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Updated: Jun 30, 2025
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
Identification of novel pathogenic variants of CUBN in patients with isolated proteinuria
Huihui Yang1, Lanfen He1, Hongjian Gong2
1Department of Nephrology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Center), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China.
Insights
Mutations in the cubilin (CUBN) gene can cause isolated proteinuria without anemia. This study identified new CUBN variants leading to non-progressive kidney disease, expanding knowledge of proteinuria.
Area of Science:
- Nephrology
- Genetics
- Molecular Biology
Background:
- Proteinuria is a risk factor for chronic kidney disease, but not all forms are detrimental.
- Isolated proteinuria can result from cubilin (CUBN) gene mutations, distinct from Imerslund-Gräsbeck syndrome (IGS).
Purpose of the Study:
- To investigate the genetic basis of non-progressive isolated proteinuria in four patients.
- To characterize novel and known CUBN variants associated with isolated proteinuria.
Main Methods:
- Whole-exome sequencing (WES) and next-generation sequencing were performed.
- CUBN variants were analyzed using cDNA-PCR sequencing, immunohistochemistry, and minigene assays.
- In silico prediction tools and 3D protein modeling were utilized.
Main Results:
- Four patients presented with isolated proteinuria and normal or elevated eGFR, lacking IGS symptoms.
- Identified CUBN variants included a homozygous splice-site mutation causing exon skipping and premature termination.
- Other identified variants were compound heterozygous splice-site, missense, and reported mutations affecting specific CUB domains.
Conclusions:
- Specific CUBN mutations can cause non-progressive isolated proteinuria.
- This expands the known spectrum of CUBN variants and aids understanding of proteinuria.
- Findings contribute to understanding the relationship between proteinuria and renal function.
Background:
Although proteinuria is long recognized as an independent risk factor for progressive chronic kidney diseases, not all forms of proteinuria are detrimental to kidney function, one of which is isolated proteinuria caused by cubilin (CUBN)-specific mutations. CUBN encodes an endocytic receptor, initially found to be responsible for the Imerslund-Gräsbeck syndrome (IGS; OMIM #261100) characterized by a combined phenotype of megaloblastic anemia and proteinuria.
Methods:
After analyzing their clinical and pathological characterizations, next-generation sequencing for renal disease genes or whole-exome sequencing (WES) was performed on four patients with non-progressive isolated proteinuria. CUBN biallelic pathogenic variants were identified and further analyzed by cDNA-PCR sequencing, immunohistochemistry, minigene assay, and multiple in silico prediction tools, including 3D protein modeling.
Results:
Here, we present four patients with isolated proteinuria caused by CUBN C-terminal biallelic pathogenic variants, all of which showed no typical IGS symptoms, such as anemia and vitamin B12 deficiency. Their urine protein levels fluctuated between +~++ and estimated glomerular filtration rate (eGFR) were normal or slightly higher. Mild mesangial hypercellularity was found in three children's renal biopsies. A homozygous splice-site variant of CUBN (c.6821+3 (IVS44) A>G) was proven to result in the exon 44 skipping and premature translation termination by cDNA sequencing and immunohistochemistry. Compound heterozygous mutations were identified among the other three children, including another novel splice-site variant (c.10764+1 (IVS66) G>A) causing the retention of first 4 nucleotides in intron 66 by minigene assay, two unreported missense mutations (c.4907G>A (p.R1636Q); c. 9095 A>G (p.Y3032C)), and two reported missense mutations in China (c.8938G>A (p.D2980N); c. 9287T>C (p.L3096P)), locating behind the vitamin B12-binding domain, affecting CUB11, CUB16, CUB22, CUB23, and CUB27 domains, respectively.
Conclusion:
These results demonstrate that above CUBN mutations may cause non-progressive and isolated proteinuria, expanding the variant spectrum of CUBN and benefiting our understanding of proteinuria and renal function.
