Mapping of Genes Involved in Neurological Disorders in Pakistani Families

Abstract

Neurological disorders are diverse group of diseases mostly induced by specific genetic factors some of which are monogenic, while others are heterogeneous in nature. The present study was aimed to investigate the genetic basis of two hereditary neurological disorders in Pakistani Families: Non-Syndromic Autosomal Recessive Intellectual Disability (NS-ARID) and Congenital Mirror Movement. Mental retardation, now referred to as intellectual disability (ID), is a neurodevelopment disorder characterized by impairment in conceptual, practical, social skills and an intelligence quotient (IQ) below 70 before the age of eighteen. It is prevalent in 1-3% of population but presumed to be higher where consanguineous marriages are common. The Mirror Movement (MRMV) refers to involuntary, synkinetic mirror reversals of an intended movement of opposite side”. MRMV is found in young children and gradually disappears within the first decade of life. If mirror movement persists after the first decade of life with no clinical features it is referred as congenital mirror movement. MRMV is a rare disorder, mainly inherited in an autosomal-dominant fashion although sporadic cases of recessive form may also exist. In this study four consanguineous Pakistani families with hereditary neurological disorder including three (A, B and C) of NS-ARID and one Family of MRMV (D) were investigated. In Families A, B, C and D, Whole Genome Single Nucleotide Polymorphism (SNP) Genotyping microarray (250K Affymatrix) identified homozygosity by decent (HBD) on chromosomes 11q25.1-q25, 7p12.1-p11.2 and xvii 7p12.1-p11.2 in families A to C respectively, and a ~3.3Mb on chromosome 22q13.1 in Family D. In Family A, analysis of genes of locus 11q25.1-q25 with Whole Genome Exome Sequences followed by Sanger Sequences revealed 678G>A splice donor site mutation in the exon-intron junction of 4 and 5 of Decapping Scavenger (DCPS) gene on chromosome 11q24.2 which resulted in alteration of splice site from GT>AT and shifting to a cryptic splice site 45bp downstream which caused incorporation of 45 nucleotide in final transcript. Another heterozygous mutation was identified in one affected individual (V:7) of Family A, where 947C>T in DCPS gene and rendering that individual as compound heterozygous. In vitro, analysis of mutant DCPS protein showed reduced expression level and enzymatic activity as compared to wild type. The locus 7p12.1-p11.2 of the Family B showed 997C>T transition in Phosphoserine phosphatise (PSPH) gene in two affected individuals (II:4 and III:4) whereas one affected (III:3) and three normal individual (II:1, II:2 and III:2) were heterozygous for this mutation. Amino acid quantification assay showed normal serine and glycine level in blood plasma of affected individuals. In Family C, COLGALT2, C1orf21, NMNAT2, RGL1, RNF2, TSEN15, ARPC5, SHCBP1L, SMG7 and NPL gene of locus 1q25.3-q31.1 were sequenced however no pathogenic sequence variation was found. In Family D, the autozygous region of ~3.3Mb on chromosome 22q13.1 (Chr22:36605976-39904648) was identified. Whole Exome Sequence (WES) reads identified a potential donor splice site mutation 2 nucleotides within intron 3 of the Dynein Axonemal Light chain 4 gene, DNAL4: chr22:39176929A>G; NM_005740.2 xviii (DNAL4_vNM_005740): c.153+2T>C. This substitution destroys the canonical “GT” splice donor site and resulted in skipping of exon 3. The removal of exon 3 results in an open reading frame of just 77 amino acid residues instead of 105, effectively a deletion of 28 amino acids (residues 24 to 51 inclusive). This variant was not in any SNP databases. Linkage analysis across the 22q region using Simwalk2 a maximum location score (directly comparable to multipoint LOD score) of 6.197 was calculated for markers D22S280 and DNAL4 (NM_005740): c.153+2T>C. Comparative protein sequence analysis for deleted stretch (residues from 24-51) of DNAL4 showed to be highly conserved across the Kingdom Animalia (or Metazoa).