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

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 patient’s son showed 5% HbF with heterozygous mutation. This is the first report from India where a homozygous mutation in KLF1 gene is implicated with high HbF in a patient with TI. Thus, mutations which affect the activity of KLF1 gene may lead to high level of fetal hemoglobin in patients presenting as TI with no HBB mutations.