Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity
8 affiliations
- 1AOM - IRCCS Ospedale Policlinico San Martino, Neuro-oncology and Mutagenesis Unit
- 2IRCCS Istituto Giannina Gaslini, Medical Genetics Unit
- 3AOM - IRCCS Ospedale Policlinico San Martino, Hereditary Cancer Unit
- 4IRCCS Istituto Giannina Gaslini, Genomics and Clinical Genetics Unit
- 5Inserm 1209, CNRS 5309, Institute for Advanced Biosciences, University Grenoble Alpes
- 6Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa
- 7IRCCS Istituto Giannina Gaslini, Oncology Unit
- 8Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento
Abstract
The TP53 gene encodes the well-known p53 tumor suppressor protein, which plays a crucial role in preventing cancer development. Germline TP53 variants cause Li–Fraumeni Syndrome (LFS), an autosomal dominant disorder associated with early-onset cancers, including breast cancer, brain tumors, leukemias, bone cancers, and soft tissue sarcomas. Here, we described a germline TP53 variant c.671A>C, located at the penultimate nucleotide of exon 6 and predicted to result in the missense substitution p.E224A. The variant was identified in a 2-year-old child with retroperitoneal rhabdomyosarcoma and with a strong family history suggestive of LFS. Functional assays in yeast and human cells demonstrated wild type-like activity of the protein p.E224A; however, in silico splicing analysis indicated potential splice defects (e.g., SpliceAI score = 0.77). Given this discrepancy, we further investigated this variant using a minigene approach, demonstrating that it causes the skipping of exon 6, likely resulting in a frameshift and the introduction of a premature stop codon. These findings supported the classification of the TP53 germline variant c.671A>C (p.E224A) as likely pathogenic, providing a definitive molecular diagnosis for family counselling. Additionally, the present results sheds light on how certain predicted TP53 missense variants can be linked to disease mechanisms through RNA splicing disruption.
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BibTeX
@article{velkova2026missense,
title = {{Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity}},
author = {Irena Velkova and Serena Cappato and Daniela Rivera and Ferruccio Romano and Deborah Schönegger and Renata Bocciardi and Anna Reymer and Pierre Hainaut and Patrizia De Marco and Viviana Gismondi and Gabriella Cirmena and Ludovica Menta and Marzia Ognibene and Alberto Garaventa and Carla Manzitti and Samuele Brugnara and Yari Ciribilli and Alessandra Bisio and Elisa Marcaccini and Paolo Malatesta and Francesca Faravelli and Paola Menichini and Valeria Capra and Paola Monti},
journal = {Scientific Reports},
year = {2026},
month = jul,
doi = {10.1038/s41598-026-62400-x},
url = {https://doi.org/10.1038/s41598-026-62400-x},
note = {CC BY},
}
RIS
TY - JOUR
TI - Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity
AU - Irena Velkova
AU - Serena Cappato
AU - Daniela Rivera
AU - Ferruccio Romano
AU - Deborah Schönegger
AU - Renata Bocciardi
AU - Anna Reymer
AU - Pierre Hainaut
AU - Patrizia De Marco
AU - Viviana Gismondi
AU - Gabriella Cirmena
AU - Ludovica Menta
AU - Marzia Ognibene
AU - Alberto Garaventa
AU - Carla Manzitti
AU - Samuele Brugnara
AU - Yari Ciribilli
AU - Alessandra Bisio
AU - Elisa Marcaccini
AU - Paolo Malatesta
AU - Francesca Faravelli
AU - Paola Menichini
AU - Valeria Capra
AU - Paola Monti
PY - 2026
DA - 2026/07/01
JO - Scientific Reports
DO - 10.1038/s41598-026-62400-x
UR - https://doi.org/10.1038/s41598-026-62400-x
AB - The TP53 gene encodes the well-known p53 tumor suppressor protein, which plays a crucial role in preventing cancer development. Germline TP53 variants cause Li–Fraumeni Syndrome (LFS), an autosomal dominant disorder associated with early-onset cancers, including breast cancer, brain tumors, leukemias, bone cancers, and soft tissue sarcomas. Here, we described a germline TP53 variant c.671A>C, located at the penultimate nucleotide of exon 6 and predicted to result in the missense substitution p.E224A. The variant was identified in a 2-year-old child with retroperitoneal rhabdomyosarcoma and with a strong family history suggestive of LFS. Functional assays in yeast and human cells demonstrated wild type-like activity of the protein p.E224A; however, in silico splicing analysis indicated potential splice defects (e.g., SpliceAI score = 0.77). Given this discrepancy, we further investigated this variant using a minigene approach, demonstrating that it causes the skipping of exon 6, likely resulting in a frameshift and the introduction of a premature stop codon. These findings supported the classification of the TP53 germline variant c.671A>C (p.E224A) as likely pathogenic, providing a definitive molecular diagnosis for family counselling. Additionally, the present results sheds light on how certain predicted TP53 missense variants can be linked to disease mechanisms through RNA splicing disruption.
SN - 2045-2322
ER -