More than 100 loci have been identified for age at menarche by genome-wide association studies; however, collectively these explain only B3% 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 fre- quencies 0.08–4.6%; effect sizes 0.08–1.25 years per allele; Po5108). In addition, we identify common X-chromosome loci at IGSF1 (rs762080, P1⁄49.41013) and FAAH2 (rs5914101, P 1⁄4 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 1⁄4 2.8 10 11), illustrating the utility of population studies to estimate the penetrance of reportedly pathogenic mutations. Collectively, these novel variants explain B0.5% variance, indicating that these overlooked sources of variation do not substantially explain the ‘missing heritability’ of this complex trait.
