We encountered a case with congenital iris coloboma, omphalocele, and developmental delay with a 2.5 Mb deletion on chromosome 4q25 encompassing <i>PITX2</i>, leading to Axenfeld-Rieger syndrome (ARS)<i>, NEUROG2</i>, and <i>ANK2</i>. Here, PITX2 is linked to Axenfeld-Rieger syndrome.