In total, 42% of the tumor samples harbor at least one mutation in a significantly mutated element: the coding region of SPOP or the promoter of PDE4DIP, NBPF10, or ZNF595, or the enhancer of HM13. We note that while our analysis reveals the non-coding regions of PDE4DIP, ZNF595, and HM13 as significantly mutated in PCa for the first time, their coding regions have been previously implicated in prostate or other cancers [70–73]. This evidence concerns the gene HM13 and urogenital neoplasm.