ArticlemedRxiv : the preprint server for health sciences2025
Analysis and Interpretation of Somatic NMD-Escaping Variants in Oncogenes and Dual-Function Genes across Adult and Pediatric Cancer Cohorts.
Article in medRxiv : the preprint server for health sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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12 authors.
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Abstract
Interpreting protein-truncating variants predicted to escape nonsense-mediated decay (NMDe) based on the 50-bp rule is challenging due to their variable consequences. The Clinical Genome Resource, Cancer Genomics Consortium, and Variant Interpretation for Cancer Consortium recommendations focus on tumor suppressor genes where NMDe variants may result in loss-of-function. However, guidance for interpreting NMDe variants in oncogenes and dual-function genes remains limited. To address this gap, we screened the Catalogue of Somatic Mutations in Cancer, focusing on oncogenes and dual-function genes with ≥10 NMDe variants supported by published functional studies. This analysis prioritized 15 genes exhibiting two distinct NMDe patterns resulting in gene activation. The first pattern and gene examples involve NMDe variants causing loss of C-terminal regulatory regions that mediate protein inhibition and/or degradation, frequently manifesting as attenuated cell surface receptor internalization/degradation (e.g.,
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