Muhammad Nasim Khan

Biallelic Truncating Mutations in FMN2, Encoding the Actin-Regulatory Protein Formin 2, Cause Nonsyndromic Autosomal-Recessive Intellectual Disability

Dendritic spines represent the major site of neuronal activity in the brain; they serve as the receiving point for neurotransmitters and undergo rapid activity-dependent morphological changes that correlate with learning and memory. Using a combination of homozygosity mapping and next-generation sequencing in two consanguineous families affected by nonsyndromic autosomal-recessive intellectual disability, we identified truncating mutations in formin 2 (FMN2), encoding a protein that belongs to the formin family of actin cytoskeleton nucleation factors and is highly expressed in the maturing brain. We found that FMN2 localizes to punctae along dendrites and that germline inactivation of mouse Fmn2 resulted in animals with decreased spine density; such mice were previously demonstrated to have a conditioned fear-learning defect. Furthermore, patient neural cells derived from induced pluripotent stem cells showed correlated decreased synaptic density. Thus, FMN2 mutations link intellectual disability either directly or indirectly to the regulation of actin-mediated synaptic spine density.

Novel protein-truncating mutations in the ASPM gene in families with autosomal recessive primary microcephaly.

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder that causes reduction in brain size. Individuals affected with the disorder show a small but architecturally normal cerebral cortex and are associated with mental retardation of mild-to severe form. MCPH is genetically heterogeneous with six loci, and four genes have been identified so far. Homozygous mutations in the ASPM gene, located at MCPH5 locus on chromosome 1q31, are the most common cause of MCPH particularly in the Pakistani population. In the present study, we have ascertained ten Pakistani and one Kashmiri family with primary microcephaly. We screened for potential mutations of the ASPM gene in seven consanguineous families (six Pakistani and one Kashmiri) linked to MCPH5 locus. Two previously reported (8508delGA, W1326X) and four novel sequence variants (Y1712X, I1717X, Y3353X, R3244X) were detected and all were predicted to be protein truncating. The degree of mental retardation in the affected individuals of the seven families varied from mild to moderate, and was not dependent on the location of mutations in the ASPM gene.

Atrichia with papular lesions resulting from a novel insertion mutation in the human hairless gene

Background.  Congenital atrichia with papular lesions is a rare, recessively inherited condition of total alopecia, characterized clinically by complete and irreversible hair loss, which begins shortly after birth with the development of the papular lesions of keratin‐filled cysts over an extensive area of the body. Mutations in the human hairless (HR) gene have been implicated in the pathogenesis of this disorder.

Novel homozygous mutations in the genes ARL6 and BBS10 underlying Bardet-Biedl syndrome.

Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder resulting from structural and functional defects in numerous organs. Frequent manifestations reported in the syndrome include obesity, renal dysplasia, cognitive impairment, postaxial polydactyly, pigmentary retinal degeneration and hypogonadism. To date, 17 genes causing BBS have been identified. Two of these BBS1 and BBS10 are the most frequently mutated genes. The present report describes two consanguineous families (A, B) with clinical manifestations of BBS. Linkage in the family A was established to ARL6 on chromosome 3q11.2, while family B showed linkage to BBS10 on chromosome 12q21.2. Sequence analysis revealed a novel homozygous missense mutation (c.281T>C, p.Ile94Thr) in the gene ARL6 in family A and a nonsense mutation (c.1075C>T, p.Gln359*) in the gene BBS10 in family B. Mutations identified in the present study extend the body of evidence implicating the genes ARL6 and BBS10 in causing Bardet-Biedl syndrome.

Novel mutations in the gene HOXC13 underlying pure hair and nail ectodermal dysplasia in consanguineous families

provides evidence that this type of AN might be due to impaired expression of the insulin receptor and supports a role for the insulin receptor in the normal physiology of the epidermis. The AN phenotype is known to be associated with the activation of tyrosine kinase growth factor receptors affecting keratinocyte proliferation; however, the mechanism for the development of the skin pigmentation and its localization to the flexural areas of the body has yet to be elucidated.

Genetic analysis of four Pakistani families with achromatopsia and a novel S4 motif mutation of CNGA3.

BackgroundTo identify the causative variants of achromatopsia (ACHM) in four Pakistani families presenting autosomal recessive ACHM.MethodsFour families (50, 55, 70 and 74) exhibiting features of achromatopsia were subjected to homozygosity mapping with STS markers flanking known ACHM loci. Mutation screening was done for two of the families linked to CNGA3 and CNGB3 by direct sequencing of the coding regions and exon-intron boundaries of genes to find the pathogenic variant.ResultsHomozygosity mapping showed co-segregation of CNGA3 in family 50 and CNGB3 in family 74. Sequencing of coding regions of CNGA3 in family 50 revealed a novel missense mutation, c.827A>G, in exon 7, which results in p.N276S substitution. N276S is located in the S4 motif of the CNGA3 protein and is conserved in all channel proteins. Bioinformatics analysis showed that the N276S substitution altered the channel conformation by shifting the helix. No pathogenic variation was identified in any affected members of family 74 in the coding sequence of CNGB3. The other two families, 55 and 70, were not linked to any known ACHM loci, indicating further heterogeneity of the ACHM phenotype.ConclusionsWe describe a novel S4 motif mutation of CNGA3 in a Pakistani family.

A novel splice site mutation in gene C2orf37 underlying Woodhouse–Sakati syndrome (WSS) in a consanguineous family of Pakistani origin

Woodhouse-Sakati Syndrome (WSS) is a rare autosomal recessive multisystemic disorder that is marked by hypogonadism, alopecia, intellectual disability, deafness, diabetes mellitus and progressive extrapyramidal defects. Mutations in the gene C2orf37 are the cause of Woodhouse-Sakati syndrome. In the present study, a four-generation consanguineous family with clinical manifestations of WSS was ascertained from a remote region of Pakistan. Linkage in the family was tested using microsatellite markers linked to several genes involved in producing WSS related phenotypes. Linkage in the family was established to the gene C2orf37, mapped on chromosome 2q22.3-2q35. DNA sequence analysis revealed a novel splice site mutation involving a homozygous G→A transition in the splice donor site of intron 3 (c.321+1G>A) of C2orf37. This study presents a first report of Woodhouse-Sakati syndrome identified in Pakistani population.

A novel recessive mutation in the gene ELOVL4 causes a neuro-ichthyotic disorder with variable expressivity

BackgroundA rare neuro-ichthyotic disorder characterized by ichthyosis, spastic quadriplegia and intellectual disability and caused by recessive mutations in ELOVL4, encoding elongase-4 protein has recently been described. The objective of the study was to search for sequence variants in the gene ELOVL4 in three affected individuals of a consanguineous Pakistani family exhibiting features of neuro-ichthyotic disorder.MethodsLinkage in the family was searched by genotyping microsatellite markers linked to the gene ELOVL4, mapped at chromosome 6p14.1. Exons and splice junction sites of the gene ELOVL4 were polymerase chain reaction amplified and sequenced in an automated DNA sequencer.ResultsDNA sequence analysis revealed a novel homozygous nonsense mutation (c.78C > G; p.Tyr26*).ConclusionsOur report further confirms the recently described ELOVL4-related neuro-ichthyosis and shows that the neurological phenotype can be absent in some individuals.

A novel chondroectodermal dysplasia mapped to chromosome 2q24.1-q31.1

Chondroectodermal dysplasias are genetically heterogeneous group of disorders involving defects in one or more ectodermal appendages (hair, nail, teeth and sweat glands) in association with anomalies of the cartilage. In the present study a novel form of chondroectodermal dysplasia, segregating in an autosomal recessive pattern in a Pakistani family, was investigated. The clinical features including proportionate short stature, osteopenia with fracturing and breaking of bones, hypodontia, hypertrophic and convex shaped nails, night blindness, watering eyes and infection of ears were observed in affected individuals of the family. Genetic linkage study mapped the novel autosomal recessive form of chondroectodermal dysplasia on human chromosome 2q24.1-q31.1. Linkage to the region was established by scanning human genome using Human Mapping 250K Nsp array. Linkage interval for chondroectodermal dysplasia on human chromosome 2q24.1-q31.1 spans 13.76 cM, which corresponds to 15.72 Mb according to the sequence-based physical map (Build 36.2). The maximum multipoint LOD score of 3.37 was obtained with several markers along the disease interval. Sequence analysis of three candidate genes (TANK, ITGB6, TBR1) located in the candidate interval did not discover potentially causal variants.

Genetic causes of MCPH in consanguineous Pakistani families.

To the Editor: Autosomal recessive primary microcephaly (MCPH) is a rare and genetic heterogeneous neurodevelopmental disorder characterized by a pronounced reduction of brain volume and intellectual disability (1, 2). To date, 13 MCPH genes have been identified [reviewed in (3)], 8 of them in the last 5 years, showing the rapid progress in this field. Still, families with an MCPH phenotype who do not carry mutations in these known MCPH genes exist, indicating further genetic heterogeneity. Here, we report the results of a genetic study on a cohort of 15 consanguineous families (46 affected individuals) with an MCPH phenotype from the Azad Jammu and Kashmir (AJK) territory in Northern Pakistan (Table 1, Fig. S1, Supporting Information). All families were examined clinically on field trips with microcephaly and intellectual disability detected in all