Missense but mis-spliced: germline TP53 variant c.671A>C (p.E224A) and the path from uncertainty to pathogenicity Article Swipe
Irena Velkova
,
Serena Cappato
,
Daniela Rivera
,
Ferruccio Romano
,
Deborah Schönegger
,
Renata Bocciardi
,
Pierre Hainaut
,
Patrizia De Marco
,
Viviana Gismondi
,
Gabriella Cirmena
,
Ludovica Menta
,
Marzia Ognibene
,
Alberto Garaventa
,
Carla Manzitti
,
S. Brugnara
,
Yari Ciribilli
,
Alessandra Bisio
,
Elisa Marcaccini
,
Paolo Malatesta
,
Francesca Faravelli
,
Paola Menichini
,
Paola Monti
,
Valeria Capra
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.07.31.25332437
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.07.31.25332437
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. Functional studies in yeast and human cells demonstrated that TP53 variants can have various effects, such as partial or complete loss of function and even gain of pro-oncogenic activities. Here, we identified a germline TP53 variant c.671A>C, resulting in the missense mutant protein p.E224A in the context of early-onset retroperitoneal rhabdomyosarcoma occurring in a child with a notable family history of cancer, suggestive of LFS. The variant was initially classified as a variant of uncertain significance (VUS). Functional assays in yeast and human cells demonstrated wild type-like activity of the protein p.E224A; however, in silico analysis predicted at RNA level a splicing defect, which we further investigated using a minigene approach. This analysis showed that the variant c.671A>C causes the skipping of exon 6, potentially introducing a frameshift in cDNA and a premature stop codon, which likely triggers nonsense-mediated mRNA decay; the loss of heterozygosity at the c.671 position in the parent’s TP53 transcript further confirmed the splicing impairment. In summary, these findings supported reclassifying the TP53 germline variant c.671A>C (p.E224A) from VUS to likely pathogenic, providing a definitive molecular diagnosis for family counseling. Additionally, this study sheds light on how certain TP53 variants that are defined as missense, can be linked to disease mechanisms through RNA splicing disruption, highlighting the need for their deep functional assessment.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.07.31.25332437
- https://www.medrxiv.org/content/medrxiv/early/2025/08/01/2025.07.31.25332437.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 45
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4412836025
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4412836025Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2025.07.31.25332437Digital Object Identifier
- Title
-
Missense but mis-spliced: germline TP53 variant c.671A>C (p.E224A) and the path from uncertainty to pathogenicityWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-08-01Full publication date if available
- Authors
-
Irena Velkova, Serena Cappato, Daniela Rivera, Ferruccio Romano, Deborah Schönegger, Renata Bocciardi, Pierre Hainaut, Patrizia De Marco, Viviana Gismondi, Gabriella Cirmena, Ludovica Menta, Marzia Ognibene, Alberto Garaventa, Carla Manzitti, S. Brugnara, Yari Ciribilli, Alessandra Bisio, Elisa Marcaccini, Paolo Malatesta, Francesca Faravelli, Paola Menichini, Paola Monti, Valeria CapraList of authors in order
- Landing page
-
https://doi.org/10.1101/2025.07.31.25332437Publisher landing page
- PDF URL
-
https://www.medrxiv.org/content/medrxiv/early/2025/08/01/2025.07.31.25332437.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.medrxiv.org/content/medrxiv/early/2025/08/01/2025.07.31.25332437.full.pdfDirect OA link when available
- Concepts
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Germline, Missense mutation, Pathogenicity, Genetics, Path (computing), Biology, Computational biology, Computer science, Mutation, Gene, Computer network, MicrobiologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
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2025: 1Per-year citation counts (last 5 years)
- References (count)
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45Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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