A wave of deep intronic mutations in X-linked Alport syndrome

Kidney Int. 2023 Aug;104(2):367-377. doi: 10.1016/j.kint.2023.05.006. Epub 2023 May 23.


X-linked Alport syndrome (XLAS) is an inherited kidney disease caused exclusively by pathogenic variants in the COL4A5 gene. In 10-20% of cases, DNA sequencing of COL4A5 exons or flanking regions cannot identify molecular causes. Here, our objective was to use a transcriptomic approach to identify causative events in a group of 19 patients with XLAS without identified mutation by Alport gene panel sequencing. Bulk RNAseq and/or targeted RNAseq using a capture panel of kidney genes was performed. Alternative splicing events were compared to those of 15 controls by a developed bioinformatic score. When using targeted RNAseq, COL4A5 coverage was found to be 23-fold higher than with bulk RNASeq and revealed 30 significant alternative splicing events in 17 of the 19 patients. After computational scoring, a pathogenic transcript was found in all patients. A causative variant affecting COL4A5 splicing and absent in the general population was identified in all cases. Altogether, we developed a simple and robust method for identification of aberrant transcripts due to pathogenic deep-intronic COL4A5 variants. Thus, these variants, potentially targetable by specific antisense oligonucleotide therapies, were found in a high percentage of patients with XLAS in whom pathogenic variants were missed by conventional DNA sequencing.

Keywords: Alport syndrome; COL4A5; RNAseq; deep-intronic mutation; splicing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Collagen Type IV / genetics
  • Collagen Type IV / metabolism
  • Exons
  • Humans
  • Mutation
  • Nephritis, Hereditary* / diagnosis
  • Nephritis, Hereditary* / genetics
  • Nephritis, Hereditary* / pathology
  • RNA Splicing


  • Collagen Type IV