C., Taylor, K. D., Teumer, A., Thompson, D. J., Thorsteinsdottir, U., Thuesen, B. H., Tönjes, A., Tromp, G., Trompet, S., Tsafantakis, E., Tuomilehto, J., Tybjaerg-Hansen, A., Tyrer, J. P., Uher, R., Uitterlinden, A. G., Ulivi, S., van der Laan, S. W., Van Der Leij, A. R., van Duijn, C. M., van Schoor, N. M., van Setten, J., Varbo, A., Varga, T. V., Varma, R., Edwards, D. R. V., Vermeulen, S. H., Vestergaard, H., Vitart, V., Vogt, T. F., Vozzi, D., Walker, M., Wang, F., Wang, C. A., Wang, S., Wang, Y., Wareham, N. J., Warren, H. R., Wessel, J., Willems, S. M., Wilson, J. G., Witte, D. R., Woods, M. O., Wu, Y., Yaghootkar, H., Yao, J., Yao, P., Yerges-Armstrong, L. M., Young, R., Zeggini, E., Zhan, X., Zhang, W., Zhao, J. H., Zhao, W., Zhao, W., Zheng, H., Zhou, W., The EPIC-InterAct Consortium, CHD Exome+ Consortium, ExomeBP Consortium, T2D-Genes Consortium, GoT2D Genes Consortium, Global Lipids Genetics Consortium, ReproGen Consortium, MAGIC Investigators, Rotter, J. I., Boehnke, M., Kathiresan, S., McCarthy, M. I., Willer, C. J., Stefansson, K., Borecki, I. B., Liu, D. J., North, K. E., Heard-Costa, N. L., Pers, T. H., Lindgren, C. M., Oxvig, C., Kutalik, Z., Rivadeneira, F., Loos, R. J. F., Frayling, T. M., Hirschhorn, J. N., Deloukas, P., & Lettre, G.
Affiliations
  • Queen Mary University of London (GB)
  • University of North Carolina at Chapel Hill (US)
  • Montreal Heart Institute (CA)
  • University of Exeter (GB)
  • Broad Institute (US)
  • Vanderbilt University (US)
  • Icahn School of Medicine at Mount Sinai (US)
  • SIB Swiss Institute of Bioinformatics (CH)
  • University of Regensburg (DE)
  • Centre for Human Genetics (GB)
  • Washington University in St. Louis (US)
  • University of Leicester (GB)
  • Wake Forest University Health Sciences (US)
  • Harbor–UCLA Medical Center (US)
  • Radboud University Medical Center (NL)
  • Helmholtz Munich (DE)
  • University of Copenhagen (DK)
  • University of California San Diego (US)
  • Inserm (FR)
  • Hôpitaux Universitaires de Strasbourg (FR)
  • University Medical Center Utrecht (NL)
  • University of Wisconsin–Milwaukee (US)
  • University Hospital Regensburg (DE)
  • Copenhagen University Hospital (DK)
  • University of Michigan (US)
  • IFB Adiposity Diseases (DE)
  • German Institute of Human Nutrition (DE)
  • Baylor College of Medicine (US)
  • National Institutes of Health (US)
  • University of Southern Denmark (DK)
  • King's College London (GB)
  • Marshfield Clinic Research Foundation (US)
  • Erasmus MC (NL)
  • University of Washington (US)
  • University of Cambridge (GB)
  • Imperial College Healthcare NHS Trust (GB)
  • Lillebaelt Hospital (DK)
  • Harvard University (US)
  • University of Trieste (IT)
  • University of Liverpool (GB)
  • University of Edinburgh (GB)
  • Griffith University (AU)
  • Harokopio University of Athens (GR)
  • University of Minnesota (US)
  • University of Bristol (GB)
  • Memorial Sloan Kettering Cancer Center (US)
  • Oulu University Hospital (FI)
  • MRC Centre for Environment and Health (GB)
  • University of Pisa (IT)
  • University of Glasgow (GB)
  • The University of Texas Health Science Center at Houston (US)
  • Uppsala University (SE)
  • QIMR Berghofer Medical Research Institute (AU)
  • University of Iceland (IS)
  • Institute of Genetics and Cancer (GB)
  • University of Helsinki (FI)
  • Haukeland University Hospital (NO)
  • Tampere University (FI)
  • Lions Eye Institute (AU)
  • University of Aberdeen (GB)
  • Norwegian University of Science and Technology (NO)
  • Amsterdam UMC Location University of Amsterdam (NL)
  • Massachusetts General Hospital (US)
  • Umeå University (SE)
  • Frederiksberg Hospital (DK)
  • University of Southern California (US)
  • Steno Diabetes Centers (DK)
  • Finnish Institute for Health and Welfare (FI)
  • Leiden University Medical Center (NL)
  • Herlev Hospital (DK)
  • University of Oxford (GB)
  • Queen's University Belfast (GB)
  • The Netherlands Cancer Institute (NL)
  • Universitätsmedizin Greifswald (DE)
  • Fred Hutch Cancer Center (US)
  • Stellenbosch University (ZA)
  • Centre Hospitalier Universitaire de Nantes (FR)
  • University of Eastern Finland (FI)
  • Atrium Health Wake Forest Baptist (US)
  • Kaiser Permanente Washington Health Research Institute (US)
  • Taichung Veterans General Hospital (TW)
  • University of Alabama at Birmingham (US)
  • Chinese Academy of Sciences (CN)
  • Stanford Medicine (US)
  • Boston University (US)
  • University of Warwick (GB)
  • Wellcome Sanger Institute (GB)
  • German Center for Diabetes Research (DE)
  • University of Tartu (EE)
  • The University of Sydney (AU)
  • Tampere University Hospital (FI)
  • University of California, Los Angeles (US)
  • Ninewells Hospital (GB)
  • The University of Western Australia (AU)
  • University of Maryland, Baltimore (US)
  • University of Turku (FI)
  • Center for Non-Communicable Diseases (PK)
  • Kuopio University Hospital (FI)
  • Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
  • Lund University (SE)
  • Brigham and Women's Hospital (US)
  • IRCCS Materno Infantile Burlo Garofolo (IT)
  • Imperial College London (GB)
  • Duke University (US)
  • National University of Singapore (SG)
  • Alzheimer Scotland (GB)
  • Capital Region of Denmark (DK)
  • Leipzig University (DE)
  • Universität für Weiterbildung Krems (AT)
  • Dalhousie University (CA)
  • Sidra Medical and Research Center (QA)
  • Newcastle University (GB)
  • Indiana University (US)
  • University of Mississippi Medical Center (US)
  • Aarhus University (DK)
  • Memorial University of Newfoundland (CA)
  • The University of Texas Southwestern Medical Center (US)
  • Ealing Hospital (GB)
  • deCODE Genetics (Iceland) (IS)
  • Pennsylvania State University (US)
  • Statens Serum Institut (DK)
Corresponding author
  • Hirschhorn, Joel N.
  • Deloukas, Panos
  • Lettre, Guillaume
ORCID
Venue
Nature
Published
2017-02-01
Volume
542
Issue
7640
Pages
186-190
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W2584469054
Cited by
610
References
51
Citations by year
2026: 22 · 2025: 29 · 2024: 34 · 2023: 45 · 2022: 54 · 2021: 57 · 2020: 120 · 2019: 105 · 2018: 85 · 2017: 56 · 2016: 1
FWCI
66.44
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • University of Southern Denmark Research Portal (University of Southern Denmark) (publishedVersion, other-oa)
  • PubMed (publishedVersion)
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  • PubMed Central (acceptedVersion)
  • ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
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Funders
  • Doris Duke Charitable Foundation (2014105)
  • University of Southern California
  • Harvard University
  • Helsingin Yliopisto
  • University of Washington
  • European Hematology Association (TRTH136)
  • Norges Teknisk-Naturvitenskapelige Universitet
  • Wellcome Trust (068545/Z/02), 202802/Z/16/Z, 098395/Z/12/Z)
  • United Kingdom Clinical Research Collaboration
  • University of Texas Health Science Center at Houston
  • Steno Diabetes Center Copenhagen (SDCC 3.A Complications)
  • Sidra Medicine
  • National Institute for Health and Care Research (NF-SI-0512-10165, ACF-2016-19-005, NF-SI-0611-10136, NF-SI-0512-10113, NF-SI-0611-10099, NF-SI-0611-10219, NF-SI-0616-10080)
  • British Heart Foundation (SP/13/2/30111, RG/08/014/24067, RG/14/5/30893)
  • University of Exeter
  • Imperial College London
  • University College London
  • University of Oxford
  • University of Glasgow
  • University of Aberdeen
  • Menzies Research Institute Tasmania
  • University of Tasmania
  • Universiteit Leiden
  • Aalborg Universitet
  • Gentofte Hospital
  • Erasmus Medisch Centrum
  • Lunds Universitet
  • Lundbeckfonden (R190 2014-3904, R16-2007-1691)
  • Tampereen Yliopisto
  • Université de Toulouse
  • Umeå Universitet (901 87)
  • Universitetet i Bergen
  • Leids Universitair Medisch Centrum
  • Rigshospitalet
  • Region Hovedstaden
  • Università degli Studi dell'Insubria
  • Háskóli Íslands
  • Syddansk Universitet
  • Uppsala Universitet
  • Università di Pisa
  • Science for Life Laboratory
  • Novo Nordisk Fonden (NNF14OC0010497, NNF16OC0021496)
  • Haukeland Universitetssjukehus
  • Tays
  • Hjartavernd
  • Menzies Institute for Medical Research
  • Terveyden ja hyvinvoinnin laitos
  • National Institutes of Health (1s10od018522-01, UL1TR000124, KL2TR001109, n01hc95159-40-0-1, UL1TR001881)
  • School of Medicine, Stanford University
  • University of California, Los Angeles
  • University of North Carolina at Chapel Hill
  • Social Science Research Institute, Duke University
  • Medical Research Council (MR/K006584/1, MR/M501633/2, MR/L01341X/1, MR/L003120/1, MR/K002414/1, MR/L01632X/1, MR/K026992/1, MC_PC_13040, MC_UU_12015/2, MR/M501633/1, MC_PC_15018, MC_UU_12015/1, MR/K007017/1)
  • Biotechnology and Biological Sciences Research Council (BB/F019394/1)
  • Helse Sør-Øst RHF
  • Helmholtz Zentrum München
  • NIHR Oxford Biomedical Research Centre
  • Netherlands Heart Institute
  • National Heart, Lung, and Blood Institute (R01HL127564, HHSN268201300046C, N01-HC-095159, R01HL119443, R35HL135824, HHSN268201100046C, K99HL130580, K23HL114724, R01HL117078, T32HL007055)
  • National Institute of Mental Health (R01MH090553)
  • National Human Genome Research Institute (U01HG008657, U01HG007417)
  • National Eye Institute (R01EY022310)
  • National Cancer Institute (UM1CA182913, P30CA008748)
  • National Institute of General Medical Sciences (T32GM096911)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R01DK072193, R01DK089256, U01DK062370, DP3DK108220, R01DK107904, R01DK106621, R01DK075787, P30DK020572, R01DK093757, P30DK063491)
  • National Center for Advancing Translational Sciences
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD057194, P2CHD050924)
  • Carolina Population Center, University of North Carolina at Chapel Hill
  • Institute of Genetics
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Physical Performance
  • Health Sciences › Medicine › Endocrinology, Diabetes and Metabolism › Growth Hormone and Insulin-like Growth Factors
Keywords
adult height, rare coding variants, low-frequency variants, polygenic traits, STC2, PAPP-A, IGFBP-4, insulin-like growth factor, Ihh, AR, CRISPLD2, ADAMTS3, NOX4, proteoglycan synthesis, glycosaminoglycan synthesis
MeSH terms
ADAMTS Proteins, NADPH Oxidase 4, Adult, Alleles, Body Height, Female, Gene Frequency, Glycoproteins, Glycosaminoglycans, Humans, Male, Phenotype, Pregnancy-Associated Plasma Protein-A, Procollagen N-Endopeptidase, Proteoglycans, Receptors, Androgen, Somatomedins, Genetic Variation, Cell Adhesion Molecules, Genome, Human, NADPH Oxidases, Multifactorial Inheritance, Intercellular Signaling Peptides and Proteins, Interferon Regulatory Factors, Interleukin-11 Receptor alpha Subunit, Hedgehog Proteins, Proteolysis

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