Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity

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.

Authors

Institutions

Publication Details

Journal
Scientific Reports
Published
2026-07-16
DOI
https://doi.org/10.1038/s41598-026-62400-x
Primary Topic
Cancer-related Molecular Pathways
Type
article
Field-Weighted Citation Impact
0.00
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity

Renata Bocciardi, Paolo Malatesta, Marzia Ognibene, Gabriella Cirmena et al.
Scientific Reports
Cancer-related Molecular Pathways
article

Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity

Renata Bocciardi, Paolo Malatesta, Marzia Ognibene, Gabriella Cirmena, Patrizia De Marco, Pierre Hainaut, Viviana Gismondi, Paola Monti, Ferruccio Romano, Anna Reymer, Yari Ciribilli, Elisa Marcaccini, Serena Cappato, Carla Manzitti, Paola Menichini, Irena Velkova, Alberto Garaventa, Francesca Faravelli, Daniela Rivera, Ludovica Menta, Alessandra Bisio, Samuele Brugnara, Deborah Schönneger, Valeria Capra
article en

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.

Scientific Reports
Centre National de la Recherche Scientifique (FR), Inserm (FR), University of Trento (IT), Istituto Giannina Gaslini (IT), Ospedale Policlinico San Martino (IT), Istituti di Ricovero e Cura a Carattere Scientifico (IT), University of Genoa (IT), Université Grenoble Alpes (FR)
Zero hunger
Openalex Percentile: Top 11%
Cancer-related Molecular Pathways
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.