In-Silico Characterization of TP53 Splice Mutations in Somatic and Germline Tumours

Abstract

TP53 undergoes alternative splicing to produce multiple mRNA transcripts and protein isoforms, yet the effects of splice site mutations on isoform regulation, tumor-biology, and clinical outcome remain unclear. Analysis of 23,017 TP53 variants, including 18,562 somatic mutations (pan-cancer datasets - cBioPortal) and 4,455 germline variants (IARC database), identified recurrent donor (X32, X125, X224, X261, X331) and acceptor (X33, X126, X187, X225, X307, X332) splice site mutations. Germline variants showed nucleotide-specific transition biases. Most splice site mutations were associated with reduced TP53 mRNA expression; however, X32, X33, X126, and X261 maintained or elevated transcript levels. Splice mutations were associated with distinct transcriptional subsets marked by altered p53 target gene expression, elevated tumor mutation burden, increased genomic instability, and significantly reduced disease-free survival compared to missense mutations, with X126 and X331 being associated with poorest outcomes. These findings emphasize the clinical impact of TP53 splice site mutations and the need for functional classification.