Hyperglycemia Due to HNF1A-Mutation-Associated Maturity-Onset Diabetes of the Young (MODY) in a 6-Year-Old Kazakh Girl

Introduction

Maturity-onset diabetes of the young (MODY), a rare autosomal dominant form of monogenic diabetes characterized by primary defects in pancreatic β-cell function, is typically diagnosed before age 25 [1]. It constitutes approximately 5% of all cases of diabetes mellitus [2]. However, MODY represents up to 6.5% of pediatric cases, particularly among children with antibody-negative diabetes [3]. Mutations in several genes have been identified as causative; GCK, hepatocyte nuclear factor 1 alpha (HNF1A), and HNF4A are among the most commonly affected genes across at least 14 recognized MODY subtypes. Genetic testing is essential to confirm the diagnosis in patients with suspected MODY because it identifies the specific single-gene mutation and helps guide individualized treatment according to MODY subtype [2].

Family-based studies play an important role in identifying putative monogenic inheritance [4]. Motyka et al described several cases demonstrating that monogenic forms of diabetes, such as MODY, can be clarified by genetic testing [5]. We encountered a Kazakh nuclear family in which multiple cases of early-onset diabetes were detected, and whole exome sequencing (WES) was performed to define the genetic etiology. Although MODY has been extensively studied, most published data are derived from European or East Asian populations; reports describing genetically confirmed MODY cases in Central Asian populations remain limited [6]. There is increasing evidence of substantial genetic heterogeneity in HNF1A, such that variant spectra and frequencies differ across ethnic groups [7]. Accordingly, data derived from 1 population cannot be fully generalized to other populations. Thus far, MODY-associated variants in the Kazakh population have not been systematically investigated.

This report describes the case of a 6-year-old Kazakh girl who presented with hyperglycemia due to HNF1A-associated MODY.

Case Report

A 6-year-old girl of Kazakh origin was admitted in May 2024 after detection of persistent hyperglycemia during routine glucose testing. Prior to hospitalization, the patient had no history of diabetic ketoacidosis, acute metabolic decompensation, or classic symptoms of diabetes mellitus (eg, polyuria, polydipsia, or unexplained weight loss). According to the medical history obtained at admission, mild thirst and dry skin had been noted; however, the child remained clinically stable, and hyperglycemia was initially detected incidentally. The patient had no prior diagnosis of diabetes mellitus.

On admission, the patient’s general condition was satisfactory. Body temperature was 36.6°C, heart rate was 92 beats per minute, and respiratory rate was 22 breaths per minute. Anthropometric assessment showed a body mass index of 20.32 kg/m2, corresponding to approximately the 75th percentile for age and sex according to pediatric growth standards [8]. Growth and developmental parameters were appropriate for age. Physical examination revealed no signs of dehydration or acute illness. The abdomen was soft and non-tender; no hepatosplenomegaly was detected. Cardiovascular, respiratory, and neurological findings were unremarkable.

Laboratory investigations demonstrated a glycated hemoglobin level of 9.67% (reference range <5.7% according to American Diabetes Association criteria) and a fasting plasma glucose level of 10.6 mmol/L (reference range 3.3–5.6 mmol/L according to pediatric laboratory standards). Random plasma glucose levels exceeded 9 mmol/L. Serum C-peptide was 2.67 ng/mL, within the age-appropriate reference range, indicating preserved endogenous insulin secretion. Autoimmune markers associated with type 1 diabetes mellitus – including antibodies against glutamic acid decarboxylase, insulin, protein tyrosine phosphatase, islet cells, and zinc transporter 8 – showed negative findings. Urinary ketones were absent, and acid-base parameters were within normal limits, excluding diabetic ketoacidosis. Liver, renal, and thyroid function test results were within institutional pediatric reference ranges.

The patient was not insulin-dependent and showed no evidence of ketosis or severe insulin resistance. Taken together, the clinical and laboratory findings were not consistent with classical type 1 or type 2 diabetes mellitus. During hospitalization, the patient remained clinically stable without episodes of ketoacidosis. Insulin therapy was not initiated; management consisted of dietary recommendations and regular glucose monitoring. The patient was discharged with a plan for outpatient endocrinological follow-up and further genetic evaluation to clarify the etiology of diabetes. Given the atypical presentation, a detailed family history was obtained. Pedigree analysis revealed clustering of diabetes mellitus across at least 2 generations (Figure 1). Both of the proband’s parents exhibited diabetes of unspecified type, which had been diagnosed at a relatively young age. No autoimmune diseases were reported by either parent.

Additional cases of diabetes were reported on both the maternal and paternal sides of the family, including the paternal grandparents and the father’s maternal aunts, as illustrated in Figure 1. Although the exact age at diagnosis was not available for all affected relatives, the family history consistently indicated onset in adulthood rather than childhood, supporting a multigenerational pattern of disease. The distribution of affected individuals was consistent with an autosomal dominant pattern of inheritance, supporting a diagnosis of monogenic diabetes, particularly MODY. The proband’s mother had a history of 4 pregnancies, including 1 missed miscarriage and 3 live births. During her pregnancy in 2018 (resulting in birth of the proband), she had been under endocrinological supervision but did not adhere to insulin therapy, resulting in persistent hyperglycemia. The pregnancy was complicated by placental insufficiency and culminated in a preterm cesarean delivery at 35 weeks of gestation. Uncontrolled maternal hyperglycemia is a known risk factor for adverse pregnancy outcomes, further supporting the presence of an underlying inherited glycemic disorder in the family. Based on the proband’s early onset of hyperglycemia, preserved β-cell function, absence of autoimmune markers, and lack of severe obesity, along with the strong multigenerational family history, monogenic diabetes was considered the most likely diagnosis. WES was therefore performed to identify a potential genetic cause.

Peripheral blood samples (~2–3 mL each) from 3 affected individuals were collected in ethylenediaminetetraacetic-acid-containing tubes at the University Medical Center, Astana, Kazakhstan, after informed consent had been obtained. Genomic DNA was extracted using a kit from Thermo Fisher Scientific; quality was assessed using a NanoDrop™ 1000 spectrophotometer (Thermo Scientific) and a Qubit® 2.0 fluorometer with dsDNA HS Assay Kit (Invitrogen). For each sample, 50 ng of DNA were used for library preparation with the Twist Library Preparation EF Kit and target enrichment with the Twist Human Core Exome Panel (~30–50 Mbp). Sequencing was performed by Macrogen (Seoul, Republic of Korea) on the NovaSeq 6000 platform (Illumina), achieving greater than 100× mean exome coverage with paired-end 2×150 bp reads. Raw reads were subjected to quality control via FastQC and Trimmomatic, then aligned to the human reference genome (GRCh37 or GRCh38) using BWA-MEM. Variant calling was performed using Genome Analysis Toolkit; variants were annotated and filtered using ANNOVAR with reference to gnomAD, ClinVar, and Human Gene Mutation Database. Variants identified in the analyzed patients are summarized in Table 1.

There are currently more than 14 recognized subtypes of MODY, each resulting from mutations in genes that play key roles in pancreatic β-cell development, glucose sensing, or insulin secretion [4,7]. WES analysis of our Kazakh patient population revealed variants in nearly all genes associated with MODY, including HNF1A, NEUROD1, GCK, HNF4A, PDX1, HNF1B, KLF11, CEL, PAX4, INS, BLK, ABCC8, and KCNJ11; none were identified in the gene corresponding to MODY14 (Table 1). MODY3, associated with mutations in HNF1A, is the most common subtype and is characterized by progressive hyperglycemia that responds well to low-dose sulfonylureas [9].

As demonstrated in Table 1, variants were filtered to retain only missense and frameshift changes with predicted high or moderate functional impact. Most remaining variants had high minor allele frequencies and were already classified as benign [10]. Therefore, these common polymorphisms were excluded as contributors to the clinical phenotype. However, in HNF1A, a key gene underlying MODY3, a variant was detected that lacked both minor allele frequency data and a ClinVar classification but was predicted to have a high functional impact. Due to its rarity and potential clinical significance, this variant was further investigated using WES data analyzed by VarSeq.

In total, 122 902 variants were initially identified from the joint genotyping analysis (Figure 2). After application of a region-based filter to exclude noncoding variants (3′ untranslated region, 5′ untranslated region, upstream, downstream, intronic, and intergenic regions), 42 568 variants remained. Subsequent exclusion of synonymous variants reduced this number to 25 138. Further filtering against the 1000 Genomes database to remove common variants with a minor allele frequency greater than 1% resulted in 7586 variants. These remaining variants were subjected to genetic modeling based on inheritance patterns to prioritize candidates for further evaluation. WES identified a single mutation in the HNF1A gene (NM_000545.8), c.183delC, predicted to result in a premature stop codon (p.Asn62fs) (Table 2). This variant leads to truncation of the HNF1A protein and is consistent with loss of function, a known disease mechanism in MODY3. According to American College of Medical Genetics and Genomics criteria, the variant was classified as likely pathogenic.

The variant was absent from population databases, including gnomAD, and had not been previously reported in ClinVar as of January 2025, suggesting that it is rare. No rsID has been assigned to this variant. Trio-based analysis demonstrated that the HNF1A c.183delC variant was present in both the proband and her mother, indicating maternal inheritance. To confirm the presence and segregation of the variant, Sanger sequencing was performed using custom-designed primers targeting the affected region of HNF1A. Primers were designed to amplify the region encompassing the deletion site:

Polymerase chain reaction products were sequenced in both forward and reverse directions; chromatograms were analyzed to confirm the presence of the heterozygous deletion. Sanger sequencing validated the heterozygous deletion in both the proband and her mother, confirming WES findings. These genetic results provide a molecular explanation for the clinical phenotype observed in the proband and support the diagnosis of HNF1A-associated MODY.

In Figure 3A, a forward Sanger sequencing chromatogram shows the heterozygous c.183delC variant in HNF1A, in which the signal corresponding to the deleted cytosine is overlapped by subsequent nucleotide peaks, resulting in superimposed signals downstream of the deletion site. To exclude sequencing errors and assess the presence of the variant in unaffected individuals, Sanger sequencing with the same primer pair was performed in 10 unrelated healthy control samples. All control samples showed a normal sequencing pattern without evidence of the c.183delC deletion. Figure 3B demonstrates that no phase shift or overlapping peaks were observed downstream of the corresponding genomic position, confirming the absence of the variant in healthy controls.

Discussion

This case highlights the importance of considering monogenic diabetes in pediatric patients who present with atypical hyperglycemia. The combination of early disease onset, preserved β-cell function, negative autoimmune markers, and a strong family history should prompt consideration of MODY and early genetic testing. Accurate diagnosis is clinically important because misdiagnosis can lead to inappropriate treatment and delayed implementation of optimal management strategies [2]. MODY represents a heterogeneous group of monogenic disorders characterized by early-onset diabetes, preserved β-cell function, and autosomal dominant inheritance [11]. Among its subtypes, MODY3, caused by pathogenic variants in HNF1A, is the most frequently reported; it is typically associated with progressive hyperglycemia, negative autoimmune markers, and a favorable response to non-insulin therapies [12]. The present case aligns well with these established clinical features, including early disease onset, absence of ketoacidosis, preserved endogenous insulin secretion, and a strong familial background of diabetes. Additionally, the current classification framework for pediatric HNF1A variants highlights the clinical value of accurate molecular diagnosis [13].

Previous studies have shown that loss-of-function variants in HNF1A, particularly truncating and frameshift mutations, represent a well-established pathogenic mechanism underlying MODY3. The single-gene deletion identified in this report is predicted to result in premature truncation of the protein and functional haploinsufficiency [14]. Although this specific variant has not been documented in ClinVar or population databases, its predicted molecular consequence is consistent with the known disease mechanism of HNF1A-associated MODY. Importantly, segregation analysis demonstrated the presence of the variant in both the proband and her affected mother; Sanger sequencing confirmed the variant while excluding its presence in healthy controls, thus strengthening the genotype-phenotype correlation.

Our clinical case is similar to previously published observations of patients with HNF1A mutations who, after molecular confirmation of the diagnosis, were successfully treated with low-dose sulfonylurea therapy. This finding highlights the key role of genetic diagnosis in selecting the optimal therapeutic strategy. Many studies have also shown that patients initially misdiagnosed with type 1 or type 2 diabetes were able to discontinue insulin therapy after receiving a diagnosis of HNF1A-associated MODY. A review of the literature indicates that pediatric forms of HNF1A-associated MODY often present with mild or atypical clinical manifestations and are frequently misclassified as type 1 or type 2 diabetes, particularly in the absence of autoimmune markers. Reliance on clinical criteria without molecular analysis can lead to delayed or missed diagnosis [15].

In this context, our findings are consistent with previous reports demonstrating the utility of comprehensive genetic testing in complex familial diabetes cases. The absence of prior reports of this variant in individuals of Kazakh origin suggests population-level rarity and highlights the need for genetic studies in underrepresented populations. The choice of WES in the present case was guided by several factors, including the atypical clinical presentation, multigenerational family history, negative autoimmune markers, and preserved β-cell function [16]. Although targeted MODY gene panels are commonly used, they may fail to detect rare variants or may not adequately address diagnostic uncertainty when multiple candidate genes are involved. WES provides a comprehensive and unbiased approach, allowing simultaneous evaluation of all known MODY-associated genes and enabling prioritization of a clinically relevant variant [17]. This approach underscores the value of WES as a problem-solving diagnostic tool in pediatric diabetes cases that do not conform to classical classifications.

Nevertheless, several limitations should be acknowledged. The pathogenicity of the identified HNF1A variant was inferred from bioinformatic predictions, established disease mechanisms, segregation with the disease, and clinical presentation, in the absence of direct functional validation. Moreover, the present report focused on a single family, which may restrict the generalizability of the findings. Despite these limitations, the case highlights several clinically relevant implications. Identification of an HNF1A variant consistent with MODY3 has direct consequences for clinical management and genetic counseling. Accurate classification of diabetes subtype may inform therapeutic decisions, reduce unnecessary insulin exposure, and enable appropriate screening of family members. From a broader perspective, the present case contributes to the growing body of evidence that supports integration of clinical phenotyping with genomic analysis in pediatric diabetes diagnostics [4,16]. Future research should focus on expanding genotype-phenotype correlations for HNF1A variants, particularly in underrepresented populations. Long-term follow-up studies are also needed to better characterize disease progression and treatment response in pediatric MODY3. Population-based studies assessing the prevalence of similar truncating variants may further inform diagnostic strategies and clinical guidelines.

Conclusions

This case illustrates the importance of considering monogenic diabetes in pediatric patients with atypical hyperglycemia, preserved β-cell function, negative autoimmune markers, and a suggestive family history. WES enabled identification of an HNF1A mutation consistent with MODY3, supported by segregation analysis, Sanger validation, and absence in healthy controls. Rather than establishing a definitive diagnosis based solely on genetic data, this report emphasizes the value of an integrated clinical-genetic approach. The findings demonstrate how genomic analysis can refine diabetes classification, guide personalized management, and inform genetic counseling in complex cases. This report underscores the importance of integrating clinical assessment with genetic analysis in the diagnosis of monogenic diabetes. Future studies should investigate the prevalence and clinical impact of similar HNF1A variants in diverse populations and assess long-term outcomes of patients diagnosed through genomic testing.