Neurodegenerative movement disorders (NDMDs) is a heterogeneous group of neurological diseases which are caused by selective loss or death of neurons and distinct involvement of functional systems defining movement disability. Proteins with altered physicochemical properties are deposited in the human brain in NDMDs. Not only neurons but glial cells also accumulate these proteins. Intra or extra-cellular Accumulation of structurally deformed and physiologically impotent protein result in the death of neurons as well as glial cells. Neurons are the functional building blocks of the central nervous system, which includes the brain and spinal cord. Mature neurons are post-mitotic and therefore incapable of self-renewal. Morphologically a typical neuron has cell body and processes (Axons and dendrites) which mediate synaptic communication. Glial cells have complex processes extending from their cell bodies; they are generally smaller than neurons. They lack axons and dendrites, do not participate directly in synaptic interactions and electrical signaling, although their supportive functions help define synaptic contacts and maintain the signaling abilities of neurons. NDMDs are incurable and debilitating conditions that result in progressive degeneration and or death of neurons and associated cells. Parkinson‘s disease (PD) is the most common NDMD. Pathologically PD is a complex disease of the mid brain, primarily affecting the substantia nigra (SN) which is densely populated with dopaminergic neurons. The death of SN neurons results in loss of smooth and coordinated skeletal muscle movement. Parkinson‘s disease is generally considered complex and multifactorial disease. Rarely PD runs as a Mendelian trait in families. The familial form of PD is considered to be monogenic. Diverse genetic strategies have been employed to understand genetic risk factors and causes in sporadic and familial forms of PD. Since the genetics of sporadic and familial forms of PD and other NDMDs has not previously been investigated in Pakistan, the objective of this study was to elucidate the role of common genetic risks such as variants in the SNCA, LRRK2, DJ1, CYP2D6 genes in sporadic PD in the Pakistani population and to identify genetic causes of familial PD and other NDMDs in Pakistan. In summary a case-control study, was done and total of 374 subjects including 174 clinically diagnosed PD patients and 200 ethnically matched healthy controls to find Abstract Molecular Genetic Study of Neurodegenerative Movement Disorder in Pakistani Population Page xiv the possible genetic associations and risk factors for Parkinson‘s disease in this population sample. Allele specific PCR and PCR-RFLP was used for screening of previously reported pathogenic single nucleotide polymorphisms (SNPs) in SNCA, LRRK2, DJ1 and CYP2D6 genes. Randomly 20% samples were selected for bidirectional Sanger sequencing to confirm the results. No association was observed for commonly reported variants e.g., rs104893875 (G>A), rs104893877 (G>A), rs104893878(C>G) in the SNCA, rs34805604 (A>G), rs33939927(C>G/T), rs35870237 (T>C), rs34637584 (G>A), rs34778348 (G>A), in the LRRK2 and rs74315354 (G>A) in the DJ1. A strong association was observed in case of rs3892097 (G>A) in the CYP2D6. An increase in the risk of Parkinson by two fold (OR: 2.9; 95% CI 1.5 to 5.50, p = 0.02) was calculated for carriers of rs3892097 (G>A) risk allele (A-allele). Whole genome sequencing and segregation analysis was carried out for three PD families (A, B and C) an atypical Parkinsonian family (D), a Wilson‘s disease family (E) and one family with rare movement disease with periventricular white matter neurodegenerative changes (F). Family (A) with autosomal dominant PD co-segregated with GBA (exon9:c.T1301C:p.434L>P) and PSAP (exon5:c.A470G:p.157N>S) a novel coinheritance of the two genes. Family (B) co-segregated with SEMA6A (exon10:c.G860C:p.287G>A) novel gene (mutation) in autosomal dominant Parkinson‘s disease. Family (C) co-segregated with AAK1 (exon17:c.C2312G p.771P>R) novel gene (mutation) in autosomal recessive Parkinson‘s disease. One family with atypical Parkinson‘s disease Family (D) co-segregated with CSF1R (c.1237G>Ap.G413S) a novel mutation with reported gene for leukodystrophy and atypical Parkinson‘s disease. An autosomal recessive family (E) with Parkinson‘s like symptoms revealed recurrent mutation ATP7B (c.2930C>T p.T977M) for Wilson‘s disease. One family (F) with autosomal recessive movement disorder co-segregated with GPR56 g.57654049 G>C splice site mutation and PCLO exon3:c.G2473A:p.A825T. Minigene assay exclude the splice site mutation in the GPR56 g.57654049 G>C. Thus a novel mutation in PCLO (exon3:c.G2473A:p.A825T) co-segregated in this family.