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<p>The <i>CNTNAP2</i> gene encodes CASPR2, a transmembrane protein essential for neuronal development and synaptic function. Biallelic pathogenic variants cause Pitt–Hopkins–like syndrome, characterized by intellectual disability, epilepsy, and autistic features. We report two patients with a Pitt–Hopkins–like phenotype carrying compound heterozygous structural variants: an intragenic deletion in <i>trans</i> with a paracentric inversion. Short-read genome sequencing detected both variants, and long-read sequencing refined one breakpoint. Non-reccurent deletions involved exon 3, while <i>CNTNAP2</i> breakpoints for both inversions were located in intron 1. These findings broaden the mutational spectrum of <i>CNTNAP2</i> and underscore the value of genome sequencing in identifying complex structural variants.</p>

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Compound heterozygous structural variants resulting in CNTNAP2 biallelic loss-of-function: rare mechanisms unveiled by genome sequencing

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月5日

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  • Jade Fauqueux,
  • Roseline Caumes,
  • Cindy Colson,
  • Adeline Trauffler,
  • Pierre Cleuziou,
  • Caroline Thuillier,
  • Pauline Planté-Bordeneuve,
  • Marine Tessarech,
  • Jamal Ghoumid,
  • Thomas Smol

摘要

The CNTNAP2 gene encodes CASPR2, a transmembrane protein essential for neuronal development and synaptic function. Biallelic pathogenic variants cause Pitt–Hopkins–like syndrome, characterized by intellectual disability, epilepsy, and autistic features. We report two patients with a Pitt–Hopkins–like phenotype carrying compound heterozygous structural variants: an intragenic deletion in trans with a paracentric inversion. Short-read genome sequencing detected both variants, and long-read sequencing refined one breakpoint. Non-reccurent deletions involved exon 3, while CNTNAP2 breakpoints for both inversions were located in intron 1. These findings broaden the mutational spectrum of CNTNAP2 and underscore the value of genome sequencing in identifying complex structural variants.