Provided herein are compositions and methods related to conditioning a subject for a hematopoietic stem cell (HSC) transplantation using an inhibitor of a stem cell growth factor receptor (KIT). The compositions and methods described herein are particularly useful for a subject who is in need of a HSC transplantation and who is hypersensitive to at least one DNA damaging agent, e.g., a subject with fanconi anemia. Compositions and methods related to conditioning a fanconi anemia subject for HSC transplantation using an inhibitor of KIT are also provided herein.