Clinical and Functional Significance of TP53 Exon 4-Intron 4 Splice Junction Variants.

Germline splicing variants are uncommon, and their clinical relevance is unknown. However, splice-altering variants at exon 4-intron 4 junctions are relatively enriched in pediatric adrenocortical tumors (ACT). Nevertheless, family histories of cancer compatible with classic Li-Fraumeni syndrome are rarely seen in these patients. We used conventional and assays to determine protein stability, splicing, and transcriptional activity of 10 variants at exon 4-intron 4 junctions and analyzed their clinical correlates. We reviewed public databases that report the impact of variants in human cancer and examined individual reports, focusing on family history of cancer. exon 4-intron 4 junction germline variants were identified in 9 of 75 pediatric ACTs enrolled in the International Pediatric Adrenocortical Tumor Registry and Children's Oncology Group ARAR0332 study. An additional eight independent variants involving exon 4 splicing were identified in the Pediatric Cancer Genome Project ( = 5,213). These variants resulted in improper expression due to ineffective splicing, protein instability, altered subcellular localization, and loss of function. Clinical case review of carriers of exon 4-intron 4 junction variants revealed a high incidence of pediatric ACTs and atypical tumor types not consistent with classic Li-Fraumeni syndrome. Germline variants involving exon 4-intron 4 junctions are frequent in ACT and rare in other pediatric tumors. The collective impact of these germline variants on the fidelity of splicing, protein structure, and function must be considered in evaluating cancer susceptibility. IMPLICATIONS: Taken together, the data indicate that splice variants at codon 125 and surrounding bases differentially impacted p53 gene expression and function.