The most frequent somatic mutations including SNVs and INDEL mutations were found in PIM1, MYD88, CD79B, IRF4, MYH11, KMT2D, PAX5, DCC, and ERBB3, and a few splice site mutations were found in CD79B, PIM1, and PTCH1. Further, Kaplan-Meier analysis showed poor and good prognoses in somatic mutations of MYH11 and PAX5 with decreased and increased copy numbers, respectively, in PCNSL patients. The gene discussed is PIM1; the disease is primary central nervous system lymphoma.