Michael Wangler, Hugo Bellen and colleagues report the generation of 5,857 fly stocks with ethyl methanesulfonate (EMS)-induced recessive lethal mutations on the X chromosome (Cell 159, 200–214, 2014). The authors screened mutants for defects in the nervous system, as well as phenotypes affecting pigmentation, wing veins and wing notching, as these have previously been linked to neuronal pathways. They were able to map 614 mutations to 165 genes using a combination of complementation testing and whole-genome sequencing. The authors integrated this data set with whole-exome sequence data for 1,929 individuals from families with undiagnosed mendelian diseases. As a proof-of-principle study, they followed up on six families with mutations in three genes with neuronal phenotypes in fly: DNM2, CRX and ANKLE2. Variants in DNM2 cause Charcot-Marie-Tooth neuropathy type 2M and were identified in two families with clinical phenotypes consistent with this disease. CRX variants were identified in three unrelated patients with Bull's eye maculopathy, expanding the known clinical manifestations of CRX mutations. Finally, ANKLE2 was identified as a novel candidate disease gene in a family with microcephaly. Further functional studies of the CRX and ANKLE2 mutations in Drosophila showed similarities to the human phenotypes and identified potential molecular mechanisms for the pathogenicity of these alleles.