Presumed COL4A3/COL4A4 Missense/Synonymous Variants Induce Aberrant Splicing

Area of Science:

• Genetics
• Molecular Biology
• Nephrology

Background:

• Incorrect interpretation of missense and synonymous variants in COL4A3/COL4A4 genes can lead to misdiagnosis and flawed genetic counseling.
• Accurate variant classification is essential for diagnosing hereditary kidney diseases like Alport syndrome and thin basement membrane nephropathy.

Purpose of the Study:

• To evaluate the pathogenicity of presumed COL4A3/COL4A4 missense and synonymous variants detected by next-generation sequencing.
• To provide evidence for accurate molecular diagnosis and genetic counseling in patients with hereditary kidney diseases.

Main Methods:

• Retrospective analysis of clinical findings and genetic data from patients with hereditary kidney diseases.
• In vitro minigene assay to assess the effect of presumed COL4A3/COL4A4 variants on RNA splicing.
• Utilized Human Splicing Finder for initial splicing predictions.

Main Results:

• Five unclassified COL4A3/COL4A4 variants were analyzed in five patients.
• COL4A3 missense variant p.(Leu1598Arg) and synonymous variant p.(Thr255Thr) were found to affect RNA splicing.
• COL4A3 variant c.3566G>A [p.(Gly1189Glu)] and COL4A4 variants c.3990G>A [p.(Pro1330Pro)], c.4766C>T [p.(Pro1589Leu)] showed no deleterious effect on splicing.
• Patients with pathogenic variants were diagnosed with autosomal recessive Alport syndrome or suspected of having thin basement membrane nephropathy.

Conclusions:

• COL4A3 missense variant p.(Leu1598Arg) and synonymous variant p.(Thr255Thr) demonstrably affect RNA splicing.
• Transcript analysis of unclassified exonic variants is critical for precise molecular diagnosis and genetic counseling.
• The reliability of in silico splicing prediction tools for exonic substitutions requires enhancement.