The interaction of alterations among the genes with the highest number of variants in BC samples from TCGA revealed significant co-occurrence after adjustment between DONSON and MUC16 (padj = 1.054509 × 10−3); DONSON and HMCN1 (padj = 2.661866 × 10−3); PCK1 and BRCA2 (padj = 6.001709 × 10−3); PFKP and HMCN1 (padj = 8.502469 × 10−3); DONSON and TTN (padj = 9.120586 × 10−3); GPD1 and HMCN1 (padj = 9.283847 × 10−3); BRCA1 and COX20 (padj = 1.672530 × 10−2); PGK1 and HMCN1 (padj = 1.876325 × 10−2); and BRCA2 and PGK1 (padj = 4.526388 × 10−2). Here, PFKP is linked to breast cancer.