Diabetes Case Reports

HNF1A Gene Mutation (c.811del, p.Arg271Glyfs) Causing Maturity Onset of Diabetes of the Young 3: A Case Study of an Indian Patient

Neelima Chitturi^*, Satish Sunkara, Sandhya Kiran Pemmasani and Anuradha Acharya Research and Development Division, Mapmygenome India Limited, Plot No. 12/2, Royal Demeure, HUDA Techno Enclave, Sector-1, Madhapur, Hyderabad, Telangana-500081, India
^*Correspondence: Neelima Chitturi, Research and Development Division, Mapmygenome India Limited, Plot No. 12/2, Royal Demeure, HUDA Techno Enclave, Sector-1, Madhapur, Hyderabad, Telangana-500081, India, Email:

Received: 08-May-2023, Manuscript No. DCRS-23-21256; Editor assigned: 10-May-2023, Pre QC No. DCRS-23-21256(PQ); Reviewed: 30-May-2023, QC No. DCRS-23-21256; Revised: 06-Jun-2023, Manuscript No. DCRS-23-21256(R); Published: 13-Jun-2023, DOI: 10.35841/2572-5629.23.8.158

Introduction

Diabetes is of several types and Maturity-Onset Diabetes of the Young (MODY) is one among them. Its characteristics include hyperglycemia and persistent microvascular long-term consequences such as retinopathy, nephropathy, and neuropathy [1]. It is a relatively rare type of diabetes with an autosomal dominant mode of inheritance that typically manifests in adolescence or early adulthood, before the age of 25. It is estimated to have a prevalence of about 2% globally and 7.7% in India, which ranks second with highest number of diabetic patients after China [2-4]. There are several types of MODY, each caused due to mutations in different genes: MODY1 (HNF4A), MODY2 (GCK), MODY3 (HNF1A), MODY4 (PDX1), MODY5 (HNF1B), MODY6 (NEUROD1), MODY7 (KLF11), MODY8 (CEL), MODY9 (PAX4), MODY10 (INS), MODY11 (BLK), MODY13 (KCNJ11) and MODY14 (APPL1) [5, 6]. Thus, it is referred as a monogenic disorder. While many biochemical tests are used to determine the type of diabetes, whole exome sequencing helps to determine the type of diabetes, and to further plan the treatment strategy.

This study goes into great detail about the MODY3-causing mutation in the HNF1A gene. The HNF1A gene, which is located on chromosome 12, encodes a homodimeric protein that functions as a transcription factor for a number of genes unique to the pancreas and liver. It has a major role in the development of the liver and pancreas, glucose import and homeostasis, insulin production, and renal glucose absorption [6, 7]. Researchers found up to 350 distinct mutations in the gene's promoter region and exons in diabetic patients, and a few have also been found in Indians [1, 8 - 11]. The objective of this study is to demonstrate the importance of identifying underlying genetics of diabetes through whole exome sequencing.

Case Presentation

Clinical History

The patient was diagnosed with diabetes at the age of 17 years and was on insulin (12 units). The random blood sugar levels were 200 mg/dL to 300 mg/dL and HbA1c was 9.2%. The patient was recommended for MODY testing after ruling out the possibilities of type 1 and type 2 diabetes. The parents of the proband are healthy and non-diabetic. Their random blood sugar levels and HbA1c were within normal limits. The pedigree is given in Figure 1.

Figure 1: Pedigree of the proband.

All experimental and analytical procedures were performed as per standard manufacturer’s protocol. An informed written consent mentioning the use of the sample for research was taken from the proband and her family members. Research was carried out in compliance with the Helsinki declaration and the procedures had been approved by internal bio-safety committee at Mapmygenome.

Extraction of DNA from blood

Genomic DNA was extracted from the blood samples using Nucleospin DNA isolation kit from Takara Bio and quantified spectrophotometrically using QubitTM from Thermo Fisher Scientific.

Whole exome sequencing and analysis

Exome libraries were prepared using Twist Comprehensive Exome Panel, from Twist Bioscience. Sequencing was performed on a NovaSeq 6000 Illumina sequencer and paired-end reads of length 150 bases were generated. Quality of raw data was verified using fastqc tool version V0.1.1 and adapters were removed using Trimommatic software version 0.39. The trimmed paired end reads were aligned to reference human genome (hg19 version) using BWA version 0.7.17. Haplotype Caller package, of GATK version 4.2.0.0, was used to call variants as per Broad Institute’s Best Practices protocol. Variants were annotated using VEP release 104 (against the Ensembl release 75 human gene model) and data from other resources such as dbsnp, dbnsfp, snpeff, ClinVar, HGMD, OMIM and HPO. The variants were filtered using criteria: a) variants of genes associated with diabetes in general and MODY in particular b) exclude synonymous, 5’ and 3’variants c) variants with gnomAD & 1000Genomes frequency less than 5%. Variant classification was done as per American College of Medical Genetics and Genomics (ACMG) guidelines [12].

Targeted validation by Sanger sequencing

The presence or absence of variant was confirmed in samples of mother and brother using bidirectional Sanger sequencing. Father was not available and so his sample could not be tested for the identified variant.

Results and Discussion

Whole exome sequencing of the proband revealed a heterozygous frame- shift deletion in exon 4 of HNF1A gene (NM_001306179.2:c.811del, non-functional gene product and leads to nonsense mediated decay, which is an established disease mechanism (ACMG: PVS1).

This particular variation is not seen in her mother and her sibling (Figure 2) and is likely a spontaneous mutation in the proband (ACMG: PM6). The variant is not found in gnomAD population database (ACMG: PM2). Variants in other genes that are known to cause diabetes were also considered for analysis, and no other significant variants were found (ACMG: PP4). The variant was classified by ClinVar as Likely Pathogenic (ACMG: PP5) based on unpublished results [13]. Based on above ACMG criteria, we recommend this particular variant to be re-classified as ‘Pathogenic’ for MODY3.

Figure 2: Sanger sequencing confirmation of the variant in the mother and brother of the proband.

Various types of mutations in HNF1A gene have been identified in diabetic patients [8 -11]. The most common mutations are c.872dupC in exon 4 (present in 234 affected families) and c.391C>T in exon 2 (present in 29 affected families) [14]. But the variant reported in this case study has not been reported in the Indian population to the best of our knowledge. Mutations in the HNF1A gene can alter the normal functioning of the pancreas, impairing insulin synthesis and leading to high blood sugar levels. Affected people have hyperglycemia and a higher chance of developing other issues, such as diabetic nephropathy and cardiovascular problems. Patients with HNF1A mutations have been observed to respond particularly well to sulfonylurea, according to research. Its use can postpone the requirement for insulin therapy and, over time, lessen microvascular problems [15]. Though the current study could identify the genetic cause of diabetes it is limited in terms of lack of follow-up on the patient's response to sulfonylurea therapy.

Conclusion

According to 2019 predictions, 77 million Indians have diabetes, and by 2045, that number is projected to rise to 134 million. Finding the genetic basis of diabetes is crucial for effective treatment and a better prognosis. Correct therapy at the earliest phases of the illness will result in fewer health issues and better management. The case study presented here strongly supports the need for genetic testing for diabetic therapy.

Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Conflict of Interest

The authors declare no potential conflicts of interest.

Author Contributions

Material preparation and wet lab analysis was performed by (Satish Sunkara), pipeline development by (Sandhyakiran Pemmasani), in silico analysis and variant identification by (Neelima Chitturi), the first draft of the manuscript was written by (Neelima Chitturi) and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Compliance with Ethical Standards and Ethical Approval

An informed written consent mentioning the use of the sample for research was taken from the participants. Research was carried out in compliance with the Helsinki declaration and the procedures have been approved by internal bio-safety committee at Mapmygenome.

Funding

This study was not funded by any agency.

Consent to Participate and/or Consent to Publish

Informed written consent was obtained from all individual participants included in the study. The authors affirm that human research participants provided informed consent for publication of the image in Figure 2.

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