Mutation spectrum in Pakistani patients with inherited metabolic disorders

Abstract

Inherited metabolic disorders constitute a diverse class of genetic diseases caused by impairment in biochemical processes because of defective enzymes or transporters consequent upon which compromised conversion of substrate into the product takes place. These disorders are manifested phenotypically with a wide overlapping spectrum of signs and symptoms that could either be due to accumulation of toxic upstream substrates, insufficient production of downstream products or abnormal alternative substrate metabolism. Biochemical and molecular investigations help in diagnosis of hereditary metabolic disorders and that if attempted early, could improve therapeutic outcome in some cases. The current study was performed to investigate the spectrum of genetic variants in Pakistani patients with inherited metabolic disorders. A cohort of sixty-eight patients was enrolled in the study from local hospitals. Twenty-five of these patients were diagnosed with inherited unconjugated hyperbilirubinemias, one with GM1 gangliosidosis, nineteen with various types of mucopolysaccharidoses (MPS), and twenty-three with Wilson’s disease. Genomic DNA samples of these patients were subjected to Sanger sequencing of respective genes. The identified variants were confirmed in families of the patients for segregation. Sequence analysis of UGT1A1 in twenty-five patients diagnosed with inherited unconjugated hyperbilirubinemias identified 16 different variants, six of which were novel. The c.622-625dupCAGC and c.1021C>T were the most frequently observed UGT1A1 variants. DNA sequencing of GLB1 in one patient diagnosed with GM1 gangliosidosis identified a novel homozygous 2-bp deletion c.881-882delAT (p.Tyr294Terfs) in exon 8. Among nineteen patients diagnosed with various types of mucopolysaccharidoses during the study period, MPS type I was the most prevalent phenotype. DNA sequencing of IDUA in MPS type I patients revealed a diverse spectrum of variants spanning the whole gene. A missense variant c.1469T>C (p.Leu490Pro) was the most common variant identified in five patients in homozygous condition. Mutations identified in other MPS types were all private mutations and include c.1006+1G>C, c.1165C>T in IDS, c.531+5G>A in NAGLU, c.902G>A, c.1175C>T, c.IVS4-1G>A in GALNS and c.511-512delGG in ARSB. DNA sequencing in a cohort of twenty-three Wilson’s disease patients identified a diverse spectrum of 18 ATP7B variants spanning over the whole gene. The mutation detection rate was 71.7% and seven of the identified variants were novel. The most frequently observed ATP7B variant was c.3809A>G followed by c.3182G>A. To our knowledge, this is the first comprehensive study of inherited metabolic disorders from Pakistan. It should be helpful in neonatal screening, improved genetic counseling, and prenatal diagnosis in the affected families.