Clinical and genetic characterization of a cohort of proteinuric patients with biallelic CUBN variants

Identification of CUBN variants in triplets with a 20-year history of proteinuria

CUBN encodes cubilin, which plays a role in the reabsorption of glomerular-filtered albumin in the proximal tubule. CUBN-related proteinuria was recently established as a new disease concept and may be present in proteinuric cases that were previously undiagnosed either genetically or histologically. We herein report a case of triplets diagnosed with chronic benign proteinuria due to CUBN variants 20 years after its onset. The proband, the first child of triplets, tested positive for urinary protein several times during the neonatal period. A urine screening test at 3 years old was positive. Proteinuria persisted for years within a non-nephrotic range. Kidney biopsy at 8 years old revealed minor glomerular abnormalities. Renin-angiotensin system inhibitors were started for albumin-based proteinuria but were ineffective. Since the two other triplets had similar courses, analyses of the NPHS1/2 and WT1 genes were performed but revealed no abnormalities. The triplets transitioned to adult care at 15 years old. CUBN-related proteinuria was reported in 2020; therefore, we re-analyzed their DNA samples and identified compound heterozygous variants in CUBN in all three triplets. The molecular diagnosis of CUBN-related proteinuria will save patients from unnecessary treatments and concerns about renal prognosis.

Identification of novel pathogenic variants of CUBN in patients with isolated proteinuria

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.

Isolated benign persistent proteinuria with novel association of CUBN (cubilin) variants

We present two siblings with persistent proteinuria and normal kidney function, each carrying the same compound heterozygous variants in the CUBN gene. The CUBN-related phenotype appears to be dependent upon both variant type and the domain site within the gene. Knowledge of CUBN status may allow for avoidance of invasive testing.

Clinical and genetic characterization of children with cubilin variants

BACKGROUND

Cubilin is one of the receptor proteins responsible for reabsorption of albumin in proximal tubules and is encoded by the CUBN gene. We aimed to evaluate clinical and genetic characterization of six patients with proteinuria who had CUBN mutations.

METHODS

Patients' characteristics, serum creatinine, albumin, vitamin B₁₂ levels, urine analysis, spot urine protein/creatinine, microalbumin/creatinine, beta-2 microglobulin/creatinine ratios, estimated glomerular filtration rates (eGFR), treatments, kidney biopsies, and genetic analyses were evaluated.

RESULTS

Six patients (2 female, 4 male) with an incidental finding of proteinuria were evaluated. Mean admission age and follow-up time were 7.3 ± 2.9 and 6.5 ± 5.6 years, respectively. Serum albumin, creatinine, and eGFR were normal; urine analysis revealed no hematuria, and C3, C4, ANA, and anti-DNA were negative; kidney ultrasonography was normal for all patients. Urine protein/creatinine was 0.9 ± 0.3 mg/mg, and microalbumin was high in all patients. Serum vitamin B₁₂ was low in two patients and normal in four. Kidney biopsy was performed in four patients, three demonstrated normal light microscopy, and there was one focal segmental glomerulosclerosis (FSGS). Genetic tests revealed four homozygous and two compound heterozygous mutations in the C-terminal part of cubilin. All patients had normal eGFR and still had non-nephrotic range proteinuria at last visit.

CONCLUSIONS

CUBN gene mutations should be considered in patients with isolated non-nephrotic range proteinuria and normal kidney function. Diagnosing these patients, who are thought to have a better prognosis, is important in terms of avoiding unnecessary treatment and predicting prognosis. CUBN gene mutations may also present as FSGS which extends the spectrum of renal manifestation of these patients. A higher resolution version of the Graphical abstract is available as Supplementary information.

Imputation-powered whole-exome analysis identifies genes associated with kidney function and disease in the UK Biobank

Genome-wide association studies have discovered hundreds of associations between common genotypes and kidney function but cannot comprehensively investigate rare coding variants. Here, we apply a genotype imputation approach to whole exome sequencing data from the UK Biobank to increase sample size from 166,891 to 408,511. We detect 158 rare variants and 105 genes significantly associated with one or more of five kidney function traits, including genes not previously linked to kidney disease in humans. The imputation-powered findings derive support from clinical record-based kidney disease information, such as for a previously unreported splice allele in PKD2, and from functional studies of a previously unreported frameshift allele in CLDN10. This cost-efficient approach boosts statistical power to detect and characterize both known and novel disease susceptibility variants and genes, can be generalized to larger future studies, and generates a comprehensive resource ( https://ckdgen-ukbb.gm.eurac.edu/ ) to direct experimental and clinical studies of kidney disease.

Podocytopathy and Glomerular Basement Membrane Anomalies in Two Patients With Cubilin Gene Mutations

Proteinuria is a frequent finding in pediatric patients and in most cases, it is intermittent or transient. When proteinuria is moderate/severe and persistent, it may require an extensive complementary study, histopathological examination and genetic test, in order to clarify its etiology. Cubilin (CUBN) is a large glycosylated extracellular protein, initially detected in proximal tubular cells, and later in podocytes. Isolated persistent proteinuria caused by cubilin gene mutations is rare, only a few cases have been reported in the literature and even fewer patients underwent renal biopsy and electron microscopy that could help to elucidate the pathogenesis of the disease. The authors describe two pediatric clinical cases referred to pediatric nephrology consultation due to persistent proteinuria. Neither of them had any other complaints, and renal function and immunological and serological studies were normal. Renal histopathology showed podocytes changes and glomerular basal membrane alterations suggestive of Alport Syndrome. The genetic study identified two heterozygous variants in the cubilin gene in both, also later identified in their parents. They were started on ramipril, with improvement in proteinuria, and both patients remain asymptomatic and without changes in renal function. At present, due to the uncertainty of prognosis, it is suggested to keep CUBN gene mutation patients under close surveillance of proteinuria and renal function. The variable ultrastructural patterns of podocytopathy and glomerular basal membrane alterations in kidney biopsies of pediatric patients with proteinuria should lead to the diagnostic possibility of CUBN gene mutation in the differential diagnosis.

Isolated Proteinuria Caused by CUBN Gene Mutations: A Case Report and Review of the Literature

Mutations in the cubilin (CUBN) gene commonly cause Imerslund-Gräsbeck syndrome, while isolated proteinuria as a result of CUBN variations is rarely reported. The clinical manifestation is mainly chronic isolated proteinuria in the non-nephrotic range. However, findings to date suggest that isolated proteinuria associated with abnormalities in the CUBN gene is benign and does not affect long-term prognosis of kidney function. We identified 2 patients with isolated proteinuria triggered by compound heterozygous CUBN mutations. Renal functions of both patients remained normal over a 10-year follow-up period, supporting the benign nature of proteinuria caused by CUBN gene variations. Two novel mutation sites were detected, expanding the genotypic spectrum of CUBN variations. In addition, etiology, pathogenesis, clinical manifestations, auxiliary examination, and treatment of the condition were reviewed, with the aim of providing further guidance for clinical management.