In our study, the compound heterozygous variation of MPDZ, comprising the nonsense variant Ser1752Ter (in exon 39) and the frameshift variation Asp1434fs*3 (in exon 31) as null alleles, was identified in the proband of a Chinese family, and the phenotype was characterized by isolated macular coloboma in the eyes but with no brain malformation or hydrocephalus. Here, MPDZ is linked to Hydrocephalus.