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

Lunetta, K. L. et al. (2015) Rare coding variants and X-linked loci associated with age at menarche. Nature Communications, 6, p. 7756. 7756. (doi:10.1038/ncomms8756) (PMID:26239645) (PMCID:PMC4538850)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Padmanabhan, Professor Sandosh
Authors: Lunetta, K. L., Day, F. R., Sulem, P., Ruth, K. S., Tung, J. Y., Hinds, D. A., Esko, T., Elks, C. E., Altmaier, E., He, C., Huffman, J. E., Mihailov, E., Porcu, E., Robino, A., Rose, L. M., Schick, U. M., Stolk, L., Teumer, A., Thompson, D. J., Traglia, M., Wang, C. A., Yerges-Armstrong, L. M., Antoniou, A. C., Barbieri, C., Coviello, A. D., Cucca, F., Demerath, E. W., Dunning, A. M., Gandin, I., Grove, M. L., Gudbjartsson, D. F., Hocking, L. J., Hofman, A., Huang, J., Jackson, R. D., Karasik, D., Kriebel, J., Lange, E. M., Lange, L. A., Langenberg, C., Li, X., Luan, J.'a., Mägi, R., Morrison, A. C., Padmanabhan, S., Pirie, A., Polasek, O., Porteous, D., Reiner, A. P., Rivadeneira, F., Rudan, I., Sala, C. F., Schlessinger, D., Scott, R. A., Stöckl, D., Visser, J. A., Völker, U., Vozzi, D., Wilson, J. G., Zygmunt, M., Forouhi, N. G., Kerrison, N. D., Sharp, S. J., Sims, M., Barroso, I., Deloukas, P., McCarthy, M. I., Arriola, L., Balkau, B., Barricarte, A., Boeing, H., Franks, P. W., Gonzalez, C., Grioni, S., Kaaks, R., Key, T. J., Navarro, C., Nilsson, P. M., Overvad, K., Palli, D., Panico, S., Quirós, J. R., Rolandsson, O., Sacerdote, C., Sánchez, M.‐J., Slimani, N., Tjonneland, A., Tumino, R., van der A, D. L., van der Schouw, Y. T., Riboli, E., Smith, B. H., Campbell, A., Deary, I. J., McIntosh, A. M., Boerwinkle, E., Buring, J. E., Crisponi, L., Easton, D. F., Hayward, C., Hu, F. B., Liu, S., Metspalu, A., Pennell, C. E., Ridker, P. M., Strauch, K., Streeten, E. A., Toniolo, D., Uitterlinden, A. G., Ulivi, S., Völzke, H., Wareham, N. J., Wellons, M., Franceschini, N., Chasman, D. I., Thorsteinsdottir, U., Murray, A., Stefansson, K., Murabito, J. M., Ong, K. K., and Perry, J. R. B.
College/School:College of Medical Veterinary and Life Sciences > Institute of Cardiovascular and Medical Sciences
Journal Name:Nature Communications
Publisher:Nature Publishing Group
ISSN:2041-1723
ISSN (Online):2041-1723
Copyright Holders:Copyright © 2015 Macmillan Publishers Limited
First Published:First published in Nature Communications 6:7756
Publisher Policy:Reproduced under a Creative Commons License

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