Movement disorders are neurological syndromes characterized by excess or paucity of movements. They are a large group of complex and clinically heterogeneous disorders and many of them have a genetic cause. The genetics of movement disorders is understudied in Pakistan. Consanguineous families are best suited to elucidate the causes of recessively inherited disorders. Next generation sequencing technology further facilitates gene identification. Ten families with multiple affected individuals were recruited in this study. All patients in the families presented different degrees of abnormalities including complete loss of voluntary movements, abnormal postures of upper and lower limbs, unusual gait, with or without abnormal ocular movements. All the affected members were videotaped according to a standard protocol and diagnosed by medical experts in Germany. Physical tests, biochemical tests, and neuroimaging were performed for the affected participants. Whole exome sequencing was performed for two to five samples from each of nine families. Variants were filtered based on zygosity, their frequency in public databases and prioritized based on their effect on the encoded proteins. Only those variants were considered that were homozygous in the affected individuals and segregated with the phenotype. Candidate variants were sequenced in all available family members for validation and segregation analyses. A functional assay was performed for a missense variant to check the localization of mutant protein in cells. The genetic causes of the disorder in five of nine families were identified. A novel nonsense variant in APTX was identified in family RDHM-02 and the disorder was diagnosed as ataxia with oculomotor apraxia type 1. Clinical phenotypic variability was observed among the affected members of the family. A novel single base pair duplication in SACS was identified in family RDHM-01. SACS variants have been described previously in spastic ataxia of the Charlevoix-Saguenay (ARSACS). All affected members of family RDHM-01 had ataxia, bradykinesia including hypomimia, mild dystonic postures of the upper limbs, supranuclear gaze palsy, and spasticity. Brain MRI of one affected individual showed severe vermal atrophy, the characteristic feature of ARSACS patients, and other brain structures abnormalities including global subcortical atrophy. Global white matter atrophy was not observed in previously reported ARSACS patients. A novel seven base pair deletion in ATCAY was found in family RDHR-04. ATCAY variants have only been reported in a few individuals with Cayman cerebellar ataxia from Cayman Island. The phenotype in all affected members of family RDHR-04 was characterized by a wide-based ataxic gait and dystonic postures of the upper limbs. They also had strabismus and apraxia, as well as some cognitive impairment. The mild bibrachial dystonia observed in RDHR-04 was a new feature associated with Cayman ataxia. Severe cerebellum atrophy was observed in cranial MRI of two affected individuals. A novel missense variant of MCOLN1 was identified in family RDHM-03, which encodes mucolipin 1. Both affected individuals had adolescent onset generalized dystonia, mild ataxia and were mildly bradykinetic. Of note, MCOLN1 variants have been reported as a cause of mucolipidosis IV, which is a neurodegenerative lysosomal storage disorder characterized by psychomotor retardation and ophthalmologic abnormalities. MCOLN1 variant (c.551T>C, p.Ile184Thr) did not affect the localization of mucolipin 1 when transfected into fibroblast cells as compared to wild-type. It indicates that the variant affects the protein by a different pathway. This finding perhaps explains the association of this variant with a different phenotype as compared to that reported for variants resulting in mucolipidosis IV. Finally, a novel missense variant in ECEL1 was found in family RDHR-01. ECEL1 variants have been reported to cause an autosomal recessive disorder known as distal arthrogryposis, type 5D Affected individuals in family RDHR-01 presented a phenotype associated with an unusual gait, ptosis, limbs contracture, curved fingers, and adducted thumbs. The affected individuals were initially enrolled on the basis of the dystonic postures of their upper and lower limbs. However, the identification of the genetic cause of the disorder helped in the correct diagnosis of these individuals from family RDHR-01, which was not possible solely based on the phenotype. The current study has revealed a high rate of clinical and genetic heterogeneity among the enrolled families. This suggests that only the clinical phenotypes are not sufficient to distinguish and diagnose a particular rare movement disorder. Therefore, this complexity can be resolved by exome sequencing which leads to the ultimate detection of disease-causing variants for highly heterogeneous disorders. These rare genetic variants are involved in pathogenesis and also expand the phenotypic spectrum of some of these movement disorders. The families in which no genetic cause was identified demonstrate that some pathogenic variant can be missed by exome sequencing. These families could be molecularly characterized by genome sequencing in future. These findings will reveal new variants in known genes or implicate variants in new genes, perhaps with novel disease mechanisms. This will increase the understanding of involved genes and their pathophysiology in movement disorders.