What question did this study set out to answer?

This research aims to analyze genetic variations in Indonesian thalassemia patients and evaluate their functional effects using in silico methods.

February 12, 2026F1000Research1 citationsOpen Access

Mutational and Functional Impact of β-globin Gene Mutation in Indonesian Thalassemia Patients using in Silico Method

SASri Mufti Ardani NRNadhifa Tazkia Ramadhani YAYulia Ariani

Key Points

This research aims to analyze genetic variations in Indonesian thalassemia patients and evaluate their functional effects using in silico methods.
Recruited 20 Indonesian thalassemia patients for genetic analysis.
Extracted genomic DNA from blood samples using a commercial kit.
Amplified β-globin gene using Polymerase Chain Reaction (PCR) with specific primers.
Sequenced DNA using Sanger Sequencing and analyzed variants with bioinformatics tools.
Identified ten pathogenic variants and one rare variant in the β-globin gene.
Documented genetic variations included mutations like IVS1nt.1, IVS2nt.654, and Cd15.
Found that identified mutations had clinically relevant impacts on amino acid interactions.

Abstract

Introduction Indonesia is located along the “Thalassemia Belt, ” a hotspot region for hemoglobinopathies, including beta thalassemia, with approximately 3–10% of the Indonesian population diagnosed with this disease. Thalassemia was diagnosed using the Hb analysis results. However, the single nucleotide variant (SNVs) database for the Indonesian population, which leads to β-thalassemia disease, has not been extensively studied. This study aimed to profile the genetic variations in Indonesian β-thalassemia patients and conduct in silico characterization of their functional effects. Methods Twenty thalassemia patients were recruited for this study. The sample collected from the respondents was whole blood in EDTA tubes, with a minimum collection time of 14 days after blood transfusion. Genomic DNA (gDNA) was extracted using a commercial kit, directly amplified using Polymerase Chain Reaction (PCR) with specific primers for β-globin and sequenced using Sanger Sequencing. All variants located in exon regions were analyzed using FinchTV, BioEdit, and Biovia Discovery Studio to determine their functional impact. Results Ten reported pathogenic variants were observed along with one rare variant. Genetic variations found according to its common name and nomenclature based on Human Genome Variation Society (HGVS) are IVS1nt. 1 (HGVS: c. 92+1G>A), IVS1nt. 1 (HGVS: c. 92+1G>T), IVS1nt. 2 (HGVS: c. 92+2G>T), IVS1nt. 5 (HGVS: c. 92+5G>C), IVS2nt. 654 (HGVS: c. 316-197C>T), Cd15 (HGVS: c. 47G>A), Cd26 (HGVS: c. 79G>A), Cd30 (HGVS: c. 92G>C), Cd41/42 (c. 126₁29delCTTT), and Cd35 (HGVS: c. 110delC). Analysis of amino acid interactions revealed that disease-causing mutations were clinically relevant in each subject. Conclusions This study has bioinformatically proven the effect of genetic mutations and predicted their effect on amino acid interactions. These findings contribute to the study of Indonesian thalassemia and require further research.

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