These so-called “wild-type” (WT) GIST had predicted deleterious variants in SUFU and GLI1. Taken together, somatic mutations in a subset of Hedgehog pathway genes were found in about 10% of GIST that we analyzed, raising the possibility that these genes may act as modifier genes in the development and progression of GIST. Here, GLI1 is linked to gastrointestinal stromal tumor.