A homozygous KLF1 gene mutation presenting as mild Thalassemia Intermedia unraveled by targeted Next Generation Sequencing

  1. Neetu Rani1,
  2. Manu Jamwal1,
  3. Jasbir Kaur1,
  4. Pankaj Malhotra2,
  5. Prashant Sharma1,
  6. Arindam Maitra3,
  7. Ranvir Singh4,
  8. Subhash Varma2 ,
  9. Reena Das1

Authors Affiliation(s)

  • 1Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, INDIA
  • 2Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, INDIA
  • 3National Institute of Biomedical Genomics, Kalyani, West Bengal, INDIA
  • 4Panjab University, Chandigarh, INDIA

Can J Biotech, Volume 1, Special Issue, Page 85, DOI: https://doi.org/10.24870/cjb.2017-a72

Presenting author: 23.neeturoyal@gmail.com


The krupple-like factor 1 (KLF1) is a crucial transcription factor that is responsible for the proper maturation of the erythroid cells. Recent studies have demonstrated that mutations in KLF1 gene may lead to increased fetal hemoglobin (HbF) and reduced or borderline hemoglobin A2 (HbA2) levels. Increased HbF levels and concomitant α-thalassemia are two main modifiers that can ameliorate the clinical and hematological severity of β-thalassemia. Mutations in KLF1 have been found in association with β thalassemia. DNA was extracted with QIAmp DNA Blood kit and quantified spectrophotometrically. Gap PCR was used to screen common HPFH deletions and Sanger’s sequencing was done to screen β-globin (HBB) mutations. Libraries were prepared using TruSight One sequencing panel and sequenced on MiSeq Sequencing System. MiSeq Reporter and Variant Studio were used for data analysis. A 56 years male presented with splenomegaly and unconjugated hyperbilirubinemia with normal hematological indices. Hemoglobin high performance liquid chromatography revealed 72.3% HbF, 0.5% HbA2 and 25.2% HbA0. Patient was found to be clinically consistent with mild TI. No mutation/s in HBB was found by Sangers sequencing. Hereditary Persistence of Fetal Hemoglobin (HPFH) deletions [HPFH1, HPFH2, HPFH3, ChineseG deletion, Asian-Indian inversion-deletion] were also found to be negative. Targeted resequencing revealed a novel homozygous probably causative mutation in KLF1 [c. 943C>T (p.Arg301Cys)]. This mutation was found to be probably damaging via PolyPhen2 and SIFT. The patients son showed 5% HbF with heterozygous mutation. This is the first report from India where a homozygous mutation in KLF1 gene isimplicated with high HbF in a patient with TI. Thus, mutations which affect the activity of KLF1 gene may lead to high level offetal hemoglobin in patients presenting as TI with no HBB mutations.