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. This evidence concerns the gene CD79B and primary central nervous system lymphoma.