Table 1.

Functional consequences of alternative splicing in breast cancer

Gene/proteinCancer-relevant gene functional tendencyType of change to reading frameAS removes % of proteinDomain(s) removed by alternative splicingFully spliced (all exons incorporated) in
CD40Pro-proliferativeFrameshift95Cytokine receptor domainCancer
TUBA4AMitosisFrameshift80Tubulin domainCancer
CCL4ProinvasiveFrameshift70Cytokine domainCancer
DBF4BPro-proliferativeFrameshift60Zinc finger domainCancer
MCL1AntiapoptoticFrameshift30Bcl2 domainCancer
F3ProinvasiveFrameshift30Cytokine receptor domainCancer
HMGA1ProneoplasticIns/del20DNA-binding domainCancer
DNMT3BAntiapoptotic oncogenicIns/del10Methylase domainCancer
FGFR2Proinvasive mitosis and differentiationIns/del10Ig-like domainCancer
SHC1ProproliferativeIns/del5Phosphotyrosine-binding domainCancer
PTPRBCell signalingIns/del5Fibronectin-like domainCancer
FN1Migration and metastasisIns/del4IIICSCancer
POLBDNA maintenanceFrameshift95Polymerase domainNormal
PAXIP1Genome stabilityFrameshift90BRCA1 C terminal domainNormal
BTCGrowth factorIns/Del30EGF-like domainNormal
DSC3Tumor suppressor cell adhesionFrameshift10Cadherin domainNormal
CLIP1Tumor suppressor cytoskeletonIns/del10Chromosome segregation domainNormal
PCSK6ProinvasiveIns/del5Protease-associated domainNormal
NOTCH3Pro-proliferativeIns/del2EGF-like domainNormal
  • Column 1, 19 markers for which the alternative splice event alters a known functional domain. Column 2, the cancer-relevant function of the corresponding protein. Columns 3 to 5 list the effect of alternative splicing on the reading frame: (3) whether it is truncated by a frameshift or undergoes an internal insertion or deletion (ins/del); (4) the approximate proportion of the protein removed in the short form; and (5) the known protein domains affected. The final column indicates whether breast tumors or normal breast has an increased amount of the full-length (likely the fully functional) form.