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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.* ; Mägi, R.* ; Morrison, A.C.* ; Padmanabhan, S.* ; Pirie, A.* ; Polasek, O.* ; Porteous, D.J.* ; 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.* ; EPIC-Interact Consortium (*) ; Generation Scotland Consortium (*) ; 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.* ; Perry, J.R.*

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

Nat. Commun. 6:7756 (2015)

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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.

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