Khadim Shah

Homozygous SLCO2A1 Translation Initiation Codon Mutation in a Pakistani Family with Recessive Isolated Congenital Nail Clubbing (ICNC).

Isolated congenital nail clubbing (ICNC; OMIM 119900) is a rare genodermatosis in which bilateral, symmetric enlargement of the nail plate and terminal segments of fingers and/or toes results from excessive proliferation of connective tissue between the nail matrix and distal phalanx. Loss of the normal angle between the nail and posterior nail fold is associated with a shiny, hypoplastic, thick-ended, long, broad nail. The thumbs are almost always involved, though some fingers or toes may be spared. Both autosomal dominant and autosomal recessive forms of ICNC have been described, sometimes associated with other systemic anomalies, which may include primary hypertrophic osteoarthropathy (PHO), the similar disorder pachydermoperiostitis (PDP), as well as cardiovascular, gastrointestinal, pulmonary and metabolic disorders.1,2 This article is protected by copyright. All rights reserved.

A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family

BackgroundPure hair and nail ectodermal dysplasia (PHNED) is a congenital disorder of hair abnormalities and nail dysplasia. Both autosomal recessive and dominant inheritance fashion of PHNED occurs. In literature, to date, five different forms of PHNED have been reported at molecular level, having three genes known and two loci with no gene yet.MethodsIn this study, a four generations consanguineous family of Pakistani origin with autosomal recessive PHNED was investigated. Affected members exhibited PHNED phenotypes with involvement of complete hair loss and nail dysplasia. To screen for mutation in the genes (HOXC13, KRT74, KRT85), its coding exons and exons-intron boundaries were sequenced. The 3D models of normal and mutated HOXC13 were predicted by using homology modeling.ResultsThrough investigating the family to known loci, the family was mapped to ectodermal dysplasia 9 (ECTD9) loci with genetic address of 12q13.13. Mutation screening revealed a novel missense mutation (c.929A > C; p.Asn310Thr) in homeobox DNA binding domain of HOXC13 gene in affected members of the family. Due to mutation, loss of hydrogen bonding and difference in potential energy occurs, which may resulting in alteration of protein function.ConclusionThis is the first mutation reported in homeodomain, while 5th mutation reported in HOXC13 gene causing PHNED.

Exome sequencing revealed a splice site variant in the IQCE gene underlying post-axial polydactyly type A restricted to lower limb.

Polydactyly is characterized by an extra supernumerary digit/toe with or without bony element. To date variants in four genes GLI3, ZNF141, MIPOL1 and PITX1 have been implicated in developing non-syndromic form of polydactyly. The present study involved characterization of large consanguineous family of Pakistani origin segregating post-axial polydactyly type A, restricted to lower limb, in autosomal recessive pattern. DNA of two affected members in the family was subjected to exome sequencing. Sanger sequencing was then followed to validate segregation of the variants in the family members. A homozygous splice acceptor site variant (c.395-1G>A) was identified in the IQCE gene, which completely co-segregated with post-axial polydactyly phenotype within the family. The homozygous variant was absent in different public variant databases, 7000 in-house exomes, 130 exomes from unrelated Pakistani individuals and 215 ethnically matched controls. Mini-gene splicing assay was used to test effect of the variant on function of the gene. The assay revealed loss of first nucleotide of exon 6, producing a −1 frameshift and a premature stop codon 22 bases downstream of the variant (p.Gly132Valfs*22). The study provided the first evidence of involvement of the IQCE gene in limbs development in humans.

Exome sequencing revealed a novel biallelic deletion in the DCAF17 gene underlying Woodhouse Sakati syndrome.

Woodhouse Sakati syndrome (WSS, MIM 241080) is a rare autosomal recessive genetic condition characterized by alopecia, hypogonadism, hearing impairment, diabetes mellitus, learning disabilities and extrapydamidal manifestations. Sequence variants in the gene DCAF17, encoding nucleolar substrate receptor, were identified as the underlying cause of inherited WSS. Considerable phenotypic heterogeneity exists in WSS with regard to severity, organs involvement and age of onset, both in inter‐familial and intra‐familial cases. In this study, the genetic characterization of a consanguineous pedigree showing mild features of WSS was performed, followed by structural analysis of truncated protein. Exome sequencing identified a novel single base deletion variant (c.270delA; K90Nfs8*) in third exon of the gene DCAF17 (RefSeq; NM_025000), resulting in a truncated protein. Structural analysis of truncated DCAF17 revealed absence of amino acid residues crucial for interaction with DDB1. Taken together, the data confirmed the single base pair deletion as the underlying cause of this second report of WSS from Pakistan. This signifies the vital yet unexplored role of DCAF17 both in development and maintenance of adult tissues homeostasis.

Molecular and in silico analyses validates pathogenicity of homozygous mutations in the NPR2 gene underlying variable phenotypes of Acromesomelic dysplasia, type Maroteaux

Homozygous and/or heterozygous loss of function mutations in the natriuretic peptide receptor B (NPR2) have been reported in causing acromesomelic dysplasia, type Maroteaux with variable clinical features and idiopathic short stature with nonspecific skeletal deformities. On the other hand, gain of function mutations in the same gene result in overgrowth disorder suggesting that NPR2 and its ligand, natriuretic peptide precursor C (CNP), are the key players of endochondral bone growth. However, the precise mechanism behind phenotypic variability of the NPR2 mutations is not fully understood so far. In the present study, three consanguineous families of Pakistani origin (A, B, C) with variable phenotypes of acromesomelic dysplasia, type Maroteaux were evaluated at clinical and molecular levels. Linkage analysis followed by Sanger sequencing of the NPR2 gene revealed three homozygous mutations including p.(Leu314 Arg), p.(Arg371*), and p.(Arg1032*) in family A, B and C, respectively. In silico structural and functional analyses substantiated that a novel missense mutation [p.(Leu314 Arg)] in family A allosterically affects binding of NPR2 homodimer to its ligand (CNP) which ultimately results in defective guanylate cyclase activity. A nonsense mutation [p.(Arg371*)] in family B entirely removed the transmembrane domain, protein kinase domain and guanylate cyclase domains of the NPR2 resulting in abolishing its guanylate cyclase activity. Another novel mutation [p.(Arg1032*)], found in family C, deteriorated the guanylate cyclase domain of the protein and probably plundered its guanylate cyclase activity. These results suggest that guanylate cyclase activity is the most critical function of the NPR2 and phenotypic severity of the NPR2 mutations is proportional to the reduction in its guanylate cyclase activity.

Novel sequence variants in the LIPH and LPAR6 genes underlies autosomal recessive woolly hair/hypotrichosis in consanguineous families: Variants in the LIPH and LPAR6 genes

Autosomal‐recessive woolly hair/hypotrichosis (ARWH/H) is a rare genetic disorder of hair caused by variants in the LIPH and LPAR6 genes. The disease is characterized by congenital tightly curled hair leading to sparse hair later in life. In the present report genetic characterization of three consanguineous families of Pakistani origin, displaying clinical features of ARWH/H, was performed. Haplotype and DNA sequence analysis of the LIPH gene revealed a novel homozygous nonsense variant (c.688C > T; p.Gln230*) in family A. In two other families, B and C, sequence analysis of the LPAR6 gene revealed a novel homozygous frameshift variant (c.68_69dupGCAT; p.Phe24Hisfs*29) and a previously reported missense variant (c.188A > T; p.Asp63Val), respectively. Taken together, our findings will expand the spectrum of variants reported in the LIPH and LPAR6 genes.

Novel autosomal recessive LAMA3 and PLEC variants underlie junctional epidermolysis bullosa generalized intermediate and epidermolysis bullosa simplex with muscular dystrophy in two consanguineous families

F. Ahmad, K. Shah, M. Umair, A. Jan, Irfanullah, S. Khan, D. Muhammad, S. Basit, S. M. Wakil, K. Ramzan and W. Ahmad Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology [KUST], Kohat, Khyber Pakhtunkhwa, Pakistan; Chandka Medical College, Shaheed Mohtarma Benazir Bhutto Medical University, Larkana, Sindh, Pakistan; Center for Genetics and Inherited Diseases, Taibah University Al Madinah Al Munawarah, Medina, Saudi Arabia; and Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia

Novel digenic inheritance of PCDH15 and USH1G underlies profound non-syndromic hearing impairment

BackgroundDigenic inheritance is the simplest model of oligenic disease. It can be observed when there is a strong epistatic interaction between two loci. For both syndromic and non-syndromic hearing impairment, several forms of digenic inheritance have been reported.MethodsWe performed exome sequencing in a Pakistani family with profound non-syndromic hereditary hearing impairment to identify the genetic cause of disease.ResultsWe found that this family displays digenic inheritance for two trans heterozygous missense mutations, one in PCDH15 [p.(Arg1034His)] and another in USH1G [p.(Asp365Asn)]. Both of these genes are known to cause autosomal recessive non-syndromic hearing impairment and Usher syndrome. The protein products of PCDH15 and USH1G function together at the stereocilia tips in the hair cells and are necessary for proper mechanotransduction. Epistasis between Pcdh15 and Ush1G has been previously reported in digenic heterozygous mice. The digenic mice displayed a significant decrease in hearing compared to age-matched heterozygous animals. Until now no human examples have been reported.ConclusionsThe discovery of novel digenic inheritance mechanisms in hereditary hearing impairment will aid in understanding the interaction between defective proteins and further define inner ear function and its interactome.

GLY67ARG substitution in RSPO4 disrupts the WNT signaling pathway due to an abnormal binding pattern with LGRs leading to anonychia

R-Spondins regulate the WNT/β-catenin signaling pathway by interacting with leucine rich-repeat containing G-protein coupled receptors (LGR4–6). These receptors share unique sequence and structural similarities with each other. Here, we report comparative binding analysis of R-Spondin-4 (RSPO4) with LGRs through structural characterization of a missense variant (GLY67ARG) identified in two consanguineous families of Pakistani origin. The modeled structure of RSPO4 comprises two contiguous Furin-like cysteine-rich domains that are involved in binding with LGRs. We observed an overall conservation of overlapping interacting residues among LGRs which recognized RSPO4 at two specific parallel positions (sites ‘a’ and ‘b’). The residual contributions of RSPO4 reconciled previously defined interactions of RSPO1 with LGRs. To check the comparative expression pattern of β-catenin, we quantified β-catenin levels in normal and anonychia patients. β-catenin level was significantly reduced in the patients exhibiting mutated RSPO4 as compared to control individuals. These findings confirm that RSPO4 modulates the LGR-dependent WNT/β-catenin signaling pathway and may have therapeutic potential in anonychia patients.

A novel homozygous mutation disrupting the initiation codon in the SLURP1 gene underlies mal de Meleda in a consanguineous family

Mal de Meleda (MDM) is a palmoplantar keratoderma (PPK), characterized by hyperkeratosis of the palms and soles, and keratotic skin lesions. Patients with MDM can develop perioral erythema, keratotic and lichenoid plaques over the joints (including the elbows and knees), nail abnormalities, joint contractures and stiffness, brachydactyly, sclerodactyly, pseudoainhum, and malodorous maceration. MDM is associated with mutations in the SLURP1 gene. We report a consanguineous family in which MDM was inherited in an autosomal recessive manner. Genotyping using microsatellite markers established linkage in the family to the SLURP1 gene, which has been mapped previously to chromosome 8q24.3. Sequence analysis revealed a homozygous missense mutation (c.2T>C, p.Met1Thr) in affected family members. Molecular docking studies using a ZDOCK server predicted disruption of binding of the mutant variant to its target α7‐nAChR. This study further supports the previously reported findings that homozygous mutations in the SLURP1 gene cause MDM.