Deciphering the complexity: a case of kidney failure with co-inheritance of COL4A5 and APOE variants

Abstract

Background

Alport syndrome (AS) is the most common inherited glomerular disease among patients with chronic kidney disease. With exome sequencing now widely used in clinical practice, pathogenic variants in Alport-related genes (COL4A3/COL4A4/COL4A5) are increasingly identified in patients with diverse phenotypes, including proteinuria‑predominant disease and kidney failure of unknown etiology. Diagnostic complexity further increases when COL4A3/COL4A4/COL4A5 variants are co‑inherited with pathogenic variants associated with other genetic kidney disorders.

Case presentation

We reported a 31‑year‑old male presenting with kidney failure, significant proteinuria, familial hematuria and hyperlipidemia. Whole‑exome sequencing (WES) identified two pathogenic variants: a hemizygous COL4A5 variant (c.2105G > A; p.Gly702Asp) and a heterozygous APOE Kyoto variant (c.127C > T; p.Arg43Cys). Given the potential dual diagnosis of AS and lipoprotein glomerulopathy (LPG), a kidney biopsy was performed. Histologic examination revealed uneven thickness of the glomerular basement membrane consistent with the diagnosis of AS, but no LPG-related lesions were observed, indicating incomplete penetrance of APOE Kyoto variant. Cascade family screening detected APOE Kyoto variant in the patient’s father and elder sister, both of whom lacked proteinuria until follow-up period.

Conclusion

This case highlights the complementary role of kidney biopsy alongside WES in AS with complex genetic mechanisms. It also illustrates the incomplete penetrance of APOE Kyoto, common among Chinese carriers.

Introduction

Genetic testing has revolutionized the diagnosis and management of genetic kidney diseases (GKD). With the adoption of next-generation sequencing strategies—including customized gene panels, whole-exome sequencing (WES), and whole-genome sequencing—diagnostic yields of GKD have reached up to 65% in pediatric and early-onset chronic kidney disease (CKD) patients [1], and 9.3%-25% in adult-onset CKD patients [2–4].

Among all known causative genes of GKD except for polycystic kidney disease, Alport syndrome (AS) genes-COL4A3/COL4A4/COL4A5(COL4A3/4/5) are among the most frequently identified GKD genes in both adult and pediatric CKD patients [2, 5]. The phenotypic spectrum associated with COL4A3/4/5 has broadened considerably, ranging from isolated hematuria to progressive loss of kidney function, with or without sensorineural hearing loss and ocular abnormalities, and even to proteinuria-dominant presentations such as focal segmental glomerulosclerosis (FSGS) [6]. Adding to this complexity, there is a growing number of reported cases involving co-inheritance of COL4A3/4/5 variants and pathogenic variants in other GKDs, as well as AS patients with concurrent primary or secondary renal conditions [7]. In such scenarios, kidney biopsy remains indispensable for clarifying the underlying disease etiology.

We herein described a 31-year-old male presenting with kidney failure, significant proteinuria, familial hematuria, and hyperlipidemia. WES identified two pathogenic variants: a hemizygous COL4A5 variant (c.2105G > A; p.Gly702Asp) and a heterozygous APOE Kyoto variant (c.127C > T; p.Arg43Cys). Subsequent kidney biopsy confirmed histological features consistent with AS. Nevertheless, no histopathological findings suggestive of lipoprotein glomerulopathy (LPG) associated with the APOE Kyoto were observed, indicating incomplete penetrance of APOE Kyoto in this patient.

Case presentation

A 31-year-old male patient (II-2) was admitted to our hospital with exercise-induced rhabdomyolysis, characterized by markedly elevated serum creatine kinase (46,198 U/L, reference range 50–310 U/L) and myoglobin levels (4,070 ng/mL, reference < 121 ng/mL). His serum creatinine (sCr) was also elevated, ranging from 3.02 to 3.52 mg/dL (reference 0.49–1.30 mg/dL). After initial management with fluid resuscitation and urine alkalinization, sCr reduced to 2.51 mg/dL, corresponding to an estimated glomerular filtration rate (eGFR) of 33 mL/min/1.73 m². Laboratory evaluation further revealed microscopic hematuria (18–20 red blood cells per high-power field [HPF], reference 0–3/HPF) and prominent proteinuria (3.75 g/24 h, reference < 0.15 g/24 h). Serum albumin was within the normal range at 41 g/L (reference 35–55 g/L). Lipid profiling indicated mixed hyperlipidemia, with elevated triglycerides (3.23 mmol/L, reference < 2.5 mmol/L), total cholesterol (5.37 mmol/L, reference < 3.6 mmol/L), and low-density lipoprotein (LDL) cholesterol (3.13 mmol/L). Renal ultrasound showed no structural abnormalities. The patient had a 2-year history of hypertension, and his body mass index was 29 kg/m². No extra-renal manifestations, such as sensorineural hearing loss or ocular abnormalities, were identified.

Given the proband’s presentation and a family history of glomerular hematuria (in his 33-year-old elder sister and mother) and hyperlipidemia (in his father), WES was performed. Analysis of 385 known CKD-related genes [3] identified two pathogenic variants: a maternally inherited, hemizygous COL4A5 variant (c.2105G > A; p.Gly702Asp) and a paternally inherited, heterozygous APOE variant (c.127C > T; p.Arg43Cys) (Fig. 1). According to the American College of Medical Genetics and Genomics (ACMG) guidelines [8], the COL4A5 variant (c.2105G > A; p.Gly702Asp) was categorized as likely pathogenic (PM1 + PM2 + PP1 + PP3 + PP4). The APOE variant (c.127C > T; p.Arg43Cys), also categorized as likely pathogenic (PS3 + PM2 + PP3), was historically designated as APOE Kyoto [9]. Subsequent APOE genotyping [10] revealed ε3/ε4 genotypes in the proband and his sister, ε3/ε3 in their mother, and ε2/ε4 in their father.

Fig. 1.

Family pedigree with clinical phenotypes (a) and sequencing chromatograms (b)

The coexistence of both pathogenic variants prompted a diagnostic kidney biopsy to assess for possible concurrent AS and LPG. Light microscopy (LM) revealed FSGS involving 4 of 7 glomeruli. No cellular proliferation, lipid droplets, or myoglobin casts were observed. Moderate tubular atrophy and interstitial fibrosis were present. Vascular changes included arteriolar hyalinosis and intimal fibrosis with luminal stenosis. Immunofluorescence showed segmental granular mesangial C3 deposition. Oil Red O staining was negative. Electron microscopy demonstrated irregular glomerular basement membrane (GBM) thickening with alternating thin and thickened segments, along with partial effacement of podocyte foot processes. Neither electron-dense deposits or lipoprotein thrombi were observed (Fig. 2).

Fig. 2.

Kidney biopsy findings. (a) Diffuse interstitial inflammation with tubular atrophy (hematoxylin-eosin [HE], ×200). (b) Segmental glomerulosclerosis (yellow arrow) (periodic acid-Schiff [PAS], ×400). (c) Oil Red O staining on frozen sections showing negative lipid deposition (Oil red O, ×400). (d) Electron microscopy showing uneven GBM thickness with focal basket-weave appearance (orange arrow), along with partial podocyte foot process effacement (yellow arrows); no electron-dense deposits or lipoprotein thrombi were observed. (e) Electron microscopy demonstrating a thin GBM, with the thinnest segments approximately 0.11–0.18 μm (yellow arrows)

The histopathological findings confirmed the diagnosis of AS and indicated the incomplete penetrance of APOE Kyoto in this case. Accordingly, the patient was started on a triple regimen of valsartan, dapagliflozin and finerenone (with appropriate disclosure regarding the off-label use of finerenone), in combination with fenofibrate and atorvastatin. Over the ensuing 6-month follow-up period, lipid profiles showed consistent improvement and eGFR increased to 37 mL/min/1.73 m², although proteinuria remained largely unchanged (Fig. 3). During the follow-up period, the sister didn’t present with proteinuria and the father didn’t present with hematuria or proteinuria, and neither of them had decreased eGFR.

Fig. 3.

Longitudinal follow-up of the patient. (a) Changes in serum creatinine (sCr), estimated glomerular filtration rate (eGFR), and proteinuria during the subsequent 6-month follow-up. (b) Changes in total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and ApoE levels during the subsequent 6-month follow-up

Discussion and conclusion

Different from co-occurrent AS and LPG case described previously demonstrating typical phenotypes of both diseases [11], the co-inheritance of APOE Kyoto variant in our X-linked Alport syndrome (XLAS) case apparently didn’t have an additive effect on AS phenotype as kidney biopsy didn’t show the evidence of LPG. Our case illustrated the correct diagnostic workup of a patient with suspected GKD favoring genetic testing prior to kidney biopsy. Otherwise, APOE Kyoto variant might be missed if a physician orders phenotype-driven panel sequencing not including the APOE gene or simply orders COL4A3/4/5 Sanger sequencing based on the histological characteristics of AS.

Current clinical guidelines [12] recommend genetic testing as a first-line diagnostic tool for patients presenting with CKD or kidney failure, particularly when accompanied by a family history of kidney disease or extra-renal features suggestive of a genetic etiology. This recommendation is supported by mounting evidences demonstrating the diagnostic utility of approaches such as WES and targeted gene panel sequencing in patients with suspected monogenic CKD. Notably, genetic testing has been shown to achieve diagnostic yields of 30–40% in patients with kidney disease of unknown etiology, especially when kidney biopsy yields inconclusive morphological findings or is contraindicated [13]. Exome sequencing has further demonstrated its utility in identifying phenocopies among patients clinically suspected of GKD. The most commonly observed phenocopies are associated with AS presenting clinically as FSGS [14]-a finding consistent with the LM diagnosis in our patient with XLAS. Given the above evidence, there remains ongoing debate within the nephrologist regarding the extent to which, and under which circumstances, genetic testing may supplant kidney biopsy. In our case with the co-inheritance of two pathogenic variants in two distinct GKD, kidney biopsy is warranted as whether AS and LPG co-occurred needed to be confirmed not only because the patient presented with the overlapping symptoms of both diseases such as prominent proteinuria and kidney failure, but also because the incomplete penetrance of APOE Kyoto among Chinese carriers is rather high (approximately 44.4%) [15]. Therefore, whether APOE Kyoto modified the phenotype of AS in our XLAS patient needed to be determined.

COL4A5 variant types, clinical and pathological factors such as proteinuria, hearing loss and type IV α5 expression on the GBM have been established as the factors altering the disease progression of XLAS [16]. Beyond these factors, modifying genetic variants as well as concurrent primary or secondary kidney diseases may account for the accelerated decline in eGFR observed in certain XLAS patients. APOE is an important apolipoprotein that plays a central role in lipoprotein metabolism. Abnormal lipoprotein metabolism caused by APOE variants may lead to APOE-related glomerular diseases including APOE2 homozygous glomerulopathy and LPG caused by heterozygous APOE variants [10]. LPG is a rare kidney disease characterized histologically by lipid deposition in glomeruli and tubular epithelial cells, and clinically manifests as moderate to severe proteinuria, hematuria, and progressive renal impairment. Cases of LPG coexisting with primary or secondary glomerulopathies-such as AS [11], IgA nephropathy [17] and collagen type III glomerulopathy [18]-have been reported in Chinese patients. Given that most LPG cases occur in the Asian populations and APOE Kyoto represents the predominant variant in China [15], such co‑occurrences warrant particular attention. Similar to our pedigree, in a previous reported case of APOE Kyoto LPG co-occurred with collagen type III glomerulopathy, three family members carrying APOE Kyoto variant didn’t have LPG-related clinical phenotype [18]. The hypnosis is that the local kidney microenvironment, defective macrophages, oxidative stress and environmental factors may contribute to the full-blown clinical presentation of LPG [19]. Given that the age at diagnosis of LPG ranges from 7 to 72 years across all reported cases [20], both the proband and the two family members carrying APOE Kyoto variant require long‑term follow‑up and systematic evaluation for possible late‑onset development of LPG.

Finerenone added to angiotensin receptor antagonist/sodium-glucose cotransporter 2 (SGLT2) blockade demonstrated the efficacy in reducing proteinuria and attenuating CKD progression in a preclinical trial in mice with AS [21]. More recently, a pilot study conducted in four AS patients also suggested that finerenone induces an appreciable reduction in proteinuria on top of dual renin-angiotensin system (RAS)/SGLT2 blockade [22]. Thus, with the aim of reducing proteinuria and delaying kidney function deterioration, we initiated triple RAS/SGLT2/mineralocorticoid receptor blockage with close monitoring of eGFR changes and serum potassium levels. Improvement of eGFR and lipid profile were observed while proteinuria remained prominent at a follow-up of 6 months. Anyhow, whether finerenone can be added to a RAS inhibitor and an SGLT2 inhibitor for treatment of AS still awaits results from prospective large scale randomized studies.

In conclusion, this case underscores the value of integrating WES and renal biopsy to resolve diagnostic uncertainty in AS cases involving complex genetic mechanisms. Clinicians should be aware of the incomplete penetrance of APOE Kyoto, which is not uncommon among Chinese carriers and justifies the need for long-term clinical surveillance.

Abbreviations

GKD

Genetic kidney disease

WES

Whole exome sequencing

CKD

Chronic kidney disease

AS

Alport syndrome

FSGS

Focal segmental glomerulosclerosis

LPG

Lipoprotein glomerulopathy

sCr

Serum creatinine

eGFR

Estimated glomerular filtration rate

HPF

High-power field

ACMG

American College of Medical Genetics and Genomics

LM

Light microscopy

GBM

Glomerular basement membrane

HE

Hematoxylin-eosin

PAS

Periodic acid- Schiff

TG

Triglycerides

TC

Total cholesterol

LDL-C

Low-density lipoprotein cholesterol

XLAS

X-linked Alport syndrome

SGLT2

Sodium-glucose cotransporter 2

RAS

Renin-angiotensin system

Author contributions

X.Y.Z. and S.J. wrote the manuscript. F.J.L. and Y.Q.S. reviewed and edited the final version. S.J. provided figures; Y.Q.S. also contributed to the clinical follow-up of the patient. X.T.D, C.L.Y and Z.Y.Z were responsible for data collection. All authors reviewed and approved the final manuscript.

Funding

This study was supported by the SJTU Research Physician Fund (2024), the National Natural Science Foundation of China Fund (82470706, 82470761, 82500817), the Shanghai Scientific and Technological Committee Fund (24YF2727300, 25ZR1402064) and the Construction Project of the “Discipline Peak Climbing Plan” of Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine (XKPF2024B301).

Data availability

The datasets generated and/or analysed during the current study are available in the [PRJCA048559] repository, [ [BIG Sub - BioProject (cncb.ac.cn)](https://ngdc.cncb.ac.cn/gsub/submit/bioproject/list)]

Declarations

Ethics statement

The study was approved by the Institutional Review Board (or Ethics Committee) of Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine (XHEC-C-2024-185-2).

Consent to participate

The present work was conducted in accordance with the Declaration of Helsinki and informed consent was obtained from the patient.

Consent for publication

Written informed consent for publication of their clinical details was obtained from the patient.

Competing interests

The authors declare no competing interests.