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Transcript analysis for variant classification resolution in a child with primary ciliary dyskinesia.

Alexander Ing1,2,3,4, Alissa Wlodaver1, Dawn Kirschmann1

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Cold Spring Harbor Molecular Case Studies
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Summary
This summary is machine-generated.

Transcriptional analysis helped reclassify variants of uncertain significance in the DNAH11 gene for primary ciliary dyskinesia (PCD). This method clarified the clinical impact of genetic variants, aiding accurate diagnosis.

Keywords:
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Area of Science:

  • Genetics
  • Molecular Biology
  • Medical Diagnostics

Background:

  • Variants of uncertain significance (VUSs) pose challenges in genetic diagnosis, particularly those affecting mRNA splicing.
  • Primary ciliary dyskinesia (PCD) is a genetic disorder affecting cilia function, often linked to DNAH11 gene mutations.
  • Accurate variant classification is crucial for diagnosing genetic disorders and predicting patient outcomes.

Purpose of the Study:

  • To investigate the clinical utility of transcriptional analysis in resolving VUSs in the DNAH11 gene.
  • To re-evaluate the pathogenicity of compound heterozygous variants (c.10691 + 2T > C and c.13523_13543dup21) in a patient with PCD.
  • To demonstrate the impact of transcriptional analysis on variant reclassification and diagnostic accuracy.

Main Methods:

  • Trio whole-exome sequencing was used to identify compound heterozygous variants in DNAH11.
  • In silico predictions were used to assess the potential impact of variants on splicing and nonsense-mediated decay (NMD).
  • Transcriptional analysis was performed to experimentally determine the in vivo effect of the identified variants on mRNA transcripts.

Main Results:

  • The variant c.10691 + 2T > C was reclassified from VUS to Likely Pathogenic due to evidence of a deleterious splicing effect.
  • The variant c.13523_13543dup21 was subsequently reclassified to Likely Pathogenic.
  • Transcriptional analysis provided critical evidence to resolve the VUS status of both DNAH11 variants.

Conclusions:

  • Transcriptional analysis is a valuable tool for resolving VUSs, especially those impacting splicing.
  • This approach can lead to accurate reclassification of genetic variants, improving diagnostic certainty for genetic disorders like PCD.
  • The study highlights the importance of functional studies in understanding the clinical significance of genetic variants.