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Mutations in PAX6/Pax6 lead to a variety of ocular anomalies in humans and mice. The aim of the study was to characterise the ocular abnormalities caused by the missense Pax6Leca4 mutation and compare them to published observations on Pax6 alleles that are functionally equivalent to Pax6− null alleles (such as Pax6Sey and Pax6Sey-Neu) and human inherited eye diseases. Ocular features of homozygous Pax6Leca4/Leca4 and heterozygous Pax6Leca4/+ embryos at E12.5–E18.5, heterozygous Pax6Leca4/+ young mice at P18 and heterozygous Pax6Leca4/+ adults at 12 weeks were analysed histologically with their wild-type Pax6+/+ littermates. Homozygous Pax6Leca4/Leca4 fetuses died perinatally with no eyes although an optic cup rudiment with pigmented cells developed. Pax6Leca4/+ mice were microphthalmic and a range of other severe ocular phenotypes affected both the anterior and the posterior segments. In contrast to Pax6+/−, the Pax6Leca4/+ eyes had no goblet cells in the corneal epithelium, the iris was not hypoplastic and there was no lens-corneal epithelial plug. However, microphthalmia was more severe, corneal vascularisation occurred earlier (during fetal stages), pigmented cells were present in the vitreous and corneal stroma and the ciliary body was malformed or abnormal. These results show that, although Pax6Leca4/+ lacked some eye abnormalities commonly seen in Pax6Sey/+ and Pax6Sey-Neu/+ eyes, in most respects their eyes were more severely affected. These differences probably reflect both differences between the Pax6Leca4 and the Pax6Sey-Neu mutations and differences in modifier gene expression in different genetic backgrounds. The presence of pigmented cells in the cornea is a novel observation. Some Pax6Leca4/+ ocular abnormalities were similar to those present in human Peters' anomaly and persistent hyperplastic primary vitreous (PHPV) so Pax6Leca4/+ mice provide a useful model for some inherited eye diseases.