1
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Nguyen TN, Tran GS, Hoang HD, Nguyen LG. A novel missense variant located within the zinc finger domain of the GLI3 gene was identified in a Vietnamese pedigree with index finger polydactyly. Mol Genet Genomic Med 2024; 12:e2468. [PMID: 38864382 PMCID: PMC11167515 DOI: 10.1002/mgg3.2468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Polydactyly, particularly of the index finger, remains an intriguing anomaly for which no specific gene or locus has been definitively linked to this phenotype. In this study, we conducted an investigation of a three-generation family displaying index finger polydactyly. METHODS Exome sequencing was conducted on the patient, with a filtration to identify potential causal variation. Validation of the obtained variant was conducted by Sanger sequencing, encompassing all family members. RESULTS Exome analysis uncovered a novel heterozygous missense variant (c.1482A>T; p.Gln494His) at the zinc finger DNA-binding domain of the GLI3 protein within the proband and all affected family members. Remarkably, the variant was absent in unaffected individuals within the pedigree, underscoring its association with the polydactyly phenotype. Computational analyses revealed that GLI3 p.Gln494His impacts a residue that is highly conserved across species. CONCLUSION The GLI3 zinc finger DNA-binding region is an essential part of the Sonic hedgehog signaling pathway, orchestrating crucial aspects of embryonic development through the regulation of target gene expression. This novel finding not only contributes valuable insights into the molecular pathways governing polydactyly during embryonic development but also has the potential to enhance diagnostic and screening capabilities for this condition in clinical settings.
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Affiliation(s)
- Thy Ngoc Nguyen
- Department of Life SciencesUniversity of Science and Technology of Hanoi, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Giang Son Tran
- Department of Information and Communication TechnologyUniversity of Science and Technology of Hanoi, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Hai Duc Hoang
- Department of OrthopedicsVietnam National Children's HospitalHanoiVietnam
| | - Long Giang Nguyen
- Department of Management Information SystemInstitute of Information Technology, Vietnam Academy of Science and TechnologyHanoiVietnam
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2
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Zhao C, Gao C, Zhu Y, Zhang Q, Lin P. A novel GLI3 frameshift mutation in a Chinese pedigree with polydactyly: A case report. Heliyon 2024; 10:e28638. [PMID: 38571622 PMCID: PMC10988035 DOI: 10.1016/j.heliyon.2024.e28638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Background GLI3 gene mutations can result in various forms of polysyndactyly, such as Greig cephalopolysyndactyly syndrome (GCPS, MIM: #175700), Pallister-Hall syndrome (PHS, MIM: #146510), and isolated polydactyly (IPD, MIM: #174200, #174700). Reports on IPD-associated GLI3 mutations are rare. In this study, a novel GLI3 mutation was identified in a Chinese family with IPD. Results We report a family with six members affected by IPD. The family members demonstrated several special phenotypes, including sex differences, abnormal finger joint development, and different polydactyly types. We identified a novel frameshift variant in the GLI3 gene (NM_000168.6: c.1820_1821del, NP_000159.3: p.Tyr607Cysfs*9) by whole-exome sequencing. Further analysis suggested that this mutation was the cause of polydactyly in this family. Conclusions The discovery of this novel frameshift variant in our study further solidifies the relationship between IPD and GLI3 and expands the previously established spectrum of GLI3 mutations and associated phenotypes.
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Affiliation(s)
- Chi Zhao
- Department of Orthopaedic Surgery, Jinhua Municipal Central Hospital, Jinhua, Zhejiang Province, 321000, China
| | - Chengcheng Gao
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang Province, 310030, China
| | - Yijun Zhu
- Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Jinhua, Zhejiang Province, 321000, China
| | - Qi Zhang
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang Province, 310030, China
| | - Ping Lin
- Department of Orthopaedic Surgery, Jinhua Municipal Central Hospital, Jinhua, Zhejiang Province, 321000, China
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3
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Khan H, Ullah K, Jan A, Ali H, Ullah I, Ahmad W. A variant in the LDL receptor-related protein encoding gene LRP4 underlying polydactyly and phalangeal synostosis in a family of Pakistani origin. Congenit Anom (Kyoto) 2023; 63:190-194. [PMID: 37563890 DOI: 10.1111/cga.12536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/07/2023] [Accepted: 06/04/2023] [Indexed: 08/12/2023]
Abstract
A family of Pakistani origin, segregating polydactyly, and phalangeal synostosis in an autosomal dominant manner, has been investigated and presented in the present report. Whole-exome sequencing (WES), followed by segregation analysis using Sanger sequencing, revealed a heterozygous missense variant [c.G1696A, p.(Gly566Ser)] in the LRP4 gene located on human chromosome 11p11.2. Homology protein modeling revealed the mutant Ser566 generated new interactions with at least four other amino acids and disrupted protein folding and function. Our findings demonstrated the first direct evidence of involvement of LRP4 in causing polydactyly and phalangeal synostosis in the same family. This study highlighted the importance of inclusion of LRP4 gene in screening individuals presenting polydactyly in hands and feet, and phalangeal synostosis in the same family.
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Affiliation(s)
- Hammal Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kifayat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abid Jan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Pakistan
| | - Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Imran Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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4
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Guo X, Shi T, Lin M, Liu B, Pan Y. Two Novel Frameshift Mutations in the GLI3 Gene Underlie Non-Syndromic Polydactyly in Chinese Families. Genet Test Mol Biomarkers 2023; 27:299-305. [PMID: 37768332 DOI: 10.1089/gtmb.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
Objective: Polydactyly is characterized by multiple distinct heterogeneous phenotypes, the etiologies of which involve several genes. This study aimed to explore the genetic defects and further clarify the molecular mechanism of polydactyly in several Chinese families. Methods: Three families with diverse phenotypes of non-syndromic polydactyly were analyzed: two were cases of familial disease, whereas one was sporadic. PCR and Sanger sequencing were used to screen for pathogenic mutations in two known disease-associated genes, GLI3 and HOXD13, while bioinformatic analyses predicted the pathogenicity of the identified variants. Reverse transcription PCR was used to analyze the splicing effect of an intronic variant. Results: Two novel heterozygous frameshift mutations (c.4478delG/p.S1493Tfs*18; c.846_c.847insC/p.R283Qfs*21) were identified in the GLI3 gene from two of the pedigrees. Both c.4478delG and c.846_c.847insC were later confirmed in affected and unaffected members and normal controls, to truncate and disrupt the integrity of the GLI3 protein, reduce its level of expression, and disrupt its biological function through nonsense-mediated mRNA decay (NMD). In addition, a deep intron mutation (c.125-47 C>A) was detected in the GLI3 gene from the sporadic case, however, both bioinformatics analysis (HSF, splice AI, and CBS) and RT-PCR indicated that the variant c.125-47 C>A had minimal if any impact on splicing of the GLI3 gene. Conclusion: Two newly identified heterozygous frameshift mutations in the GLI3 gene were detected in two families with non-syndromic polydactyly, further extending the mutational spectrum of the GLI3 gene in non-syndromic polydactyly. Moreover, our study further expanded the phenotypic spectrum of non-syndromic polydactyly.
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Affiliation(s)
- Xiaoyan Guo
- Department of Laboratory Medicine, Fuzhou Second Hospital, Fuzhou, P.R. China
- Department of Laboratory Medicine, Fuzhou Second Hospital of Xiamen University, School of Medicine, Xiamen University, Fuzhou, P.R. China
- Department of Laboratory Medicine, The Third Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Tengfei Shi
- Department of Laboratory Medicine, Fuzhou Second Hospital, Fuzhou, P.R. China
| | - Mingrui Lin
- Intensive Care Unit, The Affiliated People's Hospital of Fujian Traditional Medical University, Fuzhou, P.R. China
| | - Boling Liu
- Department of Orthopaedics, Fuzhou Second Hospital, Fuzhou, P.R. China
| | - Yuancheng Pan
- Department of Orthopaedics, Fuzhou Second Hospital, Fuzhou, P.R. China
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5
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Ahmad Z, Liaqat R, Palander O, Bilal M, Zeb S, Ahmad F, Jawad Khan M, Umair M. Genetic overview of postaxial polydactyly: Updated classification. Clin Genet 2023; 103:3-15. [PMID: 36071556 DOI: 10.1111/cge.14224] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022]
Abstract
Polydactyly or polydactylism, also known as a hyperdactyly, is a congenital limb defect with various morphologic phenotypes. Apart from physical and functional impairments, the presence of polydactyly is an indication of an underlying syndrome in the newborn. Usually, it follows as an autosomal dominant/recessive inheritance pattern with defects in the limb development's anteroposterior patterning. Although mutations in several genes have been associated with polydactyly; however, the exact underlying cause, pathways, and disease mechanisms are still unexplored, thus making it of multi-factorial origin. Polydactyly is divided into three subtypes; radial, ulnar, and central polydactyly. So far, 11 loci (PAPA1-PAPA11) and seven human genes have been reported to cause non-syndromic postaxial polydactyly in humans, including the ZNF141, GLI3, IQCE, GLI1, FAM92A1, KIAA0825, and DACH1. In this review, we discuss emerging evidences of clinical and molecular characterization of polydactyly types in term of the involvement of newly associated genes and loci for non-syndromic postaxial polydactyly, and how these might impact our understanding of the genetic mechanisms and molecular etiology involved in the cause of polydactyly.
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Affiliation(s)
- Zaheer Ahmad
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Romana Liaqat
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Oliva Palander
- Faculty of Medicine, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shah Zeb
- Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China.,College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, People's Republic of China
| | - Farooq Ahmad
- Department of Biochemistry, Women University Swabi, Swabi, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, 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 (MNGH), Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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6
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Wang Y, Hao X, Jia X, Ji W, Yuan S, Gnamey EJA, Huang M, Xu L, Zhang X, Bai J, Sun W, Fu S, Liu Y, Wu J. A novel variant of GLI3, p.Asp1514Thrfs*5, is identified in a Chinese family affected by polydactyly. Mol Genet Genomic Med 2022; 10:e1968. [PMID: 35546307 PMCID: PMC9266609 DOI: 10.1002/mgg3.1968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 04/14/2022] [Accepted: 05/03/2022] [Indexed: 11/21/2022] Open
Abstract
Background Polydactyly is a common congenital malformation characterized by the presence of supernumerary fingers or toes. In this case study, we sought to identify the causative pathogenic factor in a family from a northern region of China affected by non‐syndromic postaxial polydactyly (PAP). Methods After recruiting a three‐generation family with PAP, whole‐exome sequencing was performed to identify the causative variant. In silico analysis and Sanger sequencing were used to validate the variant. Results We identified a novel heterozygous frameshift variant (NM_000168.6:c.4540delG, p.Asp1514Thrfs*5) in the transcriptional activator (TA1) domain of the GLI3 gene. Conclusion The novel frameshift variant identified in this study further confirms the relationship between non‐syndromic PAP and GLI3 and extends the previously established mutational and phenotypic spectra of GLI3.
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Affiliation(s)
- Yusi Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Xuguang Hao
- Department of Hand Surgery the Fifth Hospital of Harbin, Harbin, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Wei Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Shuai Yuan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Estelle Judith Abla Gnamey
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Min Huang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
| | - Yong Liu
- Department of Hand Surgery the Fifth Hospital of Harbin, Harbin, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
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7
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El Mouatani A, Van Winckel G, Zaafrane-Khachnaoui K, Whalen S, Achaiaa A, Kaltenbach S, Superti-Furga A, Vekemans M, Fodstad H, Giuliano F, Attie-Bitach T. Homozygous GLI3 variants observed in three unrelated patients presenting with syndromic polydactyly. Am J Med Genet A 2021; 185:3831-3837. [PMID: 34296525 DOI: 10.1002/ajmg.a.62426] [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: 02/23/2021] [Revised: 05/01/2021] [Accepted: 06/12/2021] [Indexed: 11/08/2022]
Abstract
Polydactyly is a hallmark of GLI3 pathogenic variants, with Greig cephalopolysyndactyly syndrome and Pallister-Hall syndrome being the two main associated clinical presentations. Homozygous GLI3 variants are rare instances in the literature, and mendelian dominance is the accepted framework for GLI3-related diseases. Herein, we report three unrelated probands, presenting with polydactyly, and homozygous variants in the GLI3 gene. First, a 10-year-old girl, whose parents were first-degree cousins, presented with bilateral postaxial polydactyly of the hands, developmental delay and multiple malformations. Second, a male newborn, whose parents were first-degree cousins, presented with isolated bilateral postaxial polysyndactyly of the hands and the feet. Third, an adult male, whose parents were first-degree cousins, had bilateral mesoaxial polydactyly of the hands, with severe intellectual disability and multiple malformations. All three probands carried homozygous GLI3 variants. Strikingly, the parents also carried the child's variant, in the heterozygous state, without any clinical sign of GLI3 disease. Given the clinical presentation of our patients, the rarity and predicted high pathogenicity of the variants observed, and the absence of other pathogenic variants, we suggest that these GLI3 homozygous variants are causal. Moreover, the parents were heterozygous for the observed variants, but were clinically unremarkable, suggesting that these variants are hypomorphic alleles.
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Affiliation(s)
- Ahmed El Mouatani
- Service Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Géraldine Van Winckel
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | | | - Sandra Whalen
- Unité Fonctionnelle de Génétique Clinique, Centre de Référence Maladies Rares Anomalies du développement et syndromes malformatifs, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Amale Achaiaa
- Service Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Sophie Kaltenbach
- Service Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique - Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Andrea Superti-Furga
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Michel Vekemans
- Service Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Heidi Fodstad
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Fabienne Giuliano
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Tania Attie-Bitach
- Service Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique - Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
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8
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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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9
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Role of DZIP1-CBY-FAM92 transition zone complex in the basal body to membrane attachment and ciliary budding. Biochem Soc Trans 2021; 48:1067-1075. [PMID: 32491167 DOI: 10.1042/bst20191007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Cilia play important signaling or motile functions in various organisms. In Human, cilia dysfunctions are responsible for a wide range of diseases, called ciliopathies. Cilia assembly is a tightly controlled process, which starts with the conversion of the centriole into a basal body, leading to the formation of the ciliary bud that protrudes inside a ciliary vesicle and/or ultimately at the cell surface. Ciliary bud formation is associated with the assembly of the transition zone (TZ), a complex architecture of proteins of the ciliary base which plays critical functions in gating proteins in and out of the ciliary compartment. Many proteins are involved in the assembly of the TZ, which shows structural and functional variations in different cell types or organisms. In this review, we discuss how a particular complex, composed of members of the DZIP1, CBY and FAM92 families of proteins, is required for the initial stages of cilia assembly leading to ciliary bud formation and how their functional hierarchy contributes to TZ assembly. Moreover, we summarize how evidences in Drosophila reveal functional differences of the DZIP1-CBY-FAM92 complex in the different ciliated tissues of this organism. Whereas it is essential for proper TZ assembly in the two types of ciliated tissues, it is involved in stable anchoring of basal bodies to the plasma membrane in male germ cells. Overall, the DZIP1-CBY-FAM92 complex reveals a molecular assembly pathway required for the initial stages of ciliary bud formation and that is conserved from Drosophila to Human.
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10
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Almatrafi A, Umair M, Eldardear A, Al-Luqmani M, Hashmi JA, Albalawi AM, Alfadhel M, Ramzan K, Basit S. A homozygous missense variant in the homeobox domain of the NKX6-2 results in progressive spastic ataxia type 8 associated with lower limb weakness and neurological manifestations. J Gene Med 2020; 22:e3196. [PMID: 32246862 DOI: 10.1002/jgm.3196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Progressive spastic ataxia is a heterogeneous disorder characterized by cerebellar ataxia and limb spasticity associated with other severe neurological complications. Spastic ataxia is classified into pure and complex types, inherited in both an autosomal recessive and autosomal dominant manner. It is caused by pathogenic variants in at least eight different genes, including NKX6-2 (MIM 607063) located on chromosome 10q26.3. The present study aimed to identify the genetic variant(s) underlying progressive spastic ataxia and to establish the genotype-phenotype correlation. METHODS We collected a large consanguineous family having four affected individuals segregating progressive spastic ataxia in an autosomal recessive manner. To investigate the molecular cause of the disease, genomic DNA of three affected individuals underwent whole exome sequencing. RESULTS All of the affected individuals showed progressive clinical features such as spastic ataxia, lower limb weakness and other mild neurological abnormalities. Whole exome sequencing data were analyzed using different filters. Filtering of rare and shared homozygous variants revealed a novel homozygous missense variant (c.545C>T; p.Ala182Val) in a highly conserved homeobox domain of the NKX6-2 protein. CONCLUSIONS The findings of the present study add a novel variant to the NKX6-2 mutation spectrum and provide evidence that homozygous variants in the NKX6-2 cause progressive spastic ataxia associated with other abnormalities.
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Affiliation(s)
- Ahmad Almatrafi
- Department of Biology, College of Science, Taibah University, Almadinah Almunawwarah, Saudi Arabia
| | - 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
| | - Amr Eldardear
- College of Medicine, Taibah University, Almadinah Almunawwarah, Saudi Arabia
| | - Majid Al-Luqmani
- College of Medicine, Taibah University, Almadinah Almunawwarah, Saudi Arabia
| | - Jamil A Hashmi
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia.,Department of Biology, College of Science, King Abdulaziz University Jeddah, Jeddah, 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), King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
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11
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Ngoc NT, Duong NT, Quynh DH, Ton ND, Duc HH, Huong LTM, Anh LTL, Hai NV. Identification of novel missense mutations associated with non-syndromic syndactyly in two vietnamese trios by whole exome sequencing. Clin Chim Acta 2020; 506:16-21. [PMID: 32165123 DOI: 10.1016/j.cca.2020.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND METHODS Syndactyly is a congenital disorder caused by an irregularity in limb formation during the embryonic development. Many studies have demonstrated the critical effect of genetic factor in controlling the outcome of non-syndromic syndactyly. However the signaling pathway causing this disease has not been fully understood. The aim of this study was to identify the genetic mutations that related to syndactyly type I-c and I-d by exome sequencing. RESULTS The exome sequence from two patients revealed two novel heterozygous missense mutations: GLI3: cG1622A pT541M and GJA1: cT274C p.Y92H. Sanger sequencing result confirmed that these mutations were present under heterozygous form in the affected mothers, but not in the unaffected fathers. In-silico analyses by SIFT, Polyphen-2, PredictSNP, PhD-SNP, and PROVEAN did confirm the damaging effect of these mutations in the structure and function of the proteins. CONCLUSIONS The result suggested that the two novel mutations may be pathogenic for the disease in these families under the dominant model, provided the initial data for further functional studies to investigate whether those mutations play a disturbing role in the molecular network of syndactyly.
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Affiliation(s)
- Nguyen Thy Ngoc
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Viet Nam; University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Viet Nam.
| | - Nguyen Thuy Duong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Viet Nam; Institute of Genome Research, Vietnam Academy of Science and Technology, Viet Nam
| | - Do Hai Quynh
- Institute of Genome Research, Vietnam Academy of Science and Technology, Viet Nam
| | - Nguyen Dang Ton
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Viet Nam; Institute of Genome Research, Vietnam Academy of Science and Technology, Viet Nam
| | | | | | - Luong Thi Lan Anh
- Genetic Counseling Center, Hanoi Medical University Hospital, Hanoi Medical University, Viet Nam
| | - Nong Van Hai
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Viet Nam; Institute of Genome Research, Vietnam Academy of Science and Technology, Viet Nam
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12
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Identification of a novel biallelic missense variant in the KIAA0825 underlies postaxial polydactyly type A. Genomics 2020; 112:2729-2733. [PMID: 32147526 DOI: 10.1016/j.ygeno.2020.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/01/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023]
Abstract
Postaxial polydactyly (PAP) is characterized by development of extra digits, which mostly segregates in autosomal recessive pattern. The underlying genetic cause of recessive non-syndromic PAP type A has been associated with sequence variants in five different genes (ZNF141, IQCE, GLI1, FAM92A, KIAA0825). The present study was aimed to investigate clinical and genetic causes of PAPA in a consanguineous family of Pakistani origin. Microsatellite-based linkage analysis was used to search for the disease-causing gene. Linkage in the family was established at chromosome 5q15 harbouring a candidate gene KIAA0825. Subsequently, Sanger sequencing revealed a novel homozygous missense variant [c.50T>C; p. (Leu17Ser)] in the gene, which co-segregated with the disease within the family. Protein structural analysis predicted a substantial change in the secondary structure of the mutant protein affecting its function. This is the third disease causing variant identified in the KIAA0825. This has not only expanded spectrum of the mutations in the gene but also further substantiated its role in the limb development in human.
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13
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Albarry MA, Hashmi JA, Alreheli AQ, Albalawi AM, Khan B, Ramzan K, Basit S. Novel homozygous loss-of-function mutations in RP1 and RP1L1 genes in retinitis pigmentosa patients. Ophthalmic Genet 2019; 40:507-513. [PMID: 31833436 DOI: 10.1080/13816810.2019.1703014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background: Retinitis pigmentosa (RP) is a heterogeneous group of ocular dystrophy. It is challenging to identify the underlying genetic defect in individuals with RP due to huge genetic heterogeneity. This study was designed to delineate the genetic defect(s) underlying RP in extended Saudi families and to describe the possible disease mechanism.Materials and Methods: Fundus photography and a high definition optical coherence tomography (HD-OCT) were performed in order to detect the earlier stages of macular degeneration. Genomic DNA was extracted followed by genome-wide SNP genotyping and whole exome sequencing (WES). Exome data was filtered to identify the genetic variant(s) of interest.Results: Clinical examination showed that affected individuals manifest key features of RP. The fundus exam shows pale optic disc and bone spicules at the periphery. OCT shows macular degeneration as early as at the age of 4 years. Whole genome scan by SNPs identified multiple homozygous regions. WES identified a 10 bps novel insertion mutation (c.3544_3545insAGAAAAGCTG; p.Ala1182fs) in the RP1 gene in both affected individuals of family A. Affected individual from family B showed a large insertion of 48 nucleotides in the coding part of the RP1L1 gene (c.3955_3956insGGACTAAAGTAATAGAAGGGCTGCAAGAAGAGAGGGTGCAGTTAGAGG; p.Ala1319fs). Sanger sequencing validates the autosomal recessive inheritance of the mutations.Conclusion: The results strongly suggest that the insertion mutations in the RP1 and RP1L1 genes are responsible for the retinal phenotype in affected individuals from two families. Heterozygous individuals are asymptomatic carriers. We propose that the protective allele in other homozygous regions in heterozygous carriers contribute to the phenotypic variability in asymptomatic individuals.
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Affiliation(s)
- Maan Abdullah Albarry
- Department of Ophthalmology, College of Medicine, Taibah University Almadinah, Medina, Saudi Arabia
| | - Jamil Amjad Hashmi
- Center for Genetics and Inherited Diseases, Taibah University Almadinah, Medina, Saudi Arabia
| | - Ahdab Qasem Alreheli
- Department of Ophthalmology, College of Medicine, Taibah University Almadinah, Medina, Saudi Arabia
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University Almadinah, Medina, Saudi Arabia
| | - Bushra Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, KPK, Pakistan
| | - Khushnooda Ramzan
- Department of Genetics, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University Almadinah, Medina, Saudi Arabia
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14
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Variants in GLI3 Cause Greig Cephalopolysyndactyly Syndrome. Genet Test Mol Biomarkers 2019; 23:744-750. [DOI: 10.1089/gtmb.2019.0071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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15
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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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16
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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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