{
  "abstract": "Deep intronic variants can cause aberrant splicing, often manifested as pseudoexon inclusion, which represents a significant challenge in clinical diagnostics. Pseudoexon activations have been repeatedly described in the NF1 gene, making it a promising genomic context for studying underlying mechanisms. Here, we developed a specialized minigene assay by combining high-throughput mutagenesis and next-generation sequencing to evaluate the splicing effect of 501 deep intronic variants within NF1 intron 3. We identified and validated eleven pseudoexon-activating variants, including seven novel ones, which clustered into four activation-prone hotspots. Additionally, we detected a rare, out-of-frame wild-type pseudoexon whose inclusion was significantly enhanced by three specific mutations. Using this experimentally validated dataset, we benchmarked SpliceAI performance and ESRseq scores to refine variant prioritization. This integrated high-throughput framework offers a robust starting point for the systematic functional prioritization of deep intronic variation, providing a scalable model for variant annotation in other disease-associated genes.",
  "abstract_shown": true,
  "affiliations": [
    "Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "name": "E. Svobodova"
    },
    {
      "name": "P. Soucek"
    },
    {
      "name": "K. Reblova"
    },
    {
      "name": "Z. Kubat"
    },
    {
      "name": "M. Kratka"
    },
    {
      "name": "T. Freiberger"
    },
    {
      "affs": [
        0
      ],
      "name": "L. Kajan Grodecka"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0a7hxdh8h0ta5.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.20.760351",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.20.760351v1.full",
  "id": "0a7hxdh8h0ta5",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.20.760351v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "molecular biology"
    ],
    [
      "openalex",
      "1312|RNA Research and Splicing"
    ]
  ],
  "openalex": "W7139130897",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.20.760351v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-20",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/0a7hxdh8h0ta5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:28:46Z",
      "native_id": "10.64898/2026.10.20.760351",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.20.760351v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:molecular biology",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Decoding pseudoexon activation by deep intronic variants using a high-throughput minigene assay in the NF1 gene",
  "title_text": "Decoding pseudoexon activation by deep intronic variants using a high-throughput minigene assay in the NF1 gene",
  "type": "preprint",
  "updated_at": "2026-10-30T12:28:46Z",
  "url": "https://research.draconitic.com/paper/0a7hxdh8h0ta5",
  "venue": "bioRxiv",
  "versions": []
}