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The deletion of the third exon of the growth hormone receptor ( GHRd3 ) is one of the most common genomic structural variants in the human genome. This deletion has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of menarche, adult height, and longevity. However, its evolutionary history and the exact mechanisms through which it affects phenotypes remain unresolved. While the analysis of thousands of genomes suggests that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago, a demographic signature that roughly corresponds with the emergence of multiple modern human behaviors and a concurrent population expansion. Using a mouse line engineered to contain the deletion, pleiotropic and sex-specific effects on organismal growth, the expression levels of hundreds of genes, and serum lipid composition were documented, potentially involving the nutrient-dependent mTORC1 pathway. These growth and metabolic effects are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability. The last distinctive prehistoric shift in allele frequency might be related to newly developed technological buffers against the effects of oscillating resource levels.