Severe Clinical Phenotype in Alport Syndrome Due to 2 COL4A4 Exon-Skipping Events

Alport syndrome (AS) is a genetically heterogeneous disorder caused by mutations in COL4A3, COL4A4, or COL4A5, leading to progressive kidney dysfunction. Although genetic screening has advanced, many cases remain undiagnosed due to deep intronic splice-site variants. We report a male patient diagnosed with autosomal recessive AS, characterized by hematuria, proteinuria, and chronic kidney disease progression. Initial kidney biopsy at age 10 revealed glomerular basement membrane thinning and focal segmental glomerulosclerosis, whereas targeted deoxyribonucleic acid sequencing failed to detect pathogenic variants. Over 15 years, kidney function declined, and a second biopsy showed severe glomerular basement membrane abnormalities with multilamellated structures. Whole-transcriptome sequencing revealed 2 events of exon skipping, specifically at exons 27 and 38 of the COL4A4 gene, which were verified by exon-specific PCR and Sanger sequencing. Intronic regions analysis revealed 2 heterozygous variants positioned 78 bp downstream of exon 27 and 8 bp upstream of exon 38, though their role in aberrant splicing remains uncertain. Immunofluorescence analysis confirmed disrupted α3α4α5(IV) heterotrimer assembly. This is the first documented case of dual exon-skipping events in COL4A4, highlighting their contribution to disease severity. Our findings emphasize the need for ribonucleic acid-based diagnostics and raise questions about potential benefit of exon-skipping therapy in autosomal recessive AS.