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Deep-Intronic Variant in RUNX2 Causing Pseudo-Exon Inclusion in a Family With Cleidocranial Dysplasia.

Dorothea Stojanovic1, Dorota Garczarczyk-Asim1, Julia Vodopiutz2,3

  • 1Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria.

Clinical Genetics
|March 9, 2026
PubMed
Summary
This summary is machine-generated.

A genetic variant in the RUNX2 gene caused cleidocranial dysplasia (CCD) by creating a faulty messenger RNA (mRNA) segment. This led to reduced RUNX2 protein, explaining the condition

Keywords:
RUNX2cleidocranial dysplasialong‐read sequencingpseudo‐exon inclusion

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Area of Science:

  • Genetics
  • Molecular Biology
  • Human Disease

Background:

  • Cleidocranial dysplasia (CCD) is a skeletal disorder.
  • The RUNX2 gene plays a crucial role in bone development.

Purpose of the Study:

  • To investigate the genetic cause of CCD in a family.
  • To elucidate the molecular mechanism underlying RUNX2 haploinsufficiency in CCD.

Main Methods:

  • Sanger sequencing to identify genetic variants.
  • RT-PCR and sequencing to analyze mRNA splicing.
  • Western blotting to assess protein levels.

Main Results:

  • A deep-intronic single nucleotide variant in RUNX2 was identified.
  • The variant caused the inclusion of a pseudo-exon into the RUNX2 mRNA.
  • This pseudo-exon contained a premature stop codon, leading to mRNA decay and RUNX2 haploinsufficiency.

Conclusions:

  • Deep-intronic variants can cause genetic disorders through aberrant splicing.
  • RUNX2 haploinsufficiency due to pseudo-exon inclusion is a mechanism for CCD.
  • Understanding this mechanism aids in genetic diagnosis and counseling for CCD.