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Updated: Aug 23, 2025
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
Mutation Analysis of Thin Basement Membrane Nephropathy
Yosuke Hirabayashi1, Kan Katayama1, Mutsuki Mori1
1Department of Cardiology and Nephrology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan.
Abstract:
Thin basement membrane nephropathy (TBMN) is characterized by the observation of microhematuria and a thin glomerular basement membrane on kidney biopsy specimens. Its main cause is heterozygous mutations of COL4A3 or COL4A4, which also cause late-onset focal segmental glomerulosclerosis (FSGS) or autosomal dominant Alport syndrome (ADAS). Thirteen TBMN cases were analyzed using Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and exome sequencing. Ten heterozygous variants were detected in COL4A3 or COL4A4 in nine patients via Sanger sequencing, three of which were novel variants. The diagnostic rate of "likely pathogenic" or "pathogenic" under the American College of Medical Genetics and Genomics guidelines was 53.8% (7 out of 13 patients). There were eight single nucleotide variants, seven of which were glycine substitutions in the collagenous domain, one of which was a splice-site single nucleotide variant, and two of which were deletion variants. One patient had digenic variants in COL4A3 and COL4A4. While MLPA analyses showed negative results, exome sequencing identified three heterozygous variants in causative genes of FSGS in four patients with no apparent variants on Sanger sequencing. Since patients with heterozygous mutations of COL4A3 or COL4A4 showed a wide spectrum of disease from TBMN to ADAS, careful follow-up will be necessary for these patients.
Insights
Genetic analysis of thin basement membrane nephropathy (TBMN) revealed heterozygous mutations in COL4A3 or COL4A4 genes. These mutations are linked to a spectrum of kidney diseases, necessitating careful patient monitoring.
Area of Science:
- Nephrology
- Genetics
- Molecular Biology
Background:
- Thin basement membrane nephropathy (TBMN) presents with microhematuria and a thinned glomerular basement membrane.
- Heterozygous mutations in COL4A3 or COL4A4 are primary causes of TBMN, and can also lead to focal segmental glomerulosclerosis (FSGS) or autosomal dominant Alport syndrome (ADAS).
- Understanding the genetic basis of TBMN is crucial for diagnosing and managing associated kidney diseases.
Purpose of the Study:
- To investigate the spectrum of genetic variants in COL4A3 and COL4A4 in patients with TBMN.
- To evaluate the diagnostic yield of different genetic testing methods, including Sanger sequencing and exome sequencing.
- To correlate genetic findings with clinical phenotypes ranging from TBMN to ADAS.
Main Methods:
- Analysis of 13 TBMN cases using Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and exome sequencing.
- Variant classification based on American College of Medical Genetics and Genomics guidelines.
- Identification of single nucleotide variants, splice-site variants, deletion variants, and digenic variants.
Main Results:
- Ten heterozygous variants in COL4A3 or COL4A4 were identified in nine patients via Sanger sequencing, with three novel variants.
- The diagnostic rate for likely pathogenic or pathogenic variants was 53.8% (7/13 patients).
- Exome sequencing detected additional causative variants in four patients not identified by Sanger sequencing, including digenic variants in one patient.
Conclusions:
- Heterozygous mutations in COL4A3 or COL4A4 are key genetic drivers of TBMN and related kidney disorders.
- Exome sequencing offers a higher diagnostic yield for identifying causative variants compared to Sanger sequencing alone.
- The wide clinical spectrum from TBMN to ADAS underscores the need for long-term monitoring of affected individuals.
