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Koprulu M, Shabbir RMK, Mumtaz S, Tolun A, Malik S. Expanding OBSL1 Mutation Phenotype: Disproportionate Short Stature, Barrel Chest, Thoracic Kyphoscoliosis, Hypogonadism, and Hypospadias. Yale J Biol Med 2023; 96:367-382. [PMID: 37780995 PMCID: PMC10524810 DOI: 10.59249/rlau6003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
We present a Pakistani kinship afflicted with a syndrome with features including short stature, reduced sitting height, orofacial symptoms including prominent forehead and thick eyebrows, short and broad thorax, and variable features such as long philtrum, short broad neck, barrel chest, thoracic kyphoscoliosis, hypogonadism, and hypospadias. Phenotypic variation even within different sibships was considerable. The unique combination of the phenotypic characteristics prompted us to determine the shared homozygosity regions in patient genomes and the pathogenic variants by next generation technologies like single nucleotide polymorphism (SNP) genotyping and whole exome sequencing (WES). Through these analyses, we detected homozygous OBSL1 c.848delG (p.Gly283AlafsTer54) as the causal variant. Biallelic variants in OBSL1 are known to cause Three M Syndrome 2 (3M2), a rare disorder of growth retardation with characteristic facial dysmorphism and musculoskeletal abnormalities. Affected members of the family do not have the 3M2 hallmark features of dolichocephaly, hypoplastic midface, anteverted nares, low nasal bridge, pectus excavatum, sacral hyperlordosis, spina bifida occulta, anterior wedging of thoracic vertebrae, prominent heels, and prominent talus. Moreover, they have some variable features not typical for the syndrome such as round face, disproportionate short stature, barrel chest, thoracic kyphoscoliosis, hypogonadism, and hypospadias. Our study facilitated genetic diagnosis in the family, expanded the clinical phenotype for 3M2, and unraveled the considerable clinical variation within the same kinship. We conclude that unbiased molecular analyses such as WES should be more integrated into healthcare, particularly in populations with high parental consanguinity, given the potential of such analyses to facilitate diagnosis.
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Affiliation(s)
- Mine Koprulu
- Department of Molecular Biology and Genetics, Istanbul
Technical University, Istanbul, Türkiye
| | - Rana Muhammad Kamran Shabbir
- Human Genetics Program, Department of Zoology, Faculty
of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Zoology, Division of Science and
Technology, University of Education, Lahore, Pakistan
| | - Sara Mumtaz
- Department of Biological Sciences, National University
of Medical Sciences, Rawalpindi, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Istanbul
Technical University, Istanbul, Türkiye
| | - Sajid Malik
- Human Genetics Program, Department of Zoology, Faculty
of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Ahmad S, Ali MZ, Abbasi SW, Abbas S, Ahmed I, Abbas S, Nawaz S, Ziab M, Ahmed I, Fakhro KA, Khan MA, Akil AAS. A GHRHR founder mutation causes isolated growth hormone deficiency type IV in a consanguineous Pakistani family. Front Endocrinol (Lausanne) 2023; 14:1066182. [PMID: 36960394 PMCID: PMC10029353 DOI: 10.3389/fendo.2023.1066182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/23/2023] [Indexed: 03/09/2023] Open
Abstract
Background Isolated growth hormone deficiency (IGHD) is caused by a severe shortage or absence of growth hormone (GH), which results in aberrant growth and development. Patients with IGHD type IV (IGHD4) have a short stature, reduced serum GH levels, and delayed bone age. Objectives To identify the causative mutation of IGHD in a consanguineous family comprising four affected patients with IGHD4 (MIM#618157) and explore its functional impact in silico. Methods Clinical and radiological studies were performed to determine the phenotypic spectrum and hormonal profile of the disease, while whole-exome sequencing (WES) and Sanger sequencing were performed to identify the disease-causing mutation. In-silico studies involved protein structural modeling and docking, and molecular dynamic simulation analyses using computational tools. Finally, data from the Qatar Genome Program (QGP) were screened for the presence of the founder variant in the Qatari population. Results All affected individuals presented with a short stature without gross skeletal anomalies and significantly reduced serum GH levels. Genetic mapping revealed a homozygous nonsense mutation [NM_000823:c.G214T:p.(Glu72*)] in the third exon of the growth-hormone-releasing hormone receptor gene GHRHR (MIM#139191) that was segregated in all patients. The substituted amber codon (UAG) seems to truncate the protein by deleting the C-terminus GPCR domain, thus markedly disturbing the GHRHR receptor and its interaction with the growth hormone-releasing hormone. Conclusion These data support that a p.Glu72* founder mutation in GHRHR perturbs growth hormone signaling and causes IGHD type IV. In-silico and biochemical analyses support the pathogenic effect of this nonsense mutation, while our comprehensive phenotype and hormonal profiling has established the genotype-phenotype correlation. Based on the current study, early detection of GHRHR may help in better therapeutic intervention.
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Affiliation(s)
- Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Zeeshan Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Iftikhar Ahmed
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Shakil Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Shoaib Nawaz
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
| | - Mubarak Ziab
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
| | - Ikhlak Ahmed
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
| | - Khalid A. Fakhro
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College-Doha, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ammira Al-Shabeeb Akil
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
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Malik S, Nalbant G, Noreen M, Afzal M, Tolun A. A homozygous ROR2 variant in a family with atypical Robinow syndrome and tetramelic transverse deficiency of autopods. Am J Med Genet A 2021; 188:343-349. [PMID: 34569147 DOI: 10.1002/ajmg.a.62514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/17/2021] [Accepted: 08/30/2021] [Indexed: 11/10/2022]
Abstract
We present five members of a consanguineous Pakistani kinship with the most severe familial tetramelic transverse autopod deficiency reported to date and additionally having some of the common autosomal recessive Robinow syndrome-1 (RRS1) features including short stature, short neck, severe vertebral anomalies of kyphoscoliosis, hemivertebrae, fusion of thoracic vertebrae, broad forehead, and dental crowding. We mapped the locus of this atypical RRS and detected homozygous 8-nucleotide deletion c.1353_1360del (p.(Met452Alafs*4)) in ROR2, the gene responsible for RRS1. We did not find any other variant shared by all affected individuals that could possibly act as a modifier of limb defect. Autopods are affected in RRS1, but severe autopod deficiency is not a characteristic feature. Over 30 biallelic variants dispersed throughout the gene are known in ROR2-related RS, with no genotype-phenotype correlation for specific RRS1 features. Considering together with the sporadic case homozygous for variant p.(Arg442*) and the case homozygous for p.(Arg441Thrfs*16) in a family where heterozygous members have brachydactyly type B1, we propose that homozygous truncating variants that originate at residues 441-452 can cause severe autopod reduction anomalies, suggesting some genotype-phenotype correlation for this particular phenotype.
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Affiliation(s)
- Sajid Malik
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Gökhan Nalbant
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acıbadem Mehmet Ali Aydinlar University
| | - Moqadsa Noreen
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Afzal
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, MOBGAM, Istanbul Technical University, Istanbul, Turkey
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Abbas S, Brugger B, Zubair M, Gul S, Blatterer J, Wenninger J, Rehman K, Tatrai B, Khan MA, Windpassinger C. Exome sequencing of a Pakistani family with spastic paraplegia identified an 18 bp deletion in the cytochrome B5 domain of FA2H. Neurol Res 2020; 43:133-140. [PMID: 33246395 DOI: 10.1080/01616412.2020.1831329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hereditary spastic paraplegias (HSPs) are a diverse class of neurodegenerative disorders that mainly affect the corticospinal tract of the body and result in various clinical conditions such as lower limb spasticity and muscle weakness in the lower extremities. Worldwide, more than 70 chromosomal loci/genes have been reported to be associated with HSPs, out of which, six genes viz., ATL1, FA2H, GJC2, AP4E1, ALDH18A1 and ATP13A2 have been mapped in Pakistani families. In the present genetic study, we report on a large consanguineous Pakistani family with a complex form of HSP segregating with a 18 bp deletion in the first exon of the Fatty Acid 2-Hydroxylase (FA2H) gene (NM_024306.5:c.159_176del). The identified in-frame deletion results in loss of six amino acids (p.Arg53_Ile58del) within the cytochrome B5 domain of the protein. FA2H is required for alpha-hydroxylation of free fatty acids to form alpha-hydroxylated sphingolipids. Its cytochrome b5-like heme-binding domain, which spans from residues 15 to 85, imparts the redox activity to FA2H. This mutation has previously been reported in a Pakistani family presenting with a similar form of complex HSP. Together with our findings the pathogenic role of the observed variant is further supported. Mutation studies on additional Pakistani families for FA2H will further elucidate its mutational spectrum, which may help in developing a prenatal diagnostic test for Khyber Pakhtunkhwa resident Pakistani families.
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Affiliation(s)
- Safdar Abbas
- Gomal Center of Biochemistry and Biotechnology, Gomal University , D.I.Khan, Pakistan
| | - Beatrice Brugger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz , Graz, Austria
| | - Muhammad Zubair
- Gomal Center of Biochemistry and Biotechnology, Gomal University , D.I.Khan, Pakistan.,Department of Cell and Developmental Biology, School of Life Sciences, University of Science and Technology , Hefei, China
| | - Sana Gul
- Gomal Center of Biochemistry and Biotechnology, Gomal University , D.I.Khan, Pakistan
| | - Jasmin Blatterer
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz , Graz, Austria
| | - Julian Wenninger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz , Graz, Austria
| | - Khurram Rehman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gomal University , D.I.Khan, Pakistan
| | - Benjamin Tatrai
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz , Graz, Austria
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University , D.I.Khan, Pakistan
| | - Christian Windpassinger
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz , Graz, Austria
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Ali MZ, Blatterer J, Khan MA, Schaflinger E, Petek E, Ahmad S, Khan E, Windpassinger C. Identification of a novel protein truncating mutation p.Asp98* in XPC associated with xeroderma pigmentosum in a consanguineous Pakistani family. Mol Genet Genomic Med 2020; 8:e1060. [PMID: 31923348 PMCID: PMC7005610 DOI: 10.1002/mgg3.1060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/12/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare genetic disorder, which is characterized by hyper-sensitivity to solar ultraviolet (UV) radiation. Clinical consequences of sun exposure are skin lesions and an increased risk of developing skin cancer. Genetic studies have identified eight genes associated with xeroderma pigmentosum. The proteins encoded by these genes are mainly involved in DNA repair mechanisms. METHODS Molecular genetic characterization of patients with xeroderma pigmentosum involved positional cloning methods such as homozygosity mapping and subsequent candidate gene analysis. Mutation screening was performed through Sanger DNA sequencing. RESULTS AND DISCUSSION In this case study, we report a novel protein truncating mutation in XPC associated with autosomal recessive xeroderma pigmentosum in a consanguineous Pakistani family. Genetic mapping revealed a novel single base insertion of a thymine nucleotide NM_004628.4: c.291dupT (c.291_292insT) in the second exon of XPC. The identified mutation leads to a premature stop codon (TGA) at amino acid position 98 (p.Asp98*) and thus presumably results in a truncated protein. The Xeroderma pigmentosum, complementation group C (XPC) is located on 3p25.1 and encodes a protein involved in nucleotide excision repair. The identified mutation presumably truncates all functional domains of the XPC protein, which likely results in the loss of protein function. CONCLUSION The study expands the knowledge of the mutational spectrum of XPC and is valuable for genetic counseling of affected individuals and their families.
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Affiliation(s)
- Muhammad Z Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Jasmin Blatterer
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Muzammil A Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Erich Schaflinger
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Erwin Petek
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ejazullah Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Christian Windpassinger
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
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Khan A, Wang R, Han S, Umair M, Alshabeeb MA, Ansar M, Ahmad W, Alaamery M, Zhang X. A Novel Homozygous Nonsense Mutation p.Cys366* in the WNT10B Gene Underlying Split-Hand/Split Foot Malformation in a Consanguineous Pakistani Family. Front Pediatr 2020; 7:526. [PMID: 31998667 PMCID: PMC6970189 DOI: 10.3389/fped.2019.00526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/04/2019] [Indexed: 02/04/2023] Open
Abstract
Split hand/split foot malformation (SHFM) or ectrodactyly is characterized by a deep median cleft of the hand or foot, hypoplasia or aplasia of the metacarpals, metatarsals, and phalanges. It is a clinically and genetically heterogeneous group of limb malformations. This study aimed to identify the pathogenic variant in a consanguineous Pakistani family with autosomal recessive SHFM. Peripheral blood samples were obtained, DNA was extracted, WNT10B coding and noncoding regions were PCR amplified and Sanger sequencing was performed using workflow suggested by Thermo Fisher Scientific. A novel homozygous nonsense variant (c.1098C>A; p.Cys366*) was identified in the WNT10B gene in the index patients, which probably explains SHFM type 6 in this family in comparison with similar data from the literature.
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Affiliation(s)
- Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
- Developmental Medicine 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
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shirui Han
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Science, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mohammad A. Alshabeeb
- Developmental Medicine 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
| | - Muhammad Ansar
- 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
| | - Manal Alaamery
- Developmental Medicine 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
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
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Muzammal M, Zubair M, Bierbaumer S, Blatterer J, Graf R, Gul A, Abbas S, Badar M, Abbasi AA, Khan MA, Windpassinger C. Exome sequence analysis in consanguineous Pakistani families inheriting Bardet-Biedle syndrome determined founder effect of mutation c.299delC (p.Ser100Leufs*24) in BBS9 gene. Mol Genet Genomic Med 2019; 7:e834. [PMID: 31294530 PMCID: PMC6687644 DOI: 10.1002/mgg3.834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/11/2019] [Accepted: 05/22/2019] [Indexed: 12/29/2022] Open
Abstract
Background Bardet‐Biedl syndrome (BBS) is characterized by a heterogeneous phenotypic spectrum of retinopathy, intellectual disability (ID), obesity, polydactyly, and kidney dysfunctions as the major clinical features. Genetic investigations have reported 21 BBS genes, the products of which are mostly located at the centrosome, basal body or the ciliary transition zone. Methods In the present genetic report, we analyzed two apparently unrelated consanguineous BBS families from Dera Ismail Khan (D.I.Khan) district, Pakistan. Genetic mapping was performed using Whole exome sequencing and Sanger sequencing. Results Whole exome sequencing identified a recently reported single base deletion NM_001033604.1:c.299delC in the fourth exon of BBS9 in both families. The identified frameshift mutation is predicted to cause premature truncation of the expressed protein (p.Ser100Leufs*24). This mutation has previously been mapped in a consanguineous Pakistani family; therefore this is the second report of this particular mutation in two additional BBS families originating from different locations. Conclusion We speculate the evolutionary significance of this mutation and assume its strong founder effect in the Khaisoori tribe of D.I.Khan. Based on these findings, we suggest developing a molecular diagnostic test that may be used for premarital and prenatal screening of families at risk of BBS.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Zubair
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Sophie Bierbaumer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jasmin Blatterer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Aisha Gul
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Badar
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Ansar Ahmad Abbasi
- Department of Zoology, Mirpur University of Science and Technology (MUST), Mirpur, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
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Khan AK, Muhammad N, Khan SA, Ullah W, Nasir A, Afzal S, Ramzan K, Basit S, Khan S. A novel mutation in the HPGD gene causing primary hypertrophic osteoarthropathy with digital clubbing in a Pakistani family. Ann Hum Genet 2017; 82:171-176. [PMID: 29282707 DOI: 10.1111/ahg.12239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 11/27/2022]
Abstract
Primary hypertrophic osteoarthropathy (PHO) is a congenital multisystemic entity characterized by three major clinical symptoms: pachydermia, periostosis, and digital clubbing. Recently it has been reported that pathogenic mutations in two genes are known to be associated with PHO: HPGD and SLCO2A1. In the present study, a five-generation consanguineous Pakistani family harboring primary hypertrophic osteoarthropathy in autosomal-recessive pattern was ascertained. Whole genome single nucleotide polymorphisms (SNPs) genotyping and sequence analysis revealed a novel homozygous missense mutation (c.577T˃C) of the human HPGD gene in all affected members of the family. The study presented here demonstrate the first case of primary hypertrophic osteoarthropathy reported in Pashtun population.
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Affiliation(s)
- Anwar Kamal Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Waheed Ullah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Nasir
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Sibtain Afzal
- Prince Naif Centre for Immunology Research, College of Medicine, King Khalid University Hospitals, King Saud University Riyadh, Kingdom of Saudi Arabia
| | - 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 Almunawwarah, Saudi Arabia
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
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Yıldız Bölükbaşı E, Afzal M, Mumtaz S, Ahmad N, Malik S, Tolun A. Progressive SCAR14 with unclear speech, developmental delay, tremor, and behavioral problems caused by a homozygous deletion of the SPTBN2 pleckstrin homology domain. Am J Med Genet A 2017. [PMID: 28636205 DOI: 10.1002/ajmg.a.38332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report on nine members of a consanguineous Pakistani family with primary presentation of intellectual disability, developmental delay, limb and gait ataxia, behavioral and speech problems, and tremor. By linkage mapping and exome sequencing we identified novel homozygous splicing variant c.6375-1G>C in SPTBN2. To date, only two other SPTBN2 mutations with recessive pattern of inheritance causing SCAR14 (spinocerebellar ataxia, autosomal recessive 14) that manifest with developmental ataxia and cognitive impairment, or cerebellar ataxia, mental retardation, and pyramidal signs have been reported. The mutation we identified is predicted to lead to the deletion of just the pleckstrin homology domain; thus, the earlier onset and more progressive nature of the disease in the presented family, as compared to earlier reports, were unexpected. No other mutation that could possibly explain the features that were unusual for SCAR14-arched palate, limb hypotonia, climacophobia, and behavioral problems-was identified. The disease was more severe in males than females. Our findings expand the recessive SPTBN2 mutation phenotype. We also review SPTBN2 mutation phenotypes. The gene encodes beta-III spectrin, which forms tetramers with alpha-II spectrin. The manifestations of this third recessive mutation suggest that for recessive mutations either no mutant protein is synthesized because the transcript is subject to nonsense-mediated decay or the mutant protein does not bind membrane proteins and, thus, does not exert a negative effect in heterozygotes, whereas the dominant mutations causing SCA5 form defective tetramers that compete with the native tetramers in binding membrane proteins, but are unable to anchor them.
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Affiliation(s)
| | - Muhammad Afzal
- Human Genetics Program, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sara Mumtaz
- Human Genetics Program, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Nafees Ahmad
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Sajid Malik
- Human Genetics Program, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
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Afzal M, Zaman Q, Kornak U, Mundlos S, Malik S, Flöttmann R. Novel splice mutation in LRP4 causes severe type of Cenani-Lenz syndactyly syndrome with oro-facial and skeletal symptoms. Eur J Med Genet 2017; 60:421-425. [PMID: 28559208 DOI: 10.1016/j.ejmg.2017.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 01/19/2023]
Abstract
Cenani-Lenz syndactyly syndrome (CLSS; MIM-212780) is a rare autosomal recessive limb malformation characterized by complete osseous fusion of all fingers and toes, disorganization of phalangeal elements and severe shortening of the radius and ulna. It is occasionally associated with renal hypoplasia, oro-facial defects, scoliosis of the thoracic spine, hearing loss, and genital anomalies. Here we describe a consanguineous Pakistani kindred with a severe form of CLSS characterized by complete syndactyly and disorganization of fingers, oligo-syndactyly of toes, shortening of limbs, frontal bossing, and hypoplasia/agenesis of left kidney. The affected individuals were additionally presented with short stature, cleft-lip and hypoplastic shoulder joint with restricted upper limb movement. A novel splice variant in LRP4 (c.316+1G > A) segregated with the phenotype in a five generations family. The mutation is predicted to add 29 non-native amino acids with a premature termination, resulting in approximately 90% length reduction of the wild-type transcript. These findings not only further expand the phenotypic variability of CLSS but also indicate that early truncated and loss-of-function mutations in LRP4 lead to a more severe CLSS phenotype.
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Affiliation(s)
- Muhammad Afzal
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Qamar Zaman
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Uwe Kornak
- Institut Fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut Fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institut Fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut Fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Ricarda Flöttmann
- Institut Fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany.
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Khan AK, Muhammad N, Aziz A, Khan SA, Shah K, Nasir A, Khan MA, Khan S. A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family. BMC Med Genet 2017; 18:42. [PMID: 28403827 PMCID: PMC5389142 DOI: 10.1186/s12881-017-0402-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/04/2017] [Indexed: 02/02/2023]
Abstract
Background Pure 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. Methods In 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. Results Through 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. Conclusion This is the first mutation reported in homeodomain, while 5th mutation reported in HOXC13 gene causing PHNED.
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Affiliation(s)
- Anwar Kamal Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Aziz
- Department of Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Khadim Shah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Abdul Nasir
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry & Biotechnology, Gomal University, D.I.Khan, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan.
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Saleha S, Ajmal M, Jamil M, Nasir M, Hameed A. In silico analysis of a disease-causing mutation in PCDH15 gene in a consanguineous Pakistani family with Usher phenotype. Int J Ophthalmol 2016; 9:662-8. [PMID: 27275418 DOI: 10.18240/ijo.2016.05.04] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/06/2015] [Indexed: 11/23/2022] Open
Abstract
AIM To map Usher phenotype in a consanguineous Pakistani family and identify disease-associated mutation in a causative gene to establish phenotype-genotype correlation. METHODS A consanguineous Pakistani family in which Usher phenotype was segregating as an autosomal recessive trait was ascertained. On the basis of results of clinical investigations of affected members of this family disease was diagnosed as Usher syndrome (USH). To identify the locus responsible for the Usher phenotype in this family, genomic DNA from blood sample of each individual was genotyped using microsatellite Short Tandem Repeat (STR) markers for the known Usher syndrome loci. Then direct sequencing was performed to find out disease associated mutations in the candidate gene. RESULTS By genetic linkage analysis, the USH phenotype of this family was mapped to PCDH15 locus on chromosome 10q21.1. Three different point mutations in exon 11 of PCDH15 were identified and one of them, c.1304A>C was found to be segregating with the disease phenotype in Pakistani family with Usher phenotype. This, c.1304A>C transversion mutation predicts an amino-acid substitution of aspartic acid with an alanine at residue number 435 (p.D435A) of its protein product. Moreover, in silico analysis revealed conservation of aspartic acid at position 435 and predicated this change as pathogenic. CONCLUSION The identification of c.1304A>C pathogenic mutation in PCDH15 gene and its association with Usher syndrome in a consanguineous Pakistani family is the first example of a missense mutation of PCDH15 causing USH1 phenotype. In previous reports, it was hypothesized that severe mutations such as truncated protein of PCDH15 led to the Usher I phenotype and that missense variants are mainly responsible for non-syndromic hearing impairment.
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Affiliation(s)
- Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ajmal
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan
| | - Muhammad Jamil
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Nasir
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan
| | - Abdul Hameed
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan
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Mumtaz S, Yıldız E, Jabeen S, Khan A, Tolun A, Malik S. RBBP8 syndrome with microcephaly, intellectual disability, short stature and brachydactyly. Am J Med Genet A 2015; 167A:3148-52. [PMID: 26333564 DOI: 10.1002/ajmg.a.37299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/31/2015] [Indexed: 11/08/2022]
Abstract
Primary microcephaly is clinically variable and genetically heterogeneous. Four phenotypically distinct types of autosomal recessive microcephaly syndromes are due to different RBBP8 mutations. We report on a consanguineous Pakistani family with homozygous RBBP8 mutation c.1808_1809delTA (p.Ile603Lysfs*7) manifesting microcephaly and a distinct combination of skeletal, limb and ectodermal defects, mild intellectual disability, minor facial anomalies, anonychia, disproportionate short stature and brachydactyly, and additionally talipes in one patient.
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Affiliation(s)
- Sara Mumtaz
- Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Esra Yıldız
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Saliha Jabeen
- Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amjad Khan
- Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Sajid Malik
- Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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