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Rx is a paired-like homeodomain transcription factor that is expressed in the developing eyes, ventral forebrain, hypothalamus, posterior pituitary, and the pineal gland. In adults, Rx is primarily expressed in the neural retina, ciliary bodies, pineal gland, hypothalamus, and posterior pituitary. Rx mutations in multiple species are associated with anophthalmia. During the course if this work, we identified a human patient with anophthalmia and sclerocornea that carries mutations in the RX gene. One allele of the patient carries a Q147X mutation, which causes a truncation of the RX protein at the beginning of the homeodomain. The other allele possesses an R192Q mutation that is a substitution of a highly conserved arginine to glutamine in the DNA-binding helix of the homeodomain. We showed that the Q147X mutation ablates the RX nuclear localization signal, in addition to its inability to bind DNA, and therefore we considered this a nonfunctional allele of RX. The R192Q substitution does not affect RX localization to the nucleus but demonstrates a 10-fold decrease in the DNA-binding affinity in vitro. Targeting of the R192Q mutation into the mouse genome on the background of an Rx-null allele results in normal eye development, thus highlighting the difference between the mouse and human eye developmental processes. Despite the failure to create a mouse model for the identified human patient, an allelic series in the Rx locus was created during the process of targeting that will allow analysis of the role Rx performs in development of the eye and pituitary gland. In addition, Rx function during ventral forebrain development was studied in Rx-null mice. We showed that deletion of Rx in the ventral forebrain results in defects in the palate and cartilage and in pituitary formation. The precursor to the posterior pituitary, the infundibulum, does not form in the Rx-null embryos, with all anterior pituitary cell types present but displaced rostrally and ventrally to the roof of the mouth.