Genetic Analysis of Mental Retardation in Pakistan Genetic defects are estimated to account for more than 50% of Intellectual disability (ID) cases, which is a highly heterogeneous genetic disorder with a prevalence of 1 to 2.5% in the World. A number of mutations in more than 450 different genes have been found to be involved in the pathogenesis of Intellectual disability (ID) including X linked ID as well as Autosomal dominant ID but very few data are available for autosomal recessive syndromic as well as nonsyndromic ID. In the current study sixteen different families (namely MRQ1, MRQ2, MRQ5, MRQ8, MRQ11, MRQ12, MRQ14, MRQ15, MRQ16, MRQ17, MRQ18, MRQ19, MRQ20, D1, PKMR71 and PKMR176) were selected for molecular analysis, which also included the detailed clinical investigation of affected members. Diverse methodologies were employed to find the genetic cause among the families such as candidate gene analysis, microarray analysis and exome sequencing. Homozygosity mapping of eleven families (MRQ1, MRQ2, MRQ5, MRQ11, MRQ12, MRQ14, MRQ15, MRQ17, MRQ19, MRQ20 and D1) was performed using the Affymetrix 2.5K SNP microarray. Candidate gene analysis among the obtained homozygous regions lead to the identification of three novel mutations in three known ID genes RBBP8, BBS10 and TPO in families MRQ12, MRQ19 and MRQ18 respectively. RBBP8 sequencing identified the mutation c.919A>G, p.Arg307Gly in family MRQ12, while there was a 10bp deletion in exon 2 of BBS10, c.1958_1967del (p.Ser653Ilefsx4) in family MRQ19 and a missense substitution c.14C>G, p.Ala5Gly was found in the TPO gene. The latter was probably not the cause of ID in the family MRQ18 due to low pathogenicity score. The data of Affymetrix 2.5K SNP microarray was also analyzed for copy number variations in which three microdeletions of 607kb, 455kb and 444.26kb were found in three families i.e. MRQ12, D1 and MRQ5, respectively. The heterozygous microdeletion of 607kb in family MRQ12 encompasses the exon 13-19 of gene NRXN1 including part of α- promoter as well as the β- promoter of NRXN1, while the heterozygous microdeletion of 455kb in patient ixof family D1encompasses first seven exons of the gene NRXN1 including the α- promoter. Another heterozygous microdeletion of 444.26 kb was found in four affected members from two branches of MRQ5 in the region of chromosome 15q11.1. The region was highly polymorphic as reported in many previous studies hence the microdeletion found in the current study was probably not involved in pathogenesis of ID in family MRQ5. In three recessive families MRQ11, MRQ14 and MR15 exome sequencing revealed multiple homozygous and compound heterozygous variants, however, segregation analysis by Sanger sequencing identified three novel variants in three novel genes ZNF589, MLL4 and HHAT to be causative genes in these families. The variant in gene ZNF589 in family MRQ11 was c.1604C>A, p. L319H, while the variant c.2456C>T, p.P819H found in family MRQ14 was identified to be causing Kleefstra syndrome in this family in a unique autosomal recessive mode of inheritance. A de novo heterozygous variant c.1158G>C, p.W386C was found in family MRQ15 in HHAT. The involvement of HHAT in nonsyndromic ID has not been reported previously, however, it has been shown to cause holoprosencephaly in a mouse model. The current study reveals that ID is a highly heterogeneous disorder and there probably are many more genes which are involved in pathogenicity of this disorder and that the advance techniques such as microarray analysis and exome sequencing are powerful techniques to find the causative mutations in such genetic disorders.