Objective To analyze the genetic features of congenital aniridia in a family and to explore the characteristics of PAX6 gene mutations and differences in clinical phenotypes.Methods The medical history and clinical data of this family line were collected.Whole-exon gene sequencing and data analysis were performed,and homology modelling server SWISS-MODEL was applied to construct the corresponding protein model for analysis.Results All 4 individuals with onset in this family line had photophobia and difficulty in opening the eyes due to iris deficiency,with the same clinical phenotypes of aniridia,cataracts,and macular centro-concave dysplasia.But,there were still individual differences in phenotypes.Genetic examination showed that all 4 affected individuals were heterozygous for a heterozygous deletion shifted variant c.442_452del:p.M148Afs*48 on the PAX6 gene,which is highly conserved among species.Homozygous modeling suggested that the mutated PAX6 gene ultimately led to differential changes in protein conformation.Conclusion The newly identified PAX6 gene variant is not phenotypically identical among members of the family with congenital aniridia,and homology modeling analysis has increased the understanding that aberrant expression of PAX6 leads to structural abnormalities in the protein.Genetic examination may provide genetic evidence for this family line.