In cancer, BAP1 can function both as a Tumor suppressor and as a metastasis suppressor. Exome sequencing identified inactivating mutations in BAP1 in 47% of Uveal melanomas, and BAP1 mutation have been found to be strongly associated with metastasis. The atypical melanocytic lesions resemble Spitz nevi and have been characterized as “atypical Spitz tumors” (ASTs), although they have a unique histology and exhibit both BRAF and BAP1 mutations.

BAP1 mutations have been identified in aggressive Mesotheliomas with similar mutations as seen in melanomas. Sequencing studies have been used to identify germline mutations in BAP1 in families with genetic predispositions to mesothelioma and melanocytic skin tumors. Mutations in the tumor suppressor gene BAP1 occur in approximately 15% of clear cell renal cell carcinoma cases. Sequencing efforts demonstrated worse outcomes in patients with BAP1 mutated clear cell renal cell carcinoma. Immunohistochemistry for BAP1 is a prognostic biomarker to predict poor oncologic outcomes and adverse clinicopathological features in patients with non-metastatic clear cell renal cell carcinoma. BAP1 assessment using immunohistochemistry on needle biopsy may benefit preoperative risk stratification and guide treatment planning.