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Waheed N, Waris R, Naseer M, Razzaq A, Haider N, Shah AA, Ullah A. Mutational spectrum of CFTR in cystic fibrosis patients with gastrointestinal and hepatobiliary manifestations. Mol Biol Rep 2024; 51:573. [PMID: 38662334 DOI: 10.1007/s11033-024-09508-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) is a rare and debilitating autosomal recessive disorder. It hampers the normal function of various organs and causes severe damage to the lungs, and digestive system leading to recurring pneumonia. Cf also affects reproductive health eventually may cause infertility. The disease manifests due to genetic aberrations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study aimed to screen for CFTR gene variants in Pakistani CF patients representing variable phenotypes. METHODS Clinical exome and Sanger sequencing were performed after clinical characterization of 25 suspected cases of CF (CF1-CF25). ACMG guidelines were followed to interpret the clinical significance of the identified variants. RESULTS Clinical investigations revealed common phenotypes such as pancreatic insufficiency, chest infections, chronic liver and lung diseases. Some patients also displayed symptoms like gastroesophageal reflux disease (GERD), neonatal cholestasis, acrodermatitis, diabetes mellitus, and abnormal malabsorptive stools. Genetic analysis of the 25 CF patients identified deleterious variants in the CFTR gene. Notably, 12% of patients showed compound heterozygous variants, while 88% had homozygous variants. The most prevalent variant was p. (Met1Thr or Met1?) at 24%, previously not reported in the Pakistani population. The second most common variant was p. (Phe508del) at 16%. Other variants, including p. (Leu218*), p. (Tyr569Asp), p. (Glu585Ter), and p. (Arg1162*) were also identified in the present study. Genetic analysis of one of the present patients showed a pathogenic variant in G6PD in addition to CFTR. CONCLUSION The study reports novel and reported variants in the CFTR gene in CF patients in Pakistani population having distinct phenotypes. It also emphasizes screening suspected Pakistani CF patients for the p. (Met1Thr) variant because of its increased observance and prevalence in the study. Moreover, the findings also signify searching for additional pathogenic variants in the genome of CF patients, which may modify the phenotypes. The findings contribute valuable information for the diagnosis, genetic counseling, and potential therapeutic strategies for CF patients in Pakistan.
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Affiliation(s)
- Nadia Waheed
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Rehmana Waris
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Maryam Naseer
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Ayesha Razzaq
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Nighat Haider
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
| | - Asmat Ullah
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Khan F, Khan S, Rana N, Rahim T, Arshad A, Khan I, Ogaly HA, Ahmed DAEM, Dera AA, Zaib S. Mutational analysis of consanguineous families and their targeted therapy against dwarfism. J Biomol Struct Dyn 2024:1-18. [PMID: 38321911 DOI: 10.1080/07391102.2024.2307446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024]
Abstract
Dwarfism is a medical term used to describe individuals with a height-vertex measurement that falls below two standard deviations (-2SD) or the third percentile for their gender and age. Normal development of growth is a complicated dynamic procedure that depends upon the coordination of different aspects involving diet, genetics, and biological aspects like hormones in equilibrium. Any severe or acute pathologic procedure may disturb the individual's normal rate of growth. In this research, we examined four (A-D) Pakistani consanguineous families that exhibited syndromic dwarfism, which was inherited in an autosomal recessive pattern. The genomic DNA of each family member was extracted by using phenol-chloroform and Kit methods. Whole Exome Sequencing (WES) of affected family members (IV-11, III-5, IV-4 and III-13) from each group was performed at the Department of Medical Genetics, University of Antwerp, Belgium. After filtering the exome data, the mutations in PPM1F, FGFR3, ERCC2, and PCNT genes were determined by Sanger sequencing of each gene by using specific primers. Afterward, FGFR3 was found to be a suitable drug target among all the mutations to treat achondroplasia also known as disproportionate dwarfism. BioSolveIT softwares were used to discover the lead active inhibitory molecule against FGFR3. This research will not only provide short knowledge to the concerned pediatricians, researchers, and family physicians for the preliminary assessment and management of the disorder but also provide a lead inhibitor for the treatment of disproportionate dwarfism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Feroz Khan
- Department of Zoology Wild Life and Fishries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Sarmir Khan
- Center of Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Tariq Rahim
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Abida Arshad
- Department of Zoology Wild Life and Fishries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Hanan A Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, Saudi Arabia
| | | | - Ayed A Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
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Bilal M, Khan H, Khan MJ, Haack TB, Buchert R, Liaqat K, Ullah K, Ahmed S, Bharadwaj T, Acharya A, Peralta S, Najumuddin, Ali H, Hasni MS, Schrauwen I, Ullah A, Ahmad W, Leal SM. Variants in EFCAB7 underlie nonsyndromic postaxial polydactyly. Eur J Hum Genet 2023; 31:1270-1274. [PMID: 37684519 PMCID: PMC10620185 DOI: 10.1038/s41431-023-01450-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/14/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Polydactyly is the most common limb malformation that occurs in 1.6-10.6 per one thousand live births, with incidence varying with ancestry. The underlying gene has been identified for many of the ~100 syndromes that include polydactyly. While for the more common form, nonsydromic polydactyly, eleven candidate genes have been reported. We investigated the underlying genetic cause of autosomal recessive nonsyndromic postaxial polydactyly in four consanguineous Pakistani families. Some family members with postaxial polydactyly also present with syndactyly, camptodactyly, or clinodactyly. Analysis of the exome sequence data revealed two novel homozygous frameshift deletions in EFCAB7: [c.830delG;p.(Gly277Valfs*5)]; in three families and [c.1350_1351delGA;p.(Asn451Phefs*2)] in one family. Sanger sequencing confirmed that these variants segregated with postaxial polydactyly, i.e., family members with postaxial polydactyly were found to be homozygous while unaffected members were heterozygous or wild type. EFCAB7 displays expressions in the skeletal muscle and on the cellular level in cilia. IQCE-EFCAB7 and EVC-EVC2 are part of the heterotetramer EvC complex, which is a positive regulator of the Hedgehog (Hh) pathway, that plays a key role in limb formation. Depletion of either EFCAB7 or IQCE inhibits induction of Gli1, a direct Hh target gene. Variants in IQCE and GLI1 have been shown to cause nonsyndromic postaxial polydactyly, while variants in EVC and EVC2 underlie Ellis van Creveld and Weyers syndromes, which include postaxial polydactyly as a phenotype. This is the first report of the involvement of EFCAB7 in human disease etiology.
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Affiliation(s)
- Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hammal Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | | | - Tobias B Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rebecca Buchert
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Khurram Liaqat
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Kifayat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sohail Ahmed
- Institute of Biochemistry, University of Balochistan, Quetta, Pakistan
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Susana Peralta
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Najumuddin
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Asmat Ullah
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA.
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Gul R, Firasat S, Schubert M, Ullah A, Peña E, Thuesen ACB, Hussain M, Staeger FF, Gjesing AP, Albrechtsen A, Hansen T. Identifying the genetic causes of phenotypically diagnosed Pakistani mucopolysaccharidoses patients by whole genome sequencing. Front Genet 2023; 14:1128850. [PMID: 37091798 PMCID: PMC10113632 DOI: 10.3389/fgene.2023.1128850] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Lysosomal storage disorders (LSDs) are a group of inherited metabolic diseases, which encompass more than 50 different subtypes of pathologies. These disorders are caused by defects in lysosomal enzymes, transporters, and other non-lysosomal proteins. Mucopolysaccharidosis (MPS) is the most common subgroup of lysosomal storage disorders in which the body is unable to properly breakdown mucopolysaccharides. The aim of the present study was to identify novel genes and pathogenic variants in families from diverse regions of Pakistan with clinically diagnosed mucopolysaccharidosis type I and mucopolysaccharidosis type II.Methods: Clinical diagnosis identified 12 with mucopolysaccharidosis I and 2 with mucopolysaccharidosis II in 14 families and whole genome sequencing (WGS) was performed to identify the causative variations in 15 affected individuals. Twenty-two unaffected individuals including parents or normal siblings of patients were also sequenced. Putative causal variants were identified by co-segregation and functional annotation.Results: Analysis of whole genome sequencing data revealed ten novel and six previously reported variants in lysosomal storage disorders-associated genes (IDUA, GALNS, SGSH, GAA, IDS, ALDOB, TRAPPC4, MASP1, SMARCAL, KIAA1109, HERC1, RRAS2) and a novel candidate gene (ABCA5) for lysosomal storage disorder-like phenotypes, which has previously been associated with symptoms strongly related with lysosomal storage disorder in animal models.Conclusion: Multigenic inheritance was found in several families highlighting the importance of searching for homozygous pathogenic variants in several genes also in families with a high degree of consanguinity.
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Affiliation(s)
- Rutaba Gul
- Department of Zoology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
- *Correspondence: Sabika Firasat, ; Torben Hansen,
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Asmat Ullah
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elionora Peña
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne C. B. Thuesen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mulazim Hussain
- The Children Hospital, Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Frederik F. Staeger
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anette P. Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Sabika Firasat, ; Torben Hansen,
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A novel biallelic variant further delineates PRDX3-related autosomal recessive cerebellar ataxia. Neurogenetics 2023; 24:55-60. [PMID: 36190665 DOI: 10.1007/s10048-022-00701-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/23/2022] [Indexed: 01/01/2023]
Abstract
Cerebellar ataxias (CAs) comprise a rare group of neurological disorders characterized by extensive phenotypic and genetic heterogeneity. In the last several years, our understanding of the CA etiology has increased significantly and resulted in the discoveries of numerous ataxia-associated genes. Herein, we describe a single affected individual from a consanguineous family segregating a recessive neurodevelopmental disorder. The proband showed features such as global developmental delay, cerebellar atrophy, hypotonia, speech issues, dystonia, and profound hearing impairment. Whole-exome sequencing and Sanger sequencing revealed a biallelic nonsense variant (c.496A > T; p.Lys166*) in the exon 5 of the PRDX3 gene that segregated perfectly within the family. This is the third report that associates the PRDX3 gene variant with cerebellar ataxia. In addition, associated hearing impairment further delineates the PRDX3 associated gene phenotypes.
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Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review. Genes (Basel) 2022; 13:genes13122377. [PMID: 36553645 PMCID: PMC9778442 DOI: 10.3390/genes13122377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents.
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Naz S. Molecular genetic landscape of hereditary hearing loss in Pakistan. Hum Genet 2021; 141:633-648. [PMID: 34308486 DOI: 10.1007/s00439-021-02320-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/17/2021] [Indexed: 01/13/2023]
Abstract
Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.
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Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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Nayab A, Alam Q, Alzahrani OR, Khan R, Sarfaraz S, Albaz AA, Rafeeq MM, Sain ZM, Waqas A, Umair M. Targeted exome sequencing identified a novel frameshift variant in the PGAM2 gene causing glycogen storage disease type X. Eur J Med Genet 2021; 64:104283. [PMID: 34237446 DOI: 10.1016/j.ejmg.2021.104283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/15/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Phosphoglycerate mutase (PGAM) deficiency is associated with a rare glycogen storage disease (glycogenosis type X) in humans caused by pathogenic variants in the PGAM2 gene. Several genes causing autosomal forms of glycogen storage disease (GSD) have been identified, involved in various forms of neuromuscular anomalies. METHODS Targeted whole exome sequencing (WES) was performed on the DNA of single affected individual (IV-1) followed by Sanger sequencing confirmation of the identified variant in all available members of the family. RESULTS In the present study, the affected individual, presenting mild features of glycogen storage disease type X. Targeted exome sequencing revealed a biallelic frameshift variant (c.687dupC; p. Met230Hisfs*6) in the PGAM2 gene located on chromosome 7p13. CONCLUSION In short, we reported a novel homozygous frameshift variant as a cause of glycogen storage disease type X from Pakistani population. The work presented here proves significance of targeted WES in accurate diagnosis of known complex genetic disorders.
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Affiliation(s)
- Anam Nayab
- Hefei National Laboratory for Physical Science at the Micro Scale, School of Life Sciences, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia. Genome and Biotechnology Unit, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Ranjha Khan
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Sara Sarfaraz
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Alrayan Abass Albaz
- Department of Oncology and Human Metabolism, The Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, United Kingdom
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, 21589, Saudi Arabia
| | - Ziaullah M Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, 21589, Saudi Arabia
| | - Ahmed Waqas
- Department Zoology, Division of Science and Technology, University of Education Lahore, Multan Campus, Punjab, Pakistan.
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.
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Zaka A, Shahzad S, Rao HZ, Kanwal S, Gul A, Basit S. An intrafamilial phenotypic variability in Ellis-Van Creveld syndrome due to a novel 27 bps deletion mutation. Am J Med Genet A 2021; 185:2888-2894. [PMID: 34037314 DOI: 10.1002/ajmg.a.62360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/22/2021] [Accepted: 05/08/2021] [Indexed: 11/09/2022]
Abstract
Ellis-van Creveld (EvC) syndrome is an autosomal recessive disease, characterized by ectodermal, skeletal, and cardiac anomalies. We report intrafamilial phenotypic variability in three new EvC syndrome cases. Affected males in this study showed only ectodermal abnormalities, whereas an affected female showed the classical presentation of EvC Syndrome, including bilateral postaxial polydactyly of hands and feet, and congenital heart defects. Whole exome sequencing was performed to identify the causative variant, followed by validation and segregation analysis using Sanger sequencing. A homozygous deletion variant (c.731_757del) was identified in exon 6 of the EVC gene (NM_153717.2). The identified variant is considered to be the most likely candidate variant for the EvC syndrome in the family based on previous reports validating the role of EVC variants in the EvC syndrome. The disease correctly segregated in the family members, as all affected members were homozygous, and obligate carriers were heterozygous. Our family is remarkable in highlighting the variable expressivity of the EvC phenotype within the same family, due to a homozygous deletion mutation in the EVC gene. The variable expressivity might be due to the hypomorphic nature of mutation, or the presence of additional variants in modifier genes or in the regulatory regions of the EVC/EVC2 genes.
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Affiliation(s)
- Ayesha Zaka
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Shaheen Shahzad
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Hadi Zahid Rao
- Department of Oral and Maxillofacial Surgery, Bahria University Medical and Dental College, Karachi, Pakistan
| | - Sadia Kanwal
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Asma Gul
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Sulman Basit
- Department of Pathology, College of Medicine and Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
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Huang X, Guo Y, Xu H, Yang Z, Deng X, Deng H, Yuan L. Identification of a novel EVC variant in a Han-Chinese family with Ellis-van Creveld syndrome. Mol Genet Genomic Med 2019; 7:e885. [PMID: 31338997 PMCID: PMC6732296 DOI: 10.1002/mgg3.885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/23/2019] [Accepted: 07/01/2019] [Indexed: 12/31/2022] Open
Abstract
Background Ellis‐van Creveld syndrome (EVC), a very rare genetic skeletal dysplasia, is clinically characterized by a tetrad consisting of chondrodystrophy, polydactyly, ectodermal dysplasia, and cardiac anomalies. The aim of this study was to identify the genetic defect for EVC in a five‐generation consanguineous Han‐Chinese pedigree. Methods A five‐generation, 12‐member Han‐Chinese pedigree was enrolled in this study. Exome sequencing was applied in the proband to screen potential genetic variant(s), and then Sanger sequencing was used to identify the variant in family members and 200 unrelated ethnicity‐matched controls. Results A novel homozygous variant, c.2014C>T, p.(Q672*), in the EvC ciliary complex subunit 1 gene (EVC), was detected in the patient, which was cosegregated with the disease in the family and absent in the controls. Conclusion The identified novel homozygous EVC variant, c.2014C>T, p.(Q672*), was responsible for EVC in this Han‐Chinese pedigree. The findings in this study extend the EVC mutation spectrum and may provide new insights into EVC causation and diagnosis with implications for genetic counseling and clinical management.
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Affiliation(s)
- Xiangjun Huang
- Department of General Surgery, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Yi Guo
- Department of Medical Information, School of Life Sciences, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhijian Yang
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
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11
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A Comprehensive review of genetic skeletal disorders reported from Pakistan: A brief commentary. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Umair M, Wasif N, Albalawi AM, Ramzan K, Alfadhel M, Ahmad W, Basit S. Exome sequencing revealed a novel loss-of-function variant in the GLI3 transcriptional activator 2 domain underlies nonsyndromic postaxial polydactyly. Mol Genet Genomic Med 2019; 7:e00627. [PMID: 31115189 PMCID: PMC6625144 DOI: 10.1002/mgg3.627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 02/06/2023] Open
Abstract
Background Polydactyly is a common genetic limb deformity characterized by the presence of extra fingers or toes. This anomaly may occur in isolation (nonsyndromic) or as part of a syndrome. The disease is broadly divided into preaxial polydactyly (PPD; duplication of thumb), mesoaxial polydactyly (complex polydactyly), and postaxial polydactyly (PAP: duplication of the fifth finger). The extra digits may be present in one or both the limbs. Heterozygous variants in the GLI3, ZRS/SHH, and PITX1 have been associated with autosomal dominant polydactyly, while homozygous variants in the ZNF141, IQCE, GLI1, and FAM92A have been associated with autosomal recessive polydactyly. Pathogenic mutations in the GLI3 gene (glioma‐associated oncogene family zinc finger 3) have been associated with both nonsyndromic and syndromic polydactyly. Methods Here, we report an extended five generation kindred having 12 affected individuals exhibiting nonsyndromic postaxial polydactyly type A condition. Whole‐exome sequencing followed by variant prioritization, bioinformatic studies, Sanger validation, and segregation analysis was performed. Results Using exome sequencing in the three affected individuals, we identified a novel heterozygous frameshift variant (c.3567_3568insG; p.Ala1190Glyfs*57) in the transcriptional activator (TA2) domain of the GLI3 encoding gene. Conclusion To the best of our knowledge, the present study reports on the first familial case of nonsyndromic postaxial polydactyly due to the GLI3 variant in Pakistani population. Our study also demonstrated the important role of GLI3 in causing nonsyndromic postaxial polydactyly.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Naveed Wasif
- Institut für Human Genetik, Ulm Universität, Ulm, Germany
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital (KASCH), Riyadh, Saudi Arabia
| | - Wasim Ahmad
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
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Sabiha B, Ali J, Yousafzai YM, Haider SA. Novel deleterious mutation in MYO7A, TH and EVC2 in two Pakistani brothers with familial deafness. Pak J Med Sci 2018; 35:17-22. [PMID: 30881389 PMCID: PMC6408642 DOI: 10.12669/pjms.35.1.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective In Pakistan, 74% of consanguineous marriages are among the first cousins. Continuity of consanguineous marriages over generations increases the risk of recessive diseases such as deafness. The objective of this study was to investigate genetic origin of Pakistani deaf brothers with parents of consanguineous marriage. Methods DNA was extracted from the blood through Qiagen kit. Paired-end sequencing library was prepared according to protocol of Illumina's TruSight Rapid Capture kit and TruSight Inherited Disease Panel. Library was normalized and used for Next Generation Sequencing through MiSeq. NGS data were analyzed using various bioinformatics tools. Results Both brothers were found to have novel deleterious mutation in MYO7A (c.2476G>A) while the younger brother had additional novel deleterious mutation in TH (c.43C>T) and EVC2 (c.2614C>T) genes. Conclusion It is concluded that in addition to novel mutations in MYO7A, TH and EVC2, the CDH23 and GJB2 can also be responsible for deafness in the family with consanguineous marriages.
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Affiliation(s)
- Bibi Sabiha
- Bibi Sabiha, Center for Genomic Sciences, Rehman Medical College, Phase-V, Hayatabad, Peshawar, KP, Pakistan
| | - Johar Ali
- Johar Ali, Center for Genomic Sciences, Rehman Medical College, Phase-V, Hayatabad, Peshawar, KP, Pakistan
| | - Yasar Mehmood Yousafzai
- Yasar Mehmood Yousafzai, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Syed Adnan Haider
- Syed Adnan Haider, Center for Genomic Sciences, Rehman Medical College, Phase-V, Hayatabad, Peshawar, KP, Pakistan
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Nair P, Lama M, El-Hayek S, Abou Sleymane G, Stora S, Obeid M, Al-Ali MT, Delague V, Mégarbané A. COQ8A and MED25 Mutations in a Child with Intellectual Disability, Microcephaly, Seizures, and Spastic Ataxia: Synergistic Effect of Digenic Variants? Mol Syndromol 2018; 9:319-323. [PMID: 30800049 DOI: 10.1159/000494465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2018] [Indexed: 12/31/2022] Open
Abstract
We report on a girl, born to first-cousin Lebanese parents, with severe intellectual disability, congenital hip luxation, cardiac malformation, short stature, facial dysmorphic features including microcephaly, sparse hair, bilateral epicanthal folds, ataxia, seizures, and elevated lactate and pyruvate levels in serum. Whole exome sequencing was carried out on the patient's DNA. Potentially causal homozygous variants in the MED25 (p.Ile173Thr) and COQ8A (p.Arg512Trp) genes were found. The potential pathogenicity of these variants, and the possibility that the 2 variants could synergistically act to produce the phenotype reported, is discussed.
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Affiliation(s)
- Pratibha Nair
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - Maher Lama
- Pediatric Department El-Rassoul Hospital, Beirut, Lebanon
| | | | - Gretta Abou Sleymane
- Department of Laboratory Science and Technology, American University of Science and Technology, Beirut, Lebanon
| | | | - Marc Obeid
- Department of Laboratory Science and Technology, American University of Science and Technology, Beirut, Lebanon
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