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Background  The aim of this study is to identify the genetic defect in a Chinese family with congenital aniridia combined with cataract and nystagmus.    Methods  Complete ophthalmic examinations, including slit-lamp biomicroscopy, dilated indirect ophthalmoscopy, anterior segment photography, and anterior segment optical coherence tomography (OCT) were performed. Blood samples were collected from all family members and genomic DNA was extracted. Genome sequencing was performed in all family members and Sanger sequencing was used to verify variant breakpoints.    Results  All the thirteen members in this Chinese family, including seven patients and six normal people, were recruited in this study. The ophthalmic examination of affected patients in this family was consistent with congenital aniridia combined with cataract and nystagmus. A novel heterozygous deletion (NC_000011.10:g.31802307_31806556del) containing the 5′ region of  PAX6  gene was detected that segregated with the disease.    Conclusion  We detected a novel deletion in  PAX6  responsible for congenital aniridia in the affected individuals of this Chinese family. The novel 4.25 kb deletion in  PAX6  gene of our study would further broaden the genetic defects of  PAX6  associated with congenital aniridia.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12886-021-02120-0.

A novel 4.25 kb heterozygous deletion in PAX6 in a Chinese Han family with congenital aniridia combined with cataract and nystagmus