There have been incredible breakthroughs in the field of human genetics in the last few decades. Phenotypic diversity and genome evolution takes place due to genetic variation. Localization and identification of these genetic variants associated with disease is possible with the help of techniques used for manipulation of normal and mutant genes. Linkage analysis, haplotype analysis and DNA sequencing are used for the identification of genomic regions associated with genes and mutational analysis of genes. Pakistani population is a good candidate for genetic linkage analysis due to the large family size and higher rate of consanguineous marriages leading to higher risk of inherited diseases in this population. These large inbred families are very good candidates for mapping the genes behind the disease. The aim of this thesis is to identify the genes, mutations and regions underlying some inherited skin disorders i.e Ectodermal Dysplasia (ED), Alopecia (AP), Nail dysplasia (ND), Mal de Meleda (MDM), and Icthyosis. This Study will contribute to our understanding of human genetics and will shed light to dysfunction of genes in development and disease as the first step is always been the identification of tentative genes affecting the normal development, in this case Skin and Nails. ED comprises a heterogeneous group of developmental abnormalities constituting about 200 clinical entities. All EDs are characterized by impaired development of at least two of the epidermal appendages hair, nails, teeth and sweat glands. Approximately 30 EDs have been characterised at the molecular level. Odonto-onycho-dermal dysplasia (OODD) is a rare syndrome characterized by severe hypodontia, nail dystrophy, smooth tongue, dry skin, keratoderma and hyperhydrosis of palms and soles. A large consanguineous Pakistani pedigree comprising six individuals affected by a complete OODD syndrome was investigated. Autozygosity mapping using SNP array analysis showed that the affected individuals are homozygous for the Wnt10A gene region. Subsequent mutation screening showed a homozygous c.392C4T transition in exon 3 of Wnt10A, which predicts a p.A131V substitution in a conserved a-helix domain. First inherited missense mutation in Wnt10A with associated ectodermal features was observed. Mutations in EDA1 are underlying cause of inherited X-linked hypohidrotic ectodermal dysplasia (XLHED). A large consanguineous Pakistani kindred was investigated with hypohidrotic ED. Careful pedigree analysis suggested X-linked recessive inheritance. There were five affected male and four carrier females in the family. They presented with classical phenotype of disorder. Sequencing revealed a 4-bp insertion at nucleotide position 913 (913_914insTATA) in all affected family members investigated. The mutation is located in exon 8 and results in frameshift and a premature stop codon 2-bp downstream in the same exon. Another type of ED is “Pure hair-nail ectodermal dysplasia”: a rare subgroup with variable expression. A multigenerational consanguineous Pakistani family with four members affected by “pure hair-nail ectodermal dysplasia” was identified. Linkage was confirmed with microsatellite markers on chromosome 12 with maximum LOD score 2.92 (θ=0.0) at marker locus D12S368 suggesting linkage to this region. Further investigations associate this hair-nail type ectodermal dysplasia with novel gene present on chromosome 12p11.1-q14.3. Atrichia with papular lesions (APL) is a rare autosomal recessive form of congenital Alopecias characterized by onset of complete or near to complete irreversible alopecia or loss of hair soon after birth or in first few months of life. Diagnosis of APL involves autosomal recessive form of transmittance of disease with possible consanguinity of parents, hair either present at birth or not that never re-grow and presence of papules. APL has been mapped to 8p12 and identification of Human Hairless (HR) gene mutations are associated with its pathogenesis. Atrichea with papules has equal prevalence in both men and women but exact prevalence is still unknown. A novel homozygous missense c.2427 C>T transition in exon10 of HR gene was identified that results in p.A765V substitution and small variation of phenotype in a consanguineous Pakistani family in all affected individuals. Developmental abnormalities of the nails constitute a large and extremely heterogeneous group of disorders. These abnormalities have a wide range of appearance in form of slight and hardly noticeable change to the complete absence of nails. These can be inherited as isolated abnormality or part of complex syndromes with associated abnormalities of other ectodermal appendages. A large family with isolated congenital anonychia as sole phenotype and consanguineous pedigree with autosomal recessive inheritance was ascertained. Linkage was confirmed to 20p13 to RSPO4 gene using multi allelic microsatellite markers. A maximum two point LOD score was obtained at marker locus D20S199 (θ =0.00) 3.92 suggestive of linkage. RSPO4 gene was sequenced in two affected individual of the family, which revealed G to A transversion at nucleotide position 353 in exon 3, resulting in a (p.Cys118Tyr) amino acid substitution. Another consanguineous Pakistani family with four members affected by isolated congenital autosomal recessive nail dysplasia was investigated. Claw-like pachonychia, nail clubbing and onycholysis of both finger and toenails was present in affected individuals but no other ectodermal symptoms. Genetic analysis on the family using a 250K SNP array (Affymetrix) revealed a genomic region spanning more than 90 homozygous SNPs on chromosome 8 found to be shared by affected individuals. Linkage analysis with microsatellite markers revealed a maximum LOD score of 2.96 (θ=0) at polymorphic microsatellite marker D8S1122 chromosome 8. Recombination events restricted the candidate region to 18 Mb which spans approximately 100 genes. Sequencing revealed a nonsense c.1750G>T (p.Gly584) substitution in homozygous form in Frizzled 6 gene in exon 6. MDM or keratosis palmoplantaris transgrediens of Siemens is a rare genodermatosis which belongs to Palmo planter keratoderma PPK; a heterogeneous group of disorders by clinical and genetic definitions. Characteristic features are abnormal thickening of skin of palms and soles soon after birth and progresses to the dorsal epidermis of hands and feet with age. A consanguineous Pakistani family appeared with MDM. ARS component B gene associated with MDM phenotype found mutated in affected members. Linkage was confirmed to 8qter regions using multi allelic microsatellite marker and maximum two point LOD score was obtained at marker locus D8S161 (θ =0.00) 2.41 suggestive for linkage. Sequencing revealed a homozygous c.256 G>A transition in all 4 affected family members investigated. The mutation is located in exon 3 and results in a p.G86R substitution. Nonbullous congenital ichthyosiform erythroderma (NBCIE) is autosomal recessive congenital ichthyosis with prominent features of generalized severe white scaling all over the body and erythrodermic skin without blister formation. ABC12, causal gene is localized on chromosome 2q33-35 belongs to a subfamily of ATP-binding cassette (ABC) transporters which implicate in some autosomal recessive disorders pertaining to lipid metabolism. An extended consanguineous Pakistani family exhibiting autosomal recessive inheritance and classic phenotype of NBCIE was investigated. Sequencing revealed a novel homozygous c.4896 G>T transition in all 4 affected family members investigated. The mutation is located in exon 31 and results in a p.G1241V substitution.