Type IV collagen related nephropathy caused by heterozygous variants in the COL4A3 or COL4A4 genes shows a wide phenotypic variability, with asymptomatic individuals being relatively common. A cystic phenotype in these cases is uncommon and rarely presents with nephromegaly mimicking autosomal dominant polycystic kidney disease (ADPKD).
We report a family with hereditary kidney disease showing an autosomal dominant inheritance pattern and marked phenotypic variability. Some family members were diagnosed with urate nephropathy, others met the Ravine-Pei criteria for ADPKD, and others were labeled as having chronic kidney disease of unknown etiology; five progressed to renal replacement therapy.
The proband, who presented with bilateral renal cysts fulfilling ADPKD criteria, along with microhematuria and non-nephrotic proteinuria, tested negative for PKD1 and PKD2 variants after sequential genetic analysis. Meanwhile, another family member studied for persistent microhematuria and non-nephrotic proteinuria underwent a renal biopsy that revealed thinning of the glomerular basement membrane on electron microscopy, suggesting Alport syndrome. Genetic testing in both individuals identified the c.735+2T>C (p?) variant in the COL4A4 gene, classified as likely pathogenic due to its disruption of a splicing site.
This case illustrates the phenotypic heterogeneity of heterozygous COL4A4-related Alport syndrome and highlights the importance of implementing genetic testing in the differential diagnosis of hereditary kidney disorders to prevent diagnostic delays with potential clinical consequences.
La nefropatía asociada al colágeno tipo IV por variantes en heterocigosis en los genes COL4A3 o COL4A4 presenta una amplia variabilidad fenotípica, siendo frecuente la presencia de individuos asintomáticos. El fenotipo quístico en estos casos es poco frecuente, y rara vez se presenta con nefromegalia simulando una poliquistosis renal autosómica dominante (PQRAD).
Presentamos una familia con enfermedad renal hereditaria de patrón autosómico dominante y variabilidad fenotípica significativa. Algunos miembros fueron diagnosticados de nefropatía úrica, otros de PQRAD según criterios de Ravine-Pei y otros de enfermedad renal crónica (ERC) no filiada, donde cinco progresaron a tratamiento renal sustitutivo.
El caso índice, con quistes renales bilaterales y criterios de PQRAD, microhematuria y proteinuria no nefrótica, fue estudiado secuencialmente para PKD1 y PKD2 con resultado negativo. Paralelamente, otro familiar estudiado por microhematuria persistente y proteinuria no nefrótica, fue sometido a biopsia renal que reveló adelgazamiento de la membrana basal glomerular en microscopía electrónica, lo que sugirió el diagnóstico de síndrome de Alport (SA). El estudio genético realizado en ambos identificó la variante c.735+2T>C (p?) en el gen COL4A4, considerada probablemente patogénica por afectar a un sitio de empalme (splicing).
Este caso ilustra la heterogeneidad fenotípica del SA con variantes en heterocigosis y destaca la necesidad de implementar técnicas genéticas en el diagnóstico diferencial de la patología renal hereditaria para evitar retrasos en el diagnóstico que pueden tener implicaciones clínicas.
Hereditary kidney diseases pose a diagnostic challenge due to their frequent phenotypic overlap, especially when clinical and imaging findings do not allow precise differentiation. Among them, autosomal dominant polycystic kidney disease (ADPKD) and Alport syndrome (AS) are classically well-differentiated entities based on their clinical presentation and genetic basis. ADPKD, primarily associated with PKD1 and PKD2 variants, is characterized by progressive renal cyst formation and autosomal dominant inheritance, while AS has traditionally been considered an X-linked or autosomal recessive disease caused by pathogenic variants in COL4A5, COL4A3, or COL4A4.1
In recent years, the growing identification of heterozygous carriers of COL4A3 or COL4A4 variants has revealed a broader clinical spectrum, ranging from asymptomatic individuals to cases with microhematuria, proteinuria, or progressive chronic kidney disease (CKD).2,3 The introduction of next-generation sequencing (NGS) has enabled recognition of atypical presentations of AS, including phenotypes mimicking focal segmental glomerulosclerosis (FSGS), IgA nephropathy, or even forms with renal cysts, observed in up to 38%–42% of heterozygous carriers, although the phenotype with nephromegaly and multiple ADPKD-like cysts is uncommon.3,4
These manifestations can lead to diagnostic errors when the genetic study is limited to PKD1/PKD2, highlighting the value of broad NGS panels in recognizing AS with a cystic phenotype. We present the case of a family with hereditary CKD and marked phenotypic variability, initially attributed to various diagnoses. The application of sequencing allowed identification of a pathogenic COL4A4 variant, reclassifying the condition as heterozygous AS with cystic expression, which exemplifies the evolution of molecular diagnosis in hereditary nephropathies and underscores the utility of broad genomic approaches in kidney diseases with a cystic phenotype.
Case presentationFamily history and clinical presentationThis is a family with several generations affected by CKD showing an apparent autosomal dominant inheritance pattern and notable phenotypic variability (Table 1). A pedigree was constructed spanning five generations (Fig. 1).
Clinical manifestations of family members.
| Case | Birth date | Sex | Clin. diagnosis | Prot. | Hematuria | Kidney cysts | Liver cysts | Lithiasis | Uric | Hearing loss | RRT (age) | Genetic diagnosis |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| III-2 | 1932 | Male | UAN | – | – | – | – | Yes | Yes | – | Yes (49) | – |
| III-4 | 1936 | Male | UAN | Yes | – | – | – | No | Yes | – | Yes (45) | – |
| III-7 | 1939 | Male | ADPKD | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes (75) | – |
| III-11 | 1947 | Female | UAN | – | Yes | – | – | No | Yes | – | Yes (45) | – |
| III-12 | 1947 | Female | UAN | – | Yes | – | – | No | Yes | – | Yes (?) | – |
| IV-1 | 1959 | Male | MH | No | Yes | No | No | No | Yes | No | No | |
| IV-3 | 1962 | Female | MH | Yes | Yes | Yes | Yes | No | – | – | No | COL4A4 |
| IV-6 | 1970 | Male | MH | Yes | Yes | No | No | No | No | No | No | COL4A4 |
| IV-10 | 1966 | Male | ADPKD | Yes | Yes | Yes | – | No | Yes | No | No | COL4A4 |
| IV-12 | 1969 | Male | ADPKD | – | – | Yes | – | – | – | Yes | – | |
| V-3 | 1996 | Male | MH | Yes | Yes | No | – | No | No | No | No | COL4A4 |
| V-5 | 2009 | Female | MH | Yes | Yes | No | No | No | No | No | No | COL4A4 |
| V-8 | 2001 | Male | MH | Yes | Yes | No | No | No | No | No | No | COL4A4 |
Clin. diagnosis: clinical diagnosis; UAN: uric acid nephropathy; ADPKD: autosomal dominant polycystic kidney disease; MH: microhematuria; prot: proteinuria; RRT: renal replacement therapy.
In the third generation, three siblings developed kidney disease around the fourth decade with different diagnoses: urate nephropathy associated with hyperuricemia and gout, polycystic kidney disease due to bilateral cysts on ultrasound, and progressive CKD of undetermined etiology. Five family members progressed to end-stage kidney disease, requiring renal replacement therapy between the fourth and sixth decades of life.
Index case 1 (IV-10)A 42-year-old male, referred in 2008 for bilateral renal cysts detected on abdominal ultrasound (Fig. 2) and normal renal function (serum creatinine 1.12 mg/dL, estimated glomerular filtration rate (eGFR) 77 mL/min/1.73 m²). Physical examination revealed no cutaneous or ophthalmological findings. He denied hearing loss. Blood pressure was 120/70 mmHg.
Given the family history of cystic kidney disease and the presence of multiple bilateral cysts on ultrasound (five to six in the left kidney and three to four in the right; positive Ravine-Pei criteria), ADPKD was initially suspected. Genetic testing for PKD1 and PKD2 was performed by Sanger sequencing, with a negative result. At that time (2016), molecular diagnosis of hereditary nephropathies was performed sequentially, guided by the predominant clinical phenotype.
At follow-up, renal volumes in 2018 were 330 cc (right kidney) and 700 cc (left kidney). By 2020, both kidneys measured 13–14 cm in length, with cysts up to 5–6 cm in the left kidney and 4–5 cm in the right, resulting in a severe cystic phenotype with nephromegaly.
Index case 2 (V-3)A family member residing in another province, under evaluation since age 13 (2009) for persistent microhematuria with preserved renal function (creatinine 0.75 mg/dL, eGFR: 140 mL/min/1.73 m²). No hearing loss at the time of evaluation.
Given the persistence of hematuria and intermittent proteinuria, a renal biopsy was performed. Light microscopy and immunofluorescence showed no abnormalities, but high-resolution electron microscopy revealed diffuse thinning of the glomerular basement membrane, along with focal areas of irregularity and lamination of the lamina densa, findings suggestive of early-stage AS.
Genetic studiesAlmost simultaneously, given the suspicion of AS based on histopathological findings in case 2, a targeted study of type IV collagen genes was performed; for case 1, considering the previous negative result for PKD1/PKD2, a genetic study using a 44-gene hereditary nephropathy NGS panel was carried out (Appendix B, Supplementary Material I).
The genetic study identified in both individuals the variant NM_000092.4: c.735+2T>C (p.?) in the COL4A4 gene in heterozygosity.
This variant is registered in ClinVar as pathogenic/likely pathogenic based on criteria PVS1, PM2, PP1, and PP3 according to the American College of Medical Genetics and Genomics (ACMG).5
Family segregation studyFamily screening through targeted search for the c.735+2T>C variant confirmed its presence in six available affected family members, all with varying degrees of renal involvement. Two asymptomatic relatives (children of index case 1, aged 12 and 14 years) tested negative for the variant and had normal urinalysis and renal function.
The presence of a pathogenic COL4A4 variant in this family has given rise to a diverse phenotype including microhematuria, proteinuria, and renal cysts in some members. This AS subtype shows variable penetrance and expressivity and typically slow progression toward end-stage renal failure. In unselected cohorts, the estimated risk of stage G5 CKD is below 3% by age 60 and slightly higher by age 80, while in clinical series, progression to end-stage disease has been reported in 15%–25% of cases, generally in the seventh decade.2
Analytical dataTable 2 summarizes the analytical data of the two main cases at the time of genetic diagnosis and their subsequent evolution.
Analytical data of the two main cases at time of genetic diagnosis and evolution.
| Parameter | Case 1 | Case 1 | Case 2 | Patient 2 |
|---|---|---|---|---|
| -Initial | After 10 years | Initial | (10 years) | |
| Age (years) | 42 | 52 | 13 | 23 |
| Serum creatinine (mg/dL) | 1.12 | 1.42 | 0.75 | 0.81 |
| eGFR (mL/min/1.73 m²) | 77 | 56 | 140 | 125 |
| Proteinuria (g/24 h) | 0.2 | 1.4 | – | 0.25 |
| Hematuria (RBCs/HPF) | 15−20 | 20−30 | 30−40 | 10−30 |
| Uric acid (mg/dL) | 7.9 | 4.2 | 8.6 | 8.3 |
| Blood pressure (mmHg) | 120/70 | 144/96 | 98/51 | 108/70 |
| Audiometry | – | Bilateral sensorineural hearing loss | – | No abnormalities |
| Treatment | Telmisartan 80 mg/day | Telmisartan 80 mg/day | – | Losartan 100 mg/day |
eGFR: estimated glomerular filtration rate; RBCs/HPF: red blood cells per high-power field.
In case 1, an adult patient who begins follow-up at age 42, a progressive increase in proteinuria is observed from 0.2 g/24 h to values around 1.4 g/24 h over a decade, without reaching nephrotic range, accompanied by gradual decline in glomerular filtration rate and the onset of arterial hypertension. Hematuria, present from the outset, remains at moderate levels.
The absence of nephrotic-range proteinuria combined with the presence of cystic kidney disease contributed to prioritizing genetic testing as the diagnostic tool.
Over time, bilateral sensorineural hearing loss was documented by audiometry, a characteristic finding of AS. Treatment with a renin-angiotensin system inhibitor was maintained throughout follow-up and likely contributed to slowing disease progression and controlling proteinuria.
In contrast, case 2 is a young patient who begins follow-up at age 13 and who, after 10 years of evolution, maintains normal renal function. The clinical course over the decade shows a decline in filtration rate consistent with physiological aging, remaining within the normal range. Hematuria, persistently present but mild, constitutes the main finding, while proteinuria is minimal and does not suggest significant renal damage. This patient maintains normal blood pressure values and has no auditory abnormalities. However, given that this is a very young individual, long-term evolution cannot be predicted with certainty.
Genetic diagnosis allowed genetic counseling for the family, identifying asymptomatic carriers who require monitoring and ruling out the disease in two young members who may be considered as potential renal donors in the future if needed.
DiscussionThis case illustrates the broad phenotypic variability present in patients carrying heterozygous pathogenic variants in COL4A3/COL4A4.
For years, this syndrome was considered almost exclusively a recessive or X-linked disorder, characterized by hematuria, proteinuria, and progression to CKD. However, pathogenic heterozygous variants in COL4A3 and COL4A4 have been shown to produce AS, with a broader and more variable clinical spectrum.6
One of the possible manifestations of these dominant forms is the presence of renal cysts, a feature previously considered unrelated to type IV collagenopathies. In a single-center retrospective study, Zeni et al. observed renal cysts in approximately 38% of patients with COL4A-related nephropathies, and in approximately 3%, a severe cystic phenotype with increased renal volume similar to ADPKD. Furlano et al. confirmed in a multicenter cohort of heterozygous carriers of pathogenic COL4A3/COL4A4 variants a higher prevalence of cysts compared to the general population, although the association of multiple cysts and nephromegaly typical of ADPKD is exceptional.3,4
In our family, the presence of renal cysts in the index case, along with a family history of CKD with apparent dominant inheritance, initially pointed toward ADPKD. However, atypical features such as persistent hematuria, non-nephrotic proteinuria, and negative genetic testing for PKD1/PKD2 redirected the diagnosis toward dominant AS.
Evolution of genetic diagnosis: from sequential study to next-generation sequencing panelThis case exemplifies the evolution in the diagnostic approach to hereditary nephropathies over the past decade. In 2016, when the initial genetic study was performed for the index case, Sanger sequencing of phenotype-guided selected genes was the standard strategy, characterized by low diagnostic yield, high cumulative cost, and longer time to results.
The incorporation of NGS revolutionized this field by enabling simultaneous analysis of multiple genes in a single assay. Renkema et al. (2014) demonstrated a significant increase in diagnostic yield, with rates of 30% in adults with CKD of unknown cause and 55%–80% in AS.7 In the context of cystic diseases, NGS panels have been validated that include polycystic kidney disease genes (PKD1, PKD2) alongside other genes associated with cystic phenotypes (COL4A3-5, HNF1B, UMOD), showing diagnostic superiority over strategies targeting only PKD1/PKD2.
These findings support current recommendations to use broad hereditary nephropathy panels or clinical exome in patients with cystic kidney disease.
The current trend points toward the use of clinical exome and whole exome sequencing as first-line strategies, especially in atypical cases or those with negative panels.
Implications of recent clinical guidelinesThe recognition of the phenotypic overlap between what has traditionally been called autosomal dominant AS and ADPKD is reflected in the most recent clinical guidelines; the KDIGO 2025 guidelines on ADPKD establish that, in the differential diagnosis of cystic kidney disease, type IV collagen-related diseases should be considered, particularly when hematuria and structural abnormalities of the glomerular basement membrane coexist. The guideline recommends considering genetic testing of COL4A genes in atypical cases of cystic kidney disease.8
Simultaneously, the European guideline on AS published by Torra et al. (2024) in Nephrology Dialysis Transplantation emphasizes that renal cysts may be a feature present in individuals with COL4A3, COL4A4, and COL4A5 variants and that documented cases exist where these variants coexist with clinical manifestations or even a diagnosis of ADPKD. The guideline recommends that genetic testing via broad panels is crucial for precise diagnoses in complex clinical presentations.2
Genetic diagnosis as an alternative to renal biopsyRenal biopsy, considered the gold standard for the diagnosis of nephropathies, is an invasive procedure with risks that limit its application. Beyond the associated risks, it has significant diagnostic limitations: histological findings are often nonspecific, it is contraindicated in advanced CKD or multiple cystic disease, and it does not allow the establishment of a specific molecular etiological diagnosis. Torra et al. (2024) document that, in patients with CKD of unknown cause, biopsy was not performed in 70% of cases and, when carried out, frequently showed nonspecific findings. Molecular genetic diagnosis via clinical exome allows avoidance of biopsy and provides molecular confirmation to interpret ambiguous histological findings.9
NGS-based genetic diagnosis established the definitive molecular etiological diagnosis in both patients, avoiding biopsy in one of them and demonstrating its value as a non-invasive, safer, and more precise alternative. Current guidelines recognize that genetic testing can obviate renal biopsy in patients with high suspicion of hereditary nephropathy, reserving this procedure for cases in which genetic testing is inconclusive.
Splicing variants: clinical importance and molecular mechanismsThe variant c.735+2T>C is located in an intronic region, specifically at the splice site. At this position, the change from a thymine (T) to a cytosine (C) occurs at the second nucleotide of the intron, a highly conserved region that is part of the splice donor site, whose canonical sequence is ‘GT’.
Variants affecting positions +1 or +2 of an intron are critical for the splicing machinery to correctly recognize the boundaries between exons and introns. Therefore, an alteration in this region typically interferes with normal mRNA processing. This may result in the loss of an entire exon, intron retention, or the use of an alternative splice site. The likely result is an aberrant mRNA that generates a truncated or non-functional protein.10
Impact of diagnostic delayThis family experienced a ‘diagnostic odyssey’ of more than two decades, reflecting the limitations of pre-NGS diagnostic strategies. This delay had multiple adverse consequences:
• Absence of adequate genetic counseling: family members were unable to make informed decisions about family planning or conduct targeted screening to identify at-risk relatives.
• Unnecessary and non-risk-free diagnostic procedures: the diagnostic uncertainty led to multiple studies, and in index case 2, a renal biopsy that could have been avoided with early genetic diagnosis.
• Psychosocial impact: the lack of a definitive diagnosis generates anxiety and uncertainty in patients and families.
Schott et al. (2025)11 documented that, in adult patients with CKD of genetic cause, the median time from first CKD diagnosis to genetic evaluation was 10.4 years, with many patients progressing to end-stage kidney disease before receiving a molecular diagnosis. Our case reflects this reality, highlighting the need to integrate genetic testing earlier in the evaluation of patients with CKD, particularly when there is a family history or atypical phenotypic features.
In summary, the clinical heterogeneity in patients with heterozygous variants in COL4A3/COL4A4 underscores the need to systematically incorporate genetic techniques in the diagnosis of hereditary nephropathies, in order to avoid delays with clinical implications and to facilitate both reproductive counseling and access to clinical trials.
Ethical considerationsAll genetic studies performed were conducted with the patients' informed consent for clinical purposes, to obtain a clinical diagnosis directed at their healthcare within their clinical process. This study has the approval of the Clinical Research Ethics Committee of the Hospital Universitario Virgen de las Nieves de Granada.
Declaration of Generative AI and AI-assisted technologies in the writing processDuring the preparation of this work, the authors used ChatGPT and Perplexity in order to improve the quality of the manuscript's writing. After using said tool, the authors reviewed and edited the content as necessary, assuming full responsibility for the content of the publication.
FundingThis research did not receive any specific grants from agencies in the public, commercial, or non-profit sectors.
All authors of this manuscript declare that the results presented in this work have not been previously published in whole or in part, except in abstract format. The authors have no conflict of interests.
We would like to express our gratitude to Dr. Juan Antonio Bravo Soto for providing us with the valuable clinical data collected from the GEEPAD registry. We also wish to acknowledge the tireless efforts of all our colleagues in the molecular genetics laboratory of Hospital Virgen de las Nieves and Hospital Clínico San Cecilio in Granada.
This manuscript is acknowledged as an integral part of the doctoral thesis entitled ‘Clinical and genetic characterization of rare hereditary kidney disease’.
The following is Supplementary data to this article:
