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To explore the genetic basis for a child with ocular anomaly, microcephaly, growth retardation and intrauterine growth restriction. The patient underwent ophthalmologic examinations including anterior segment photography, fundus color photography, and fundus fluorescein angiography. The patient and her parents were subjected to whole exome sequencing. Candidate variants were verified by Sanger sequencing and bioinformatic analysis. The patient was found to have bilateral persistent pupillary membrane and coloboma of inferior iris, in