Any holoprosencephaly in which the cause of the disease is a mutation in the GLI2 gene. The disease is holoprosencephaly 9 (MONDO_0012563). Also known as: GLI2 holoprosencephaly, HPE9, holoprosencephaly caused by mutation in GLI2, holoprosencephaly type 9, holoprosencephaly with microphthalmia and first branchial arch anomalies, pituitary anomalies with holoprosencephaly-like features.