Our analysis of mice homozygous for a hypomorphic Prdm13 allele suggests that the phenotypic association of CHH with cerebellar hypoplasia occurs as a result of the central function of PRDM13 in controlling GABAergic and Kiss1 neuronal specification and differentiation in the cerebellum and hypothalamus, respectively. Here, PRDM13 is linked to cartilage-hair hypoplasia.