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Comprehensive Splice Pattern Analysis for Previously Reported OCRL Splicing Variants and Their Phenotypic

Rini Rossanti1,2, Eri Okada1, Nana Sakakibara1

  • 1Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.

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|June 9, 2025
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Summary

Genetic variants in the oculocerebrorenal syndrome of Lowe (OCRL) gene cause Dent disease-2 and Lowe syndrome. This study clarifies how OCRL splicing variants correlate with these distinct phenotypes, improving diagnostic understanding.

Keywords:
Dent disease-2Lowe syndromeOCRLSplicingisoformminigene system

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Area of Science:

  • Genetics
  • Molecular Biology
  • Human Disease Genetics

Background:

  • Dent disease-2 and Lowe syndrome are distinct phenotypes arising from oculocerebrorenal syndrome of Lowe (OCRL) gene abnormalities.
  • Truncating variants in early exons (1-7) of OCRL are associated with Dent disease-2, while variants in later exons (8-24) are linked to Lowe syndrome.
  • The role of functional OCRL isoforms and their altered initiation codons in exon 8 on phenotype variability remains unclear.

Purpose of the Study:

  • To investigate the pathogenicity of OCRL splicing variants.
  • To establish genotype-phenotype correlations for OCRL-related disorders.
  • To elucidate the impact of splicing variants on OCRL function and disease manifestation.

Main Methods:

  • Analysis of 28 previously reported OCRL splicing variants from the Human Gene Mutation Database.
  • In vitro splicing assays using a minigene system to assess mRNA level consequences.
  • Evaluation of variant compatibility with in silico algorithms and correlation with clinical phenotypes.

Main Results:

  • Aberrant splicing was confirmed in 27 out of 28 variants.
  • OCRL splicing variants in exons 1-7 consistently led to Dent disease-2, and variants in exons 9-24 to Lowe syndrome.
  • A specific variant, c.561-2 A > G in exon 8, resulted in Dent disease-2, preserving an altered initiation codon (Met206) of an OCRL isoform.

Conclusions:

  • This study provides critical data on the pathogenicity of OCRL splicing variants and their genotype-phenotype correlations.
  • The c.561-2 A > G variant's association with Dent disease-2 supports the role of altered initiation codons in exon 8 of OCRL isoforms.
  • Findings enhance understanding of OCRL variant impact on disease phenotypes, aiding in diagnosis and genetic counseling.