Familial WT1-associated nephropathy - 46, XY Frasier syndrome and 46, XX steroid-resistant nephrotic syndrome in female siblings: A case report and review of literature

Abstract

BACKGROUND

The Wilms tumor 1 (WT1) mutation is significantly associated with steroid-resistant nephrotic syndrome (SRNS) in children. It causes a spectrum of disorders, including Frasier and Denys-Drash syndromes. The WT1 gene encodes a transcription factor essential for renal, gonadal, and mesothelial development. The prevalence of Frasier syndrome is 1 in 1000000. Frasier syndrome presents with childhood onset of SRNS, progressing to end-stage kidney disease, has an XY female phenotype, delayed puberty, and gonadal tumor risk. Two siblings with identical WT1 mutations but differing phenotypes offer important clinical insights.

CASE SUMMARY

We report a rare familial occurrence of shared mutation of WT1 (at intron 9 splice site: C.1432+5G>A) and COL4A5 genes in two siblings. The elder sibling (46, XY) presented with infantile steroid-resistant nephrotic syndrome and rapidly deteriorating and progressing to end-stage kidney disease with XY karyotype. The genetic testing confirmed the diagnosis of Frasier syndrome associated with a WT1 mutation in the elder sibling. She is currently on maintenance dialysis, awaiting renal transplantation. The younger sibling presented at age four with facial edema and SRNS with slower disease progression and no apparent gonadal anomalies. Her renal biopsy revealed minimal change disease, and she maintains stable renal function under antiproteinuric therapy. Genetic testing confirmed the diagnosis of WT1 mutation with 46, XX karyotype in the younger sibling. Both siblings also carried a COL4A5 gene variant of uncertain significance. Family history reveals consanguineous marriage and a similar presentation in a sibling.

CONCLUSION

Despite identical mutations, phenotypic differences highlight complex genotype-phenotype relations, stressing the need for research, genetic counseling, and family member screening.

Key Words: Frasier syndrome; Pediatric; Steroid-resistant nephrotic syndrome; Karyotype; WT1 mutation; Case report

Core Tip: This report describes two siblings with identical pathogenic Wilms tumor 1 but distinct karyotypes (46, XY and 46, XX) leading to divergent clinical presentations. The elder sibling had classical features with early-onset steroid-resistant nephrotic syndrome with rapidly deteriorating renal function, while the younger sibling presented with steroid-resistant nephrotic syndrome only without gonadal abnormalities. This rare familial occurrence emphasizes sex-dependent phenotypic variability despite identical mutations, expanding understanding of Wilms tumor 1-related disorders. The findings underscore the importance of genetic testing, detailed family evaluation, and long-term monitoring to guide management in such rare syndromic presentations.

INTRODUCTION

Steroid-Resistant Nephrotic Syndrome (SRNS) is a challenging clinical entity in pediatric nephrology, representing a significant subset of cases that fail to respond to standard corticosteroid therapy. Approximately up to 25% of SRNS cases are attributed to mutations in genes predominantly expressed in podocytes, specialized epithelial cells essential for the integrity of the glomerular filtration barrier[1-3]. Among these genes, Wilms tumor 1 (WT1) was the first identified to harbor pathogenic variants associated with SRNS[4]. Initially recognized as a tumor suppressor gene linked to Wilms tumor. WT1 disorder is characterized by congenital or infantile onset of SNRS, mainly with glomerular lesions[5].

Frasier syndrome is a rare autosomal dominant genetic disorder caused by mutations in the WT1 gene, characterized by SRNS with onset in early childhood, progressive kidney failure, and disorders of sex development. The prevalence rate of Frasier syndrome is less than 1 in 1000000, with approximately 150 cases reported worldwide to date[6]. WT1 disorder is caused by a heterozygous pathogenic variant in the WT1 gene. The WT1 gene primarily functions in the regulation of genitourinary system development. WT1 mutations cause a wide spectrum of renal and extrarenal manifestations[5]. WT1 encodes a transcription factor containing an N-terminal transactivation domain (exon 1) and four zinc fingers at the C-terminus (exons 7-10). It serves as a regulatory transcription factor for both renal and gonadal development and plays multiple essential roles in the embryonic development of various systems, including the central nervous system and mesothelial organs[7].

Depending on the exon involved, pathogenic variants of the WT1 gene can lead to Denys-Drash syndrome (DDS) or Frasier syndrome. Both conditions are characterized by progressive glomerulopathy and a predisposition to Wilms’ tumor[8]. Frasier syndrome is caused by heterozygous mutations in the donor splice site in intron 9 of the Wilms tumor gene, resulting in insertion of the amino acids lysine (K), threonine (T) and serine (S), altering the ratio of +KTS/-KTS isoforms of WT1. A splice site at exon 9 inserts three additional amino acids between the third and the fourth zinc finger (usually referred to as the KTS splice insert). Mutations in the KTS site result in Frasier syndrome[9]. A group of mostly missense mutations in exons 8 and 9 affect the zinc-finger domains, which impair the DNA-binding capacity of WT1 and cause either DDS or Meacham syndrome[10].

Patients with Frasier syndrome have delayed or poor pubertal development. It is also associated with a high risk of developing End Stage Kidney Disease, gonadal tumors, and male pseudo hermaphroditism (female external genitalia with XY sex chromosomes) in the second or third decade of life[6,11]. The rarity and complex inheritance of WT1-related nephropathies make familial occurrences extremely uncommon. Here, we report the clinical and genetic findings in two female siblings with identical WT1 mutations who presented with differing phenotypes: One consistent with Frasier syndrome (XY karyotype) and the other with SRNS with XX karyotype. This case provides valuable insight into the spectrum of WT1-associated disorders and highlights the variable expressivity that can occur even within the same family.

CASE PRESENTATION

Chief complaints

Elder sibling: A female child presented with intermittent periorbital puffiness in the last 2 months at the age of one year (December 2015). Her parents consulted a pediatric nephrologist. After clinical examination, he advised urine examination, which revealed proteinuria, confirming the case of infantile nephrotic syndrome with right-sided hydronephrosis. She was treated with oral methylprednisolone 2 mg/kg/day for a six-week duration; however, proteinuria persisted, and she was resistant to steroids and diagnosed with SRNS. Then she was treated with calcineurin inhibitor cyclosporine (4-5 mg/kg in two divided doses) with continuous monitoring of kidney function and serum electrolytes. After an initial response, over time, the response diminished, with intermittent periods of clinical improvement. Eventually, she developed resistance to calcineurin inhibitors, and cyclosporine was discontinued.

Younger sibling: Her younger sister presented with similar symptoms, i.e. facial edema at the age of 4 years (June 2019) and was evaluated by a pediatric nephrologist. Urinalysis confirmed nephrotic syndrome. She was prescribed a full course of corticosteroids at 2 mg/kg/day for six weeks. However, the proteinuria persisted, and she was resistant to it. The pediatric nephrologist confirmed a clinical diagnosis of primary SRNS.

History of present illness

Elder girl: Her renal function progressively declined, eventually leading to chronic kidney disease.

Younger girl: She is under antiproteinuric therapy with stable renal function.

History of past illness

Elder sibling: There is no history of any past medical illness.

Younger sibling: Elder sister was diagnosed with Frasier syndrome 2 years ago (2018).

Personal and family history

No known genetic disorders have been reported in either parent’s family or the maternal lineage. The mother, of Nepali origin residing in India, has a history of consanguineous marriage and two miscarriages prior to the birth of these daughters. A similar clinical presentation was reported in a female child from her previous marriage; however, no medical records are available to verify this.

Physical examination

Elder sibling: On examination, the patient appeared alert and well-oriented. Periorbital and facial edema were noted, without generalized edema or ascites. Vital signs were stable with a normal heart rate, blood pressure, and respiratory rate. Cardiovascular, respiratory, abdominal, and neurological examinations were unremarkable. No lymphadenopathy or organomegaly was detected. Growth parameters were appropriate for age.

Younger sibling: On examination, the patient with periorbital and facial edema was noted, without generalized edema or ascites, with stable vital parameters. Cardiovascular, respiratory, abdominal, and neurological examinations were unremarkable. No lymphadenopathy or organomegaly was detected. Growth parameters were appropriate for age.

Laboratory examinations

Elder sibling: (1) Renal biopsy: In view of clinically diagnosed SRNS, the pediatric nephrologist advised her renal biopsy (January 2016), which revealed focal mesangial-proliferative glomerulonephritis; (2) Genetic analysis: As she was a case of SRNS and rapid progressive renal dysfunction, she was advised to undergo genetic testing (August 2018). Next generation sequencing for the WT1 and COL4A5 genes revealed presence of two pathogenic variants: A heterozygous variant in the WT1 gene (chr11: 32413513C>T; c.1432+5G>A, located in intron 9 at the 5’ splice site), and a hemizygous variant in the COL4A5 gene (chrX: 107846262C>G; c.2215C>G; p.Pro739Ala in exon 28). These findings are consistent with a genetic etiology of SRNS (Figure 1); and (3) Karyotype analysis: Following the genetic testing results, the nephrologist recommended karyotyping (August 2018) for further evaluation. It showed a 46, XY chromosomal complement in a phenotypic female (Figure 2).

Figure 1 The figure illustrates the genetic evaluation of the siblings. A: Whole exome sequencing of elder daughter; B: Sanger-based genome sequencing of younger daughter. Whole exome sequencing of the elder daughter, performed using next-generation sequencing, identified a heterozygous splice-site variant in intron 9 of the WT1 gene (c.1432+5G>A), which is classified as likely pathogenic and consistent with a diagnosis of Frasier syndrome. Additionally, a hemizygous variant in exon 28 of the COL4A5 gene (c.2215C>G; p.Pro739Ala) was detected in the elder sibling. In the younger daughter, Sanger-based genomic sequencing identified the same WT1 variant in a heterozygous state, along with the COL4A5 variant in a heterozygous form. WT1: Wilms tumor 1; COL4A5: The alpha5 chains of collagen type IV.

Figure 2 The figure presents the karyotype analysis of two siblings affected by primary steroid-resistant nephrotic syndrome. A: Chromosomal analysis report - elder daughter; B: Chromosomal analysis report - younger daughter. The elder sibling exhibits a male karyotype (46, XY), which supports the molecular diagnosis of Frasier syndrome associated with a WT1 gene mutation. In contrast, the younger sibling, also diagnosed with steroid-resistant nephrotic syndrome, shows a normal female karyotype (46, XX) with no detectable chromosomal abnormalities. SRN: Steroid-resistant nephrotic.

Younger sibling: (1) Renal biopsy: Due to the family history of SRNS in the elder sibling, the pediatric nephrologist advised a renal biopsy, which revealed the finding of “minimal change disease”; (2) Genetic analysis: She was advised to undergo Sanger sequence for the target gene analysis (September 2019). The test result revealed that the younger one also carries two heterozygous genetic variants: One in the WT1 gene (chr11: 32413513C>T affecting intron 9) and one in the COL4A5 gene (chrX: 107846262C>G affecting exon 28, resulting in p.Pro739Ala). These are identical to the variants identified in her elder sibling (Figure 1); and (3) Karyotype analysis: She also underwent karyotype analysis (September 2019). Unlike her elder sister, her karyotype analysis showed a normal female chromosome pattern (46, XX) (Figure 2).

Imaging examinations

Both siblings were advised to undergo abdominal ultrasonography, which revealed normal findings, with no structural abnormalities observed in the kidneys or other abdominal organs.

FINAL DIAGNOSIS

Elder sibling

Based on the clinical presentation of SRNS, a 46, XY karyotype with a female phenotype, and the identification of a WT1 mutation at the 5’ splice site of intron 9 on genetic testing, the pediatric nephrologist confirmed the diagnosis of Frasier syndrome.

Younger sibling

Based on the clinical presentation of SRNS, a 46, XX karyotype with a female phenotype, and the identification of a WT1 mutation at the 5’ splice site of intron 9 on genetic testing, the pediatric nephrologist confirmed the diagnosis of WT1-associated nephropathy.

TREATMENT

Elder sibling

Currently, she is on maintenance hemodialysis twice a week as well as an antiproteinuric protocol.

Younger sibling

She is treated with an antiproteinuric protocol with continuous monitoring of renal function.

OUTCOME AND FOLLOW-UP

Elder sibling

She is progressing to End Stage Renal Disease (ESRD). Her family was advised and counseled for renal transplantation.

Younger sibling

She remains asymptomatic with preserved renal function and is under ongoing antiproteinuric therapy.

DISCUSSION

Both siblings had pathogenic WT1 mutation at the 5’ splice site of intron 9, along with a COL4A5 variant; however, their clinical and phenotypic presentations differed markedly. The elder sibling, with a 46, XY karyotype, presented with classical features of Frasier syndrome, and had rapid progressive nephropathy leading to chronic kidney disease[12]. In contrast, the younger sibling, who had a 46, XX karyotype, exhibited isolated SRNS with a later onset and a more indolent progression of renal dysfunction, without any extrarenal manifestations. A similar pattern was observed in the cases reported by Klamt et al[13] describing two sisters - ws131 (46, XX) and ws131B (46, XY) - who carried the same +5 G→A splice-site mutation in intron 9 of the WT1 gene but demonstrated differing clinical outcomes, highlighting the variable expressivity and phenotypic spectrum associated with WT1 mutations. We have included published case reports of WT1-associated nephropathy, as shown in Table 1[9,13-24], which provide comprehensive details on both genotypic and phenotypic characteristics.

Table 1 Reported cases of Wilms tumor 1-associated syndromes with genotype-phenotype.

Ref.	WT1-mutation type	Phenotype	Karyotype	Renal pathology	Syndrome
Barbaux et al[9], 1997	IVS9+1G>A and IVS9+5G>A splice-site	Female	46, XY	FSGS, SRNS, gonadal dysgenesis	Frasier syndrome
Klamt et al[13], 1998	IVS9+5G>A splice-site	Females	46, XY and 46, XX	FSGS, SRNS	Frasier syndrome
Guaragna et al[14], 2012	WT1 IVS9+5G>A (cases 1-3), IVS9+1G>A	Female	46, XY	FSGS, SRNS, ESRF, puberty, dysgerminoma, streak gonads	Frasier syndrome
Dattolo et al[15], 2013	Exon 6 truncating (c.1012A>T, p.R338X)	Female	46, XX	FSGS, Gonadoblastoma	Atypical WT1-related syndrome
Ahn et al[16], 2017	Exon 7-9 missense and Intron 9 splice	Female and male	46, XY (Predominantly, 46, XX	FSGS, SRNS, DSD and ESRD	Denys-Drash syndrome
Akramov et al[17], 2021	Exon 7 (chr11:32417947G>A),	Male	46, XY	Nephroblastoma, ambiguous genitalia	Variant of Denys-Drash syndrome
Wang et al[18], 2021	Exon 7 novel missense (c.1420C>T, p.His474 Tyr)	Female	46, XY	Gonadoblastoma, dysgerminoma	Denys-Drash syndrome
Zhang et al[19], 2022	intron 9 of, c.1432+5G>A splice-site	Female	46, XY	FSGS, SRNS and pulmonary dysplasia	Frasier syndrome
Arroyo-Parejo et al[20], 2022	WT1	Female	46, XY	ESKD, abnormalities of the male external genitalia	Frasier syndrome
Shao Q, et al[21], 2023	WT1 intron 9 mutation (c.1447+4C>T)	Female	46, XY	SNRS with progressive nephropathy	Frasier syndrome
Al Zabali et al[22], 2024	WT1 mutations	Female and male	46, XY and 46, XX	ESRF, thrombotic microangiopathy	WT1-associated atypical hemolytic uremic syndrome
Tran Thuy et al[23], 2024	p.Arg467Gln exon 9 missense	Female and male (Neonate)	46, XY and 46, XX	ESRD within the first month of their life	Aggressive Denys-Drash syndrome variant
McTaggart SJ et al[28], 2001	T1 c.1447+4C>T (intron 9)	Female	46, XY	FSGS	Frasier syndrome
Chan et al[24], 2006	WT1 intron 9 mutation (c.1447+4C>T)	Female and male	46, XY	FSGS, SRNS, progressed to ESRD	Frasier syndrome

WT1: Wilms tumor 1; ESRD: End-stage renal disease; ESRF: End-stage renal failure; ESKD: End-stage kidney disease; FSGS: Focal segmental glomerulosclerosis; SRNS: Steroid-resistant nephrotic syndrome; DSD: Disorders or differences of sex development.

Literature review of WT1-associated nephropathies

Table 1 compiles reported cases of WT1 gene mutation-associated nephropathies. It summarizes key features, including mutation type, phenotype, karyotype, and renal pathology, helping to elucidate genotype–phenotype correlations. So far, WT1-related nephropathies have almost exclusively been associated with changes in intron 9 or exon 8 or 9, and they also include emerging atypical presentations (e.g., a novel sequence variant (c.1012A>T) of the WT1 gene in exon 6, atypical hemolytic uremic syndrome-associated WT1 mutations, offering a comprehensive view of the expanding WT1-related disease spectrum. Classic Frasier syndrome is consistently associated with intron 9 splice-site mutations (e.g.+4C>T, +5G>A) in 46, XY individuals, presenting with focal segmental glomerulosclerosis and gonadal dysgenesis[9,14-16,19,24]. DDS variants often involve exon 7-9 missense mutations, manifesting as early-onset diffuse mesangial sclerosis, having a higher risk of Wilms tumor[16-18,23]. Some incomplete or atypical presentations, including exon 6 or truncating mutations, may present later and with milder or overlapping features. Recently, novel WT1 missense variants (e.g. p.Arg467Gln) have been identified in neonatal DDS patients with extremely severe ESRD[21]. Published case series linking WT1 mutations with atypical hemolytic uremic syndrome expand the phenotypic spectrum beyond classic nephropathy[22] (Table 1).

A variety of specialized genetic databases and software tools are available to explore and interpret WT1 mutations. They are “Online Mendelian Inheritance in Man”(OMIM) (Available from: https://www.omim.org), “ClinVar” (Available from: https://www.ncbi.nlm.nih.gov/clinvar/), “Human Gene Mutation Database “(HGMD) (Available from: https://www.hgmd.cf.ac.uk), “Leiden Open Variation Database” (LOVD) (Available from: https://www.lovd.nl), “DECIPHER” (Available from: https://www.deciphergenomics.org), “Orphanet” (Available from: https://www.orpha.net), “Gene Curation Coalition” (GenCC) (Available from: https://thegencc.org) and “GeneReviews “ (Available from: https://www.ncbi.nlm.nih.gov/books/NBK1249/) provides evidence-based clinical validity of gene-disease relationships.

The COL4A5 p.Pro739Ala variant identified in these cases is currently classified as a variant of uncertain significance. The COL4A5 gene, located on the X chromosome, encodes the α5 chain of type IV collagen and is implicated in X-linked Alport syndrome when pathogenic variants are present. In hemizygous males (46, XY), pathogenic COL4A5 variants typically manifest as hematuria, progressive renal failure, sensorineural hearing loss, and ocular abnormalities, characteristic of classical X-linked Alport syndrome[25]. This variant is extremely rare and largely unreported in major population databases such as the Genome Aggregation Database, Exome Variant Server, and TOPMed, highlighting its limited recognition and unclear clinical relevance[26]. Although both siblings had a COL4A5 variant in addition to WT1 mutations, the absence of hematuria and extrarenal manifestations (such as hearing loss or ocular abnormalities) at present strongly supports a diagnosis of WT1-associated nephropathy. However, we cannot entirely exclude the potential role of X-linked inheritance or the COL4A5 variant as a phenotypic modifier, particularly in light of the evolving understanding of digenic inheritance in renal disorders; the overall phenotype aligns more closely with WT1-related glomerulopathy[25]. Frasier syndrome follows a slower course, typically progressing during adolescence or early adulthood during the second decade of life[27]. But in this case, the elder sibling’s rapidly progressive, deteriorating kidney function might be influenced or contributed to by the presence of the COL4A5 variant.

Frasier syndrome is typically suspected during adolescence when phenotypic females with a history of SRNS are evaluated for delayed puberty or absence of menstruation, since most cases have normal-looking female genitalia and are raised as girls[14]. However, diagnosis may be delayed as modest breast development can occur despite estrogen deficiency, and pubertal delay may be mistakenly attributed to chronic illness or immunosuppressive therapy. The diagnosis is confirmed by detecting WT1 mutations[28]. The elder sibling in our case represents a rare presentation of Frasier syndrome, with a 46, XY karyotype, normal-appearing external female genitalia, and no detectable gonadal abnormalities at present. A similar rare presentation of Frasier syndrome was reported by Huang et al[29] in a female sibling who had early-onset SRNS and a WT1 mutation, with no gonadal abnormalities initially, but who later developed gonadoblastoma during adolescence[3]. In our case, early diagnosis in the elder sibling was possible through genetic and karyotyping analysis before she entered adolescence. The relative rarity of 46, XX presentations may also reflect diagnostic bias, as these individuals lack the gonadal abnormalities that trigger early evaluation in 46, XY cases, leading to underdiagnosis[9,30]. Interestingly, the younger sibling had a 46, XX karyotype. However, in our case, the younger sibling with a 46, XX karyotype was diagnosed early due to a known history of Frasier syndrome in the elder sibling with similar manifestations.

The clinical management of WT1-associated SRNS is challenging, as it typically does not respond to corticosteroids or immunosuppressive therapies. Progression to ESRD is inevitable. Once ESRD develops, dialysis and, ultimately, renal transplantation remain the only definite treatment options. Notably, there have been no reported cases of nephrotic syndrome recurrence following kidney transplantation[31]. In addition to renal complications, patients with a 46, XY karyotype and gonadal dysgenesis face a significantly elevated risk of gonadal tumors, particularly in Frasier syndrome, where the risk is estimated at around 60%, compared to approximately 40% in DDS. As a result, early diagnosis and timely prophylactic bilateral gonadectomy are strongly recommended for individuals with Frasier syndrome and DDS to mitigate the risk of malignancy[14]. Until surgical removal is performed, regular monitoring with imaging studies such as pelvic ultrasound or MRI is crucial to detect any early signs of gonadal tumors. After gonadectomy, the child may require long-term hormone replacement therapy to support normal pubertal development and maintain bone health, necessitating regular follow-up with an endocrinologist. In addition, psychological counseling should be offered to support the child’s gender identity, emotional well-being, and adjustment during adolescence[9,14].

Genetic counseling is also recommended for the parents to assess the inheritance pattern. The patients have been informed about the potential risk of tumor development and advised to continue regular follow-ups with ongoing monitoring and periodic reassessment of gonadal status. Genetic analysis and long-term follow-up of such exceptional cases will advance the understanding of genotype-phenotype correlations in WT1-related disorders and improve clinical management strategies for affected families. The parents of these siblings have been advised to undergo whole exome sequencing to evaluate potential carrier status or mosaicism, which may help assess recurrence risk and guide future genetic counseling.

CONCLUSION

Two siblings within a single family shared an identical WT1 mutation, but differing clinical courses, disease progression, and karyotypic presentations highlight the complexity of genotype-phenotype correlations in WT1-associated nephropathies. This case illustrates the intricate interplay between genetics and sex determination in WT1 disorders. Early diagnosis remains challenging. Genetic counseling, long-term follow-up, and proactive monitoring are essential. With confirmed familial inheritance, parental genetic testing and counseling are strongly recommended to help anticipate future reproductive risks. Limitation: Parental genetic testing has not yet been performed, which restricts the ability to determine inheritance patterns.

ACKNOWLEDGEMENTS

We sincerely thank the hospital administration for their support, and we are also grateful to the patient’s parents for providing consent to share the clinical information for publication.