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

Germline TP53 missense variant c.671A>C disrupting splicing (exon 6 skipping) → frameshift and premature stop codon.

Characterisation of a germline TP53 variant c.671A>C, located at the penultimate nucleotide of exon 6 and predicted missense (p.E224A), identified in a 2-year-old with retroperitoneal rhabdomyosarcoma and a strong family history suggestive of Li-Fraumeni syndrome. Functional assays in yeast and human cells showed near-wild-type protein activity, but in silico analysis predicted a splicing defect (SpliceAI 0.77). A minigene approach confirmed exon 6 skipping, likely leading to a frameshift and premature stop codon. These data reclassified the variant as likely pathogenic, providing a definitive molecular diagnosis for family counselling.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

A neat demonstration that protein-level readouts can mislead: a variant that looks functionally neutral turns out pathogenic through a splicing mechanism, reconciling SpliceAI and minigene. The message is directly transferable — for a discordant TP53 missense, test splicing before concluding. The impact remains family-level (one variant, one family), hence a moderate score, but the teaching value is real.

Analysis by Dr Thibaut Benquey