Leukodystrophies (LDs) are a heterogeneous group of rare and progressive genetic diseases that affect brain, spinal cord and often the peripheral nerves. They are characterized by abnormal development or destruction of the myelin sheath of the brain. This study was aimed to search for the causative variants in three unrelated consanguineous families presented with LD. Detailed clinical investigations were carried out on probands in three unrelated consanguineous families of Pakistani origin. Targeted gene sequencing and Whole Exome Sequencing (WES) were performed for variant identification. Candidate variants were checked for co-segregation with the phenotype using Sanger sequencing. Public databases including ExAC, gnomAD, dbSNP and the 1,000 Genome Project were searched to determine frequencies of the alleles. Conservation of the missense variants was ensured by aligning orthologous protein sequences from diverse vertebrate species. Targeted gene sequencing identified a novel homozygous missense mutation [c.2135G>A, p.(Arg712His) in the ATP Binding Cassette Subfamily D Member 1 (ABCD1; OMIM# 300371) in three affected siblings in family A.WES followed by validation by Sanger sequencing revealed previously reported homozygous missense variants [c.162C>A; p.(Asn54Lys)] in ASPA (OMIM# 608034) in family B and [c.361G>C,p.(Gly121Arg)] in ARSA (OMIM# 607574) in family C. Investigation of three families underlies importance of WES as an amazing diagnostic tool for conclusive determination of a specific type of LD. Further, the study would assist in carrier testing and prenatal diagnosis of the affected families. In addition, searching for common variants in the genes causing LD would help in designing low-cost targeted variation testing in patients.