Exploring genotype–phenotype correlations in three pediatric patients with IL10RA variants and very early-onset inflammatory bowel disease

Abstract

Background

Very early onset inflammatory bowel disease (VEO-IBD) is a severe chronic intestinal inflammatory disorder with onset in infancy. Mutations in the interleukin-10 (IL-10) receptor A (IL10RA) gene represent a key pathogenic mechanism of VEO-IBD; however, the genotype–phenotype correlations remain unclear.

Objective

This study aims to describe and compare the clinical features, genotypes, and family segregation data of three pediatric patients with IL10RA mutation-associated VEO-IBD to explore potential associations between different IL10RA mutation sites and types (compound heterozygous or homozygous) and clinical phenotypes.

Methods

Three VEO-IBD patients harboring IL10RA mutations diagnosed at our hospital from July 2022 to December 2024 were retrospectively enrolled. Genetic testing and family segregation analysis were performed for all patients. Detailed clinical data, including age of onset, manifestations, examinations, and treatment were collected. Phenotypic features were summarized and compared among different mutation types to establish genotype–phenotype relationships.

Results

All patients developed symptoms within six months, mainly diarrhea, perianal abscesses, and fistulas. Patient 1 had a homozygous c.301 C > T(p.Arg101Trp) mutation with severe perianal disease. Patient 2 carried compound heterozygous c.301 C > T(p.Arg101Trp) and c.537G > A(p.Thr179Thr) mutations, exhibiting recurrent oral ulcers, perianal lesions, and growth retardation, exhibiting a severe phenotype linked to compound/homozygous mutations. Patient 3 had a novel compound heterozygous IL10RA c.421G > A(p.Gly141Arg) mutation along with (c.301 C > T(p.Arg101Trp), with milder symptoms with a perianal disease and growth delay.

Conclusion

Our study identified homozygous or compound heterozygous IL10RA mutations associated with the VEO-IBD phenotype, with severe clinical features. The newly discovered c.421G > A(p.Gly141Arg) mutation may broadens the genetic spectrum associated with the disease.Although small in scale, this case series provides a meaningful contribution to the growing body of evidence on VEO-IBD.

Introduction

Very early-onset inflammatory bowel disease (VEO-IBD) refers to IBD with an onset before six years old, with a subset of patients presenting symptoms before two years old [1–3]. These cases are often severe and very progressive, frequently exhibiting poor response to conventional immunosuppressive therapy, suggesting a possible monogenic etiology [3]. In recent years, with the widespread application of high-throughput sequencing technologies, genetic variants in the interleukin-10 (IL-10) signaling pathway—particularly in IL-10 receptor A (IL10RA) and IL-10 receptor B (IL10RB)—have gained increasing attention for their pathogenic roles in VEO-IBD [4, 5]. IL-10 is a critical anti-inflammatory cytokine, whose receptor comprises two subunits, IL10RA and IL10RB [6]. Mutations in IL10RA lead to immune cells, such as macrophages, becoming insensitive to IL-10 signaling, triggering excessive intestinal inflammation and resulting in early-onset IBD characterized by refractory diarrhea, perianal abscesses, oral ulcers, and delayed growth [7–10].

Although IL10RA mutations have been confirmed as pathogenic in VEO-IBD, phenotypic differences among various mutation types remain to be elucidated. The homozygous c.301 C > T(p.Arg101Trp) (p.R101W) mutation is relatively common and is associated with a typical severe phenotype [11, 12]. However, whether compound heterozygous mutations, such as c.301 C > T(p.Arg101Trp) combined with c.537G > A(p.Thr179Thr) or c.421G > A(p.Gly141Arg), result in distinct clinical spectra remains underexplored.

This study retrospectively collected three VEO-IBD patients diagnosed at our center with different IL10RA variants. We integrated clinical features, laboratory and imaging results, and performed familial segregation analysis to investigate potential genotype–phenotype correlations. Our goal is to provide that may more case materials for gene related early-onset inflammatory bowel disease.

Materials and methods

Study subjects

This study included three pediatric patients diagnosed with VEO-IBD at our hospital between July 2022 and December 2024. Patients were enrolled if they met all of the following criteria: (1) clinical features consistent with VEO-IBD, including persistent diarrhea, hematochezia, perianal lesions, and oral ulcers; (2) detection of IL10RA gene mutations via whole-exome sequencing (WES); (3) completion of familial genetic verification, with genetic testing of both parents and relevant family members to establish inheritance patterns; and (4) exclusion of other conditions with similar symptoms, such as primary immunodeficiency, infectious enteritis, lactose intolerance, and inborn errors of metabolism.

Clinical data collection

Clinical data were extracted by the attending physicians from electronic medical records and follow-up documentation to ensure completeness and accuracy. The following information was collected in detail: (1) Birth and perinatal history (gestational age, parity, birth weight); (2) age at onset and initial symptoms; (3) main clinical manifestations, including diarrhea, hematochezia, perianal lesions, oral ulcers, and growth in weight and height; (4) hospitalization and treatment history, including medications used and treatment responses; (5) laboratory findings, such as complete blood counts, biochemical profiles, immunologic evaluations (immunoglobulin levels, lymphocyte subsets), stool studies and cultures, and inflammatory markers; (6) imaging and endoscopic findings, including colonoscopy and histopathological reports; and (7) genetic testing results and family segregation analysis. All data were de-identified to ensure patient confidentiality.

Genetic testing and familial analysis

Informed consent was obtained from all patients and their parents, and the study protocol was approved by the institutional ethics committee. Peripheral blood samples were collected for genomic DNA extraction. WES was performed on a high-throughput sequencing platform (e.g., Illumina NovaSeq) for exome capture and sequencing. Raw data underwent quality control, alignment, variant calling, and annotation using standard bioinformatics pipelines. Variant filtering focused on mutations in the IL10RA gene. Public databases, including ClinVar, the Human Gene Mutation Database, and the Genome Aggregation Database, were consulted to assess variant frequency and pathogenicity. Pathogenicity was classified according to the guidelines of the American College of Medical Genetics and Genomics. Candidate variants identified by WES were validated by Sanger sequencing. DNA samples from both parents were analyzed in parallel to perform segregation analysis and determine the mode of inheritance (homozygous, compound heterozygous, or de novo).

Clinical phenotype analysis

Based on the IL10RA mutation types (homozygous or compound heterozygous) and specific mutation sites, we systematically summarized and compared patients’ clinical manifestations, organ involvment, laboratory abnormalities, treatment responses, and disease progression. Our objective was to preliminarily establish genotype–phenotype correlations and explore how different mutation combinations may influence disease severity and clinical presentation.

Results

All three patients developed VEO-IBD during infancy, with definitive diagnoses attributed to pathogenic IL10RA mutations. Gastrointestinal symptoms appeared within weeks to months after birth, accompanied by varying degrees of perianal disease (Table 1). Genetic testing confirmed pathogenic IL10RA variants in all cases, and familial analysis established autosomal recessive inheritance (Table 2; Fig. 1).

Table 1.

Main clinical features of the three pediatric patients

Age at onset	Case 1	Case 2	Case 3
	20 days after birth	6 months after birth	2 months after birth
Diarrhea	+ (watery stool)	+ (moderate)	+ (frequent with blood)
Perianal lesions	++ (granulomatous, stenosis)	+ (recurrent abscess)	+ (abscess)
Oral ulcers	−	+	−
Growth retardation	+	+/−	+++
Family history	None	None	Monozygotic twin also had diarrhea
IL-10 level (pg/mL)	144.6	113.8	97.87
Treatment	Severe perianal stenosis and lesions; underwent sigmoidostomy followed by stem cell transplantation	Stem cell transplantation	Early thalidomide therapy with poor response; later received stem cell transplantation

Table 2.

Genetic characteristics and familial validation of three patients and the pathogenicity score genetic

	IL10RA Mutation Type	Inheritance Pattern	Familial Validation	Variant Type	Pathogenicity of mutation sites(Missense Variant)			Pathogenicity of mutation sites(Synonymous Variant)
					CADD Score	Polyphen Score	Vest4 Score	SpliceAI Score	dbscSNV_ADA Score	dbscSNV_RF Score
Case 1	c.301 C > T(p.Arg101Trp) (homozygous)	Autosomal recessive	Both parents were carriers	Missense Variant	27	1	0.91	-	-	-
Case 2	c.301 C > T(p.Arg101Trp) / c.537G > A(p.Thr179Thr) (compound heterozygous)	Autosomal recessive	Each parent was a heterozygous carrier	Missense Variant / Synonymous Variant	27	1	0.91	0.9	1	0.99
Case 3	c.301 C > T(p.Arg101Trp) / c.421G > A(p.Gly141Arg) (compound heterozygous)	Autosomal recessive	Each parent was a heterozygous carrier	Missense Variant	27/32	1 / 1	0.91 / 0.79	-	-	-

Fig. 1.

Sanger sequencing results of the three cases

Case 1 was a female infant with the earliest onset. She developed diarrhea at 20 days of age, characterized by frequent watery stools. Conservative treatment, including antibiotics and amino acid-based formula, was ineffective. Progressive perianal erythema advanced to granulomatous lesions, and digital rectal examination revealed marked anal canal stenosis, suggesting distal rectal involvement. Colonoscopy and histopathology confirmed extensive chronic inflammatory changes. Serum IL-10 levels were markedly elevated (144.6 pg/mL), the highest among the three patients. Genetic analysis identified a homozygous c.301 C > T(p.Arg101Trp) mutation; both parents were heterozygous carriers, confirming the pathogenicity of this variant.

Case 2 was a female infant who developed symptoms at approximately 6 months of age, initially presenting with perianal erythema that progressed to recurrent abscesses and fistulas. She subsequently developed recurrent watery diarrhea, occasionally mixed with blood, and multiple oral ulcers, suggesting mucosal immune dysregulation. Colonoscopy revealed multiple colonic erosions and areas of inflammation. Histopathology identified moderate-to-severe chronic inflammatory cell infiltration with glandular architectural distortion, consistent with IBD. IL-10 levels were markedly elevated (113.8 pg/mL), accompanied by increased IL-6, indicating active inflammation. Genetic analysis identified compound heterozygous mutations (c.301C>T(p.Arg101Trp) and c.537G>A(p.Thr179Thr)); each parent carried one of the variants, confirming autosomal recessive inheritance.

Case 3 was a male infant, the smaller twin of a dichorionic pregnancy, delivered at 34^+ 1 weeks via cesarean section due to intrauterine growth restriction, with a birth weight of 1.65 kg. At 2 months of age, he developed more than ten episodes of diarrhea per day with variable stool consistency, occasionally containing blood. He also suffered from recurrent perianal abscesses with skin breakdown and exhibited marked growth failure. By 6 months, his weight was only 3.7 kg, significantly below age norms, indicating malabsorption and chronic inflammation. Laboratory evaluation revealed elevated IL-10 (97.87 pg/mL) and IL-6 levels. Genetic analysis revealed compound heterozygous IL10RA mutations (c.301 C > T(p.Arg101Trp) and c.421G > A(p.Gly141Arg)), with each parent identified as a heterozygous carrier. Notably, his monozygotic twin brother also developed diarrhea and anal fistulas, further supporting a strong genetic etiology.

To further support the pathogenicity of the identified IL10RA variants, multiple in silico prediction tools were applied (Table 2. The missense variant c.301 C > T(p.Arg101Trp) showed consistently high pathogenicity scores, including a CADD score of 27, PolyPhen-2 score of 1.0 (probably damaging), and a Vest4 score of 0.91, supporting its strong deleterious effect on protein function.Similarly, the novel missense variant c.421G > A(p.Gly141Arg) demonstrated high in silico pathogenicity scores (CADD 32, PolyPhen-2 score 1.0, Vest4 score 0.79), suggesting a potentially damaging impact on IL10RA protein structure and function.For the synonymous variant c.537G > A(p.Thr179Thr), splice prediction tools indicated a high likelihood of aberrant splicing, with a SpliceAI score of 0.90, dbscSNV_ADA score of 1.0, and dbscSNV_RF score of 0.99, consistent with previously reported functional evidence.

All three patients developed symptoms within the first year of life and exhibited a clinical phenotype dominated by diarrhea and perianal disease, with individual differences in associated features (Table 3). Case 1 developed granulomatous perianal lesions and anal stenosis, indicating deep rectal and anal canal involvement. Case 2 presented with prominent oral ulcers, suggesting extraintestinal mucosal involvement. Case 3 experienced severe growth retardation and persistent underweight status, reflecting the nutritional impact of chronic inflammation. These findings underscore the marked clinical heterogeneity of IL10RA-associated VEO-IBD.

Table 3.

Correlation Between IL10RA mutations and clinical phenotypes

Genotype	Severity of Mucosal Damage	Systemic Symptoms	Distinctive Features
c.301 C > T(p.Arg101Trp) (homozygous)	++++	++++	Anal canal stenosis, granulomatous lesions
c.301 C > T(p.Arg101Trp) / c.537G > A(p.Thr179Thr)	++	++	Oral ulcers
c.301 C > T(p.Arg101Trp) / c.421G > A(p.Gly141Arg)	+++	++	Marked growth retardation

Immunologic studies demonstrated significantly elevated IL-10 levels in all patients, consistent with heightened proinflammatory cytokine activity. IL10RA mutations impair IL-10 signaling, rendering it ineffective in controlling intestinal inflammation and thereby driving persistent immune activation and chronic intestinal disease. The clinical manifestations observed in these patients align with this pathogenic mechanism and highlight the pivotal role of IL10RA mutations in the development of VEO-IBD.

Discussion

This study systematically analyzed the clinical and genetic characteristics of three patients with IL10RA mutation-associated VEO-IBD. While all patients exhibited the typical clinical phenotype of VEO-IBD, notable differences were observed in age of onset, symptom presentation, growth patterns, laboratory findings, and treatment responses, underscoring the marked phenotypic heterogeneity of this condition. We further sought to explore potential underlying mechanisms in relation to mutation type, locus variation, and familial background.

IL-10R is primarily expressed in the monocyte–macrophage system and lamina propria immune cells, mediating the anti-inflammatory effects of IL-10 [13]. The IL10RA gene encodes the α-subunit of IL-10R, a critical component of the IL-10 signaling pathway [14]. Binding of IL-10 to IL10RA activates the JAK1/STAT3 pathway, downregulating proinflammatory cytokines such as TNF-α, IL-6, and IL-1β, thereby maintaining intestinal immune homeostasis [15, 16]. In our study, all three patients carried the c.301 C > T(p.Arg101Trp) (p.R101W) variant, a well-characterized loss of function mutation that abolishes IL-10-induced signal transduction and is the most commonly reported pathogenic variant in IL10RA [11, 17]. Previous research has shown that R101W impairs STAT3 phosphorylation in response to IL-10, leading to persistent macrophage-mediated release of inflammatory mediators and continuous intestinal mucosal injury [12, 18, 19]. Case 1 harbored a homozygous mutation, while cases 2 and 3 had compound heterozygous mutations. Homozygous R101W has been associated with treatment-refractory infantile IBD [12]. Correspondingly, Case 1 exhibited the most severe mucosal lesions, extensive disease involvement, highest IL-10 levels, and poorest response to conventional therapy, consistent with the “classic IL10RA-deficient VEO-IBD” phenotype. These findings suggest a “dosage effect” mutation, in which c.301 C > T(p.Arg101Trp) homozygosity correlates with greater phenotypic severity.

In contrast, patients with compound heterozygous mutations (Cases 2 and 3) exhbited relatively milder symptoms, suggesting that different mutation combinations may preserve partial IL-10 signaling activity. A review of IL10/IL10R-deficient patients indicated that heterozygous IL10RA mutations may not result in complete loss of function but can still significantly affect IL-10/IL10R signaling, consistent with our observations [11]. For example, the c.537G > A(p.Thr179Thr) variant has been reported in a patient with neonatal-onset Crohn’s disease presenting initially with oral ulcers. This patient carried the same compound heterozygous combination (c.301 C > T(p.Arg101Trp) / c.537G > A(p.Thr179Thr)) as our Case 2 and similarly exhibited prominent oral ulcers and recurrent perianal abscesses, along with extraintestinal involvement, suggesting this genotype may predispose to oral mucosal damage [20]. By comparison, the c.421G > A(p.Gly141Arg) mutation is novel and has not been reported in public databases or prior IBD studies. A case report incidentally identified this variant in a patient with Gitelman syndrome who developed an acute perianal abscess, hinting that c.421G > A(p.Gly141Arg) may influence the intestinal immune microenvironment or inflammatory regulation, potentially contributing to disease pathogenesis [21]. Additionally, the pronounced growth retardation observed in Case 3 reflects systemic inflammation and nutritional malabsorption, further demonstrating the widespread impact of disrupted IL-10 signaling.

If c.537G > A(p.Thr179Thr) and c.421G > A(p.Gly141Arg) represent residual-function or hypomorphic mutations, compound heterozygosity may lead to only partial loss of IL-10 signaling. In this scenario, immune effector cells, such as macrophages and dendritic cells, may retain limited anti-inflammatory capacity. This could explain why the phenotypes of Cases 2 and 3 fall between classic VEO-IBD and milder autoimmune enteropathy: significant perianal and intestinal symptoms are present, but systemic inflammation is less severe, and growth impairment is milder compared with the homozygous case. Thus, our study reinforces the pathogenic severity of c.301 C > T(p.Arg101Trp) and highlights the potential phenotypic heterogeneity associated with c.537G > A(p.Thr179Thr) and c.421G > A(p.Gly141Arg) in compound heterozygous states. Further structural modeling and in vitro functional assays are warranted to clarify the specific effects of these “borderline pathogenic” mutations and establish more precise genotype–phenotype correlations. Such insights may facilitate early identification of high-risk patients and inform individualized therapeutic strategies.

Based on our clinical experience, infants presenting with recurrent diarrhea, perianal disease, and poor response to conventional therapy should raise suspicion for monogenic IBD, particularly IL10RA-related cases. Early genetic testing and definitive diagnosis can provide a critical therapeutic window, especially for hematopoietic stem cell transplantation. However, given the small sample size of this study, the genotype–phenotype associations reported remain preliminary and require validation in larger, multicenter cohorts. The pathogenic mechanism of the novel c.421G > A(p.Gly141Arg) mutation remains and warrants further investigation through cellular functional assays, structural simulation, and IL-10/STAT3 pathway activity.

However, due to the sample size of only three cases, our study has limitationsand the findings should be interpreted with caution.This precludes any definitive statistical analysis, prevents generalization of our observations to the broader population of IL10RA-deficient VEO-IBD patients, and limits the power to draw firm conclusions about causal relationships between specific variants and clinical manifestations.Our study is primarily clinical and genetic. We did not perform functional assays (e.g., on patient-derived cells) to validate the molecular consequences of the identified mutations on IL-10 signaling pathway activity. Such functional data would strengthen the causal link between genotype and phenotype.Despite these limitations, detailed case reports like these are crucial for building the foundational knowledge of ultra-rare disorders. They generate hypotheses for future research. Our findings highlight the clinical diversity within IL10RA deficiency and underscore the need for large, international, prospective registries to aggregate data systematically. Future studies integrating deep genotype, comprehensive phenotype, and functional validation are essential to establish robust genotype-phenotype correlations and guide personalized management.

Conclusion

This study systematically analyzed the clinical and genetic features of three patients with IL10RA mutation-associated VEO-IBD, demonstrating that mutation type can influence residual IL-10 signaling function, thereby affecting age at onset, disease severity, and treatment response. Homozygous c.301 C > T(p.Arg101Trp) mutations were associated with earlier onset, more severe disease, and poorer response to conventional therapy, whereas compound heterozygous mutations, such as c.301 C > T(p.Arg101Trp)/c.537G > A(p.Thr179Thr) or c.301 C > T(p.Arg101Trp)/c.421G > A(p.Gly141Arg), were associated with intermediate or milder phenotypes, suggesting partial functional retention. Notably, c.421G > A(p.Gly141Arg) is a novel variant whose pathogenicity requires further functional validation. These findings offer valuable insights into the classification, diagnosis, and mechanistic understanding of IL10RA mutation-related VEO-IBD.

Authors’ contributions

Qiu Rubiao: methodology, validation, formal analysis, data curation, writing–original draft, and visualization. Zhang Mengxu: endoscopic procedure, methodology，data curation. Li Tingting: data collection; data analysis. Wang Yumei: resources, writing–review and editing, and supervision. Liang Yanping: data curation, formal analysis, resources. Xu Songtao: conceptualization, resources, writing–review and editing, supervision, project administration.

Funding

None.

Data availability

The data and images in this article can be obtained from the author upon reasonable request.

Declarations

Ethics approval and consent to participateconsen

The research protocol has been approved by the Medical Ethics Committee of The Third Affiliated Hospital of Zhengzhou University (2025-179-01).All participants provided informed consent.

Competing interests

The authors declare no competing interests.