Rare coding variants and X-linked loci associated with age at menarche.

Kathryn L Lunetta, Felix R Day, Patrick Sulem, Katherine S Ruth, Joyce Y Tung, David A Hinds, Tõnu Esko, Cathy E Elks, Elisabeth Altmaier, Chunyan He, Jennifer E Huffman, Evelin Mihailov, Eleonora Porcu, Antonietta Robino, Lynda M Rose, Ursula M Schick, Lisette Stolk, Alexander Teumer, Deborah J Thompson, Michela Traglia, Carol A Wang, Laura M Yerges-Armstrong, Antonis C Antoniou, Caterina Barbieri, Andrea D Coviello, Francesco Cucca, Ellen W Demerath, Alison M Dunning, Ilaria Gandin, Megan L Grove, Daniel F Gudbjartsson, Lynne J Hocking, Albert Hofman, Jinyan Huang, Rebecca D Jackson, David Karasik, Jennifer Kriebel, Ethan M Lange, Leslie A Lange, Claudia Langenberg, Xin Li, Jian'an Luan, Reedik Mägi, Alanna C Morrison, Sandosh Padmanabhan, Ailith Pirie, Ozren Polasek, David Porteous, Alex P Reiner, Fernando Rivadeneira, Igor Rudan, Cinzia F Sala, David Schlessinger, Robert A Scott, Doris Stöckl, Jenny A Visser, Uwe Völker, Diego Vozzi, James G Wilson, Marek Zygmunt, Eric Boerwinkle, Julie E Buring, Laura Crisponi, Douglas F Easton, Caroline Hayward, Frank B Hu, Simin Liu, Andres Metspalu, Craig E Pennell, Paul M Ridker, Konstantin Strauch, Elizabeth A Streeten, Daniela Toniolo, André G Uitterlinden, Sheila Ulivi, Henry Völzke, Nicholas J Wareham, Melissa Wellons, Nora Franceschini, Daniel I Chasman, Unnur Thorsteinsdottir, Anna Murray, Kari Stefansson, Joanne M Murabito, Ken K Ong, John R B Perry

Journal: Nature communications 2016;6():7756

PMID: 26239645

Abstract

More than 100 loci have been identified for age at menarche by genome-wide association studies; however, collectively these explain only ∼3% of the trait variance. Here we test two overlooked sources of variation in 192,974 European ancestry women: low-frequency protein-coding variants and X-chromosome variants. Five missense/nonsense variants (in ALMS1/LAMB2/TNRC6A/TACR3/PRKAG1) are associated with age at menarche (minor allele frequencies 0.08-4.6%; effect sizes 0.08-1.25 years per allele; P<5 × 10(-8)). In addition, we identify common X-chromosome loci at IGSF1 (rs762080, P=9.4 × 10(-13)) and FAAH2 (rs5914101, P=4.9 × 10(-10)). Highlighted genes implicate cellular energy homeostasis, post-transcriptional gene silencing and fatty-acid amide signalling. A frequently reported mutation in TACR3 for idiopathic hypogonatrophic hypogonadism (p.W275X) is associated with 1.25-year-later menarche (P=2.8 × 10(-11)), illustrating the utility of population studies to estimate the penetrance of reportedly pathogenic mutations. Collectively, these novel variants explain ∼0.5% variance, indicating that these overlooked sources of variation do not substantially explain the 'missing heritability' of this complex trait.

Address: 1] Boston University School of Public Health, Department of Biostatistics, Boston, Massachusetts 02118, USA [2] NHLBI's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA.; MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.; deCODE genetics/Amgen, Inc., Reykjavik IS-101, Iceland.; Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK.; 23andMe Inc., 1390 Shorebird Way, Mountain View, California 94043, USA.; 1] Estonian Genome Center, University of Tartu, Tartu 51010, Estonia [2] Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA [3] Department of Genetics, Harvard Medical School, Boston, MA 02115, USA [4] Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140, Cambridge, MA 02142, USA.; 1] Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany [2] Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany.; 1] Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN 46202, USA [2] Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA.; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.; Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.; 1] Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy [2] University of Sassari, Department of Biomedical Sciences, Sassari, Sassari 07100, Italy [3] Center for Statistical Genetics, Ann Arbor, University of Michigan, Michigan 48109-2029, USA.; Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste 34137, Italy.; Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215.; Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109-1024, USA.; Department of Internal Medicine, Erasmus MC, Rotterdam 3015GE, the Netherlands.; Institute for Community Medicine, University Medicine Greifswald, Greifswald 17475, Germany.; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK.; Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano 20132, Italy.; School of Women's and Infants' Health, The University of Western Australia, WA-6009, Australia.; Program in Personalized Medicine, Division of Endocrinology, Diabetes and Nutrition-University of Maryland School of Medicine, Baltimore, MD 21201, USA.; Boston University School of Medicine, Department of Medicine, Sections of Preventive Medicine and Endocrinology, Boston, MA, USA.; 1] Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy [2] University of Sassari, Department of Biomedical Sciences, Sassari, Sassari 07100, Italy.; Division of Epidemiology &Community Health, University of Minnesotta, Minneapolis, MN 55455, USA.; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK.; 1] Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste 34137, Italy [2] Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Trieste 34149, Italy.; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.; 1] deCODE genetics/Amgen, Inc., Reykjavik IS-101, Iceland [2] School of Engineering and Natural Sciences, University of Iceland, Reykjavik IS-101, Iceland.; Musculoskeletal Research Programme, Division of Applied Medicine, University of Aberdeen, Aberdeen AB25 2ZD, UK.; Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam 3015 GE, the Netherlands.; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.; Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.; 1] Hebrew SeniorLife Institute for Aging Research, Boston, MA 02131, USA [2] Harvard Medical School, Boston, MA 02115, USA.; 1] Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany [2] German Center for Diabetes Research, Neuherberg 85764, Germany.; 1] Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA [2] Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA.; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.; British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.; Faculty of Medicine, University of Split, Split, Croatia.; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.; 1] Department of Internal Medicine, Erasmus MC, Rotterdam 3015GE, the Netherlands [2] Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam 3015 GE, the Netherlands.; Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland.; National Institute on Aging, Intramural Research Program, Baltimore, MD 20892, USA.; Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17475, Germany.; Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA.; Department of Obstetrics and Gynecology, University Medicine Greifswald, Greifswald 17475, Germany.; 1] Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215 [2] Harvard Medical School, Boston, MA 02115, USA.; Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy.; 1] Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK [2] Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK.; 1] Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA [3] Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA.; Departments of Epidemiology and Medicine Brown University, Brown University, Providence, RI 02912, USA.; 1] Estonian Genome Center, University of Tartu, Tartu 51010, Estonia [2] Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia.; 1] Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany [2] Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich 81377, Germany.; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA.; Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.; 1] deCODE genetics/Amgen, Inc., Reykjavik IS-101, Iceland [2] Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland.; 1] NHLBI's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA [2] Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA 02118, USA.; 1] MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK [2] Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK.
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