Distal enhancers are thought to play important roles in the spatiotemporal regulation of gene expression during embryonic development, but few predicted enhancer elements have been shown to affect transcription of their endogenous genes or to alter phenotypes when disrupted. Here, we demonstrate that a 123.6-kb deletion within the mouse gene is associated with reduced transcription of , a gene located 660 kb away. Mice homozygous for the deletion mutation [named hyperspin ()] have malformed inner ears and are deaf with balance defects, whereas previously reported knockout mice showed no phenotypic abnormalities. Inner ears of mice have malformations similar to those of embryos, and expression is severely reduced in the otocyst but not the branchial arches of embryos, indicating that the deletion affects otic-specific enhancers of In addition, transheterozygous mice exhibit noncomplementation with inner ear dysmorphologies similar to those of and embryos, verifying a -acting effect of the deletion on expression. CRISPR/Cas9-mediated deletions of putative enhancer elements located within the deleted region failed to phenocopy the defects of mice, suggesting the possibility of multiple enhancers with redundant functions. Our findings in mice suggest that analogous enhancer elements in the human gene may regulate expression and underlie the hearing loss that is associated with split-hand/-foot malformation 1 syndrome. mice provide a new animal model for studying long-range enhancer effects on expression in the developing inner ear.