Cancer transcriptomes contain abundant alternative splice junctions, but the existence of an abnormal RNA does not establish an altered protein product, still less a therapeutically exploitable dependency. This integrative review follows evidence from splice-site choice and transcript fate through mass-spectrometric protein identification, isoform-specific function, and intervention. Genomic and RNA-based studies reveal recurrent splicing disruption, whereas proteogenomic analyses show that the transition from junction detection to uniquely assigned protein species is selective and method dependent. Mechanistic examples reveal distinct outcomes: degradation of aberrant transcripts with loss of normal protein, stable isoforms with altered signaling or cell states, and changes in antigen presentation. Perturbation studies can support vulnerability at the level of a splice-regulatory process, a downstream pathway, or a particular isoform; these are not interchangeable claims. This review therefore proposes an evidence-resolved interpretation that explicitly separates RNA association, protein identity, functional causation, and context-dependent therapeutic response. It identifies decisive experiments for resolving ambiguous peptide assignments, separating competing molecular mechanisms, and determining whether findings in model systems survive tumor heterogeneity and clinical translation. The practical conclusion is that therapeutic relevance depends on the experimentally demonstrated molecular entity and intervention context, not on the apparent abundance of alternative splicing alone.
