Alport syndrome cold cases: Missing mutations identified by exome sequencing and functional analysis

Area of Science:

• Genetics
• Molecular Biology
• Nephrology

Background:

• Alport syndrome (AS) is an inherited kidney disease caused by mutations in COL4A3, COL4A4, and COL4A5 genes.
• Standard genetic screening often fails to identify causative mutations in a significant portion of AS patients.
• Whole-exome sequencing (WES) offers a comprehensive approach to identify genetic variants.

Observation:

• WES was applied to three Italian families with AS who had negative results from candidate-gene analyses.
• Novel pathogenic variants were identified in COL4A5 and COL4A3 genes, including intronic splicing variants and missense mutations.
• Functional studies confirmed the pathogenicity of identified variants, including disruption of splicing and protein secretion.

Findings:

• A novel intronic COL4A5 variant disrupting exon 29 splicing was identified and functionally validated.
• A new hemizygous COL4A5 missense mutation (p.Gly491Asp) segregating with the AS phenotype was detected.
• A homozygous in-frame deletion in COL4A3 exon 1, affecting the signal peptide, was found in a recurrent AS mutation.

Implications:

• WES is crucial for achieving molecular diagnosis in AS families with previously unidentified genetic causes.
• Identifying novel variants expands the understanding of AS genetic heterogeneity and diagnostic capabilities.
• Functional validation of variants is essential for confirming pathogenicity and correlating genotype with phenotype in inherited kidney diseases.