Unique near-complete deletion of GLI2 in a patient with combined pituitary hormone deficiency and post-axial polydactyly

•GLI2 is crucial for the formation of the midline, including the pituitary•Large phenotypic variability, not yet understood•Patients with larger deletions or truncating mutations present with ‘brain phenotype’ more frequently than missense mutations•We found a unique near-complete deletion of GLI2 in a patient without ‘brain phenotype’•Genotype-phenotype analysis shows that brain phenotype only occurs when adjacent genes are affected