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Paracentric inversion disrupting the SHANK2 gene.

Jolien Huyghebaert1, Bregje Christiaenssen1, Marjan De Rademaeker2

  • 1Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.

European Journal of Medical Genetics
|March 8, 2025
PubMed
Summary

A large chromosomal inversion on chromosome 11 was identified in a girl with developmental delays. This genetic finding, disrupting the SHANK2 gene, offers a likely molecular diagnosis for her neurodevelopmental disorder (NDD).

Keywords:
Chromosome inversionIntellectual disabilityOptical genome mappingSHANK2Whole genome sequencing

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Area of Science:

  • Genetics and Genomics
  • Neurodevelopmental Disorders
  • Molecular Diagnostics

Background:

  • Intellectual disability (ID), speech and language delays, motor development delays, and attention deficit hyperactivity disorder (ADHD) can present with complex genetic etiologies.
  • Balanced de novo paracentric inversions are a type of structural variation that can disrupt gene function and lead to various phenotypes.
  • The SHANK2 gene plays a critical role in synaptic function and has been implicated in neurodevelopmental disorders (NDDs).

Purpose of the Study:

  • To identify the precise breakpoints of a large de novo paracentric inversion on chromosome 11.
  • To investigate the potential genetic cause of a patient's neurodevelopmental phenotype, including mild intellectual disability, speech and language delays, motor development delay, and ADHD.
  • To determine if the identified inversion disrupts any critical genes associated with neurodevelopmental disorders.

Main Methods:

  • Utilized a combination of short-read whole genome sequencing (WGS) analyzed with Delly software.
  • Employed cytogenomic analysis using Bionano technology for high-resolution mapping.
  • Confirmed breakpoints using Sanger sequencing for precise genetic characterization.

Main Results:

  • Identified a balanced de novo paracentric inversion on chromosome 11 (inv11q13.3; q25) spanning approximately 64 Mb.
  • The inversion breakpoints were found to disrupt the SHANK2 gene, crucial for postsynaptic scaffolding proteins, and the LINC02714 long non-coding RNA (lncRNA).
  • No other genetic variants that could explain the patient's phenotype were identified.

Conclusions:

  • The combined genomic techniques successfully pinpointed the breakpoints of a large chromosomal inversion.
  • Disruption of the SHANK2 gene due to the inversion is proposed as the likely molecular cause for the patient's neurodevelopmental disorder.
  • This study highlights the importance of integrating multiple sequencing and cytogenomic approaches for diagnosing complex genetic conditions.