1
|
Latif M, Hashmi JA, Alayoubi AM, Ayub A, Basit S. Identification of Novel and Recurrent Variants in BTD, GBE1, AGL and ASL Genes in Families with Metabolic Disorders in Saudi Arabia. J Clin Med 2024; 13:1193. [PMID: 38592052 PMCID: PMC10932034 DOI: 10.3390/jcm13051193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 04/10/2024] Open
Abstract
Background and Objectives: Inherited metabolic disorders (IMDs) are a group of genetic disorders characterized by defects in enzymes or transport proteins involved in metabolic processes. These defects result in an abnormal accumulation of metabolites and thus interfere with the body's metabolism. A variety of IMDs exist and differential diagnosis is often challenging. Our objective was to gain insight into the genetic basis of IMDs and the correlations between specific genetic mutations and clinical presentations in patients admitted at various hospitals in the Madinah region of the Kingdom of Saudi Arabia. Material and Methods: Whole exome sequencing (WES) has emerged as a powerful tool for diagnosing IMDs and allows for the identification of disease-causing genetic mutations in individuals suspected of IMDs. This ensures accurate diagnosis and appropriate management. WES was performed in four families with multiple individuals showing clinical presentation of IMDs. Validation of the variants identified through WES was conducted using Sanger sequencing. Furthermore, various computational analyses were employed to uncover the disease gene co-expression and metabolic pathways. Results: Exome variant data analysis revealed missense variants in the BTD (c.1270G > C), ASL (c.1300G > T), GBE1 (c.985T > G) and AGL (c.113C > G) genes. Mutations in these genes are known to cause IMDs. Conclusions: Thus, our data showed that exome sequencing, in conjunction with clinical and biochemical characteristics and pathological hallmarks, could deliver an accurate and high-throughput outcome for the diagnosis and sub-typing of IMDs. Overall, our findings emphasize that the integration of WES with clinical and pathological information has the potential to improve the diagnosis and understanding of IMDs and related disorders, ultimately benefiting patients and the medical community.
Collapse
Affiliation(s)
- Muhammad Latif
- Department of Basic Medical Sciences, College of Medicine, Taibah University, Madinah 42353, Saudi Arabia; (J.A.H.); (A.M.A.)
- Center for Genetics and Inherited Diseases, Taibah University, Madinah 42353, Saudi Arabia
| | - Jamil Amjad Hashmi
- Department of Basic Medical Sciences, College of Medicine, Taibah University, Madinah 42353, Saudi Arabia; (J.A.H.); (A.M.A.)
- Center for Genetics and Inherited Diseases, Taibah University, Madinah 42353, Saudi Arabia
| | - Abdulfatah M. Alayoubi
- Department of Basic Medical Sciences, College of Medicine, Taibah University, Madinah 42353, Saudi Arabia; (J.A.H.); (A.M.A.)
| | - Arusha Ayub
- Department of Medicine, School of Health Sciences, University of Georgia, Tbilisi, P. O. Box-0171, Georgia;
| | - Sulman Basit
- Department of Basic Medical Sciences, College of Medicine, Taibah University, Madinah 42353, Saudi Arabia; (J.A.H.); (A.M.A.)
- Center for Genetics and Inherited Diseases, Taibah University, Madinah 42353, Saudi Arabia
| |
Collapse
|
2
|
Wang J, Yu Y, Cai C, Zhi X, Zhang Y, Zhao Y, Shu J. The biallelic novel pathogenic variants in AGL gene in a chinese patient with glycogen storage disease type III. BMC Pediatr 2022; 22:284. [PMID: 35578201 PMCID: PMC9109368 DOI: 10.1186/s12887-022-03252-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycogen storage disease type III (GSD III) is a rare autosomal recessive glycogenolysis disorder due to AGL gene variants, characterized by hepatomegaly, fasting hypoglycemia, hyperlipidemia, elevated hepatic transaminases, growth retardation, progressive myopathy, and cardiomyopathy. However, it is not easy to make a definite diagnosis in early stage of disease only based on the clinical phenotype and imageology due to its clinical heterogeneity. CASE PRESENTATION We report a two-year-old girl with GSD III from a nonconsanguineous Chinese family, who presented with hepatomegaly, fasting hypoglycemia, hyperlipidemia, elevated levels of transaminases. Accordingly, Sanger sequencing, whole‑exome sequencing of family trios, and qRT-PCR was performed, which revealed that the patient carried the compound heterogeneous variants, a novel frameshift mutation c.597delG (p. Q199Hfs*2) and a novel large gene fragment deletion of the entire exon 13 in AGL gene. The deletion of AGL was inherited from the proband's father and the c.597delG variant was from the mother. CONCLUSIONS In this study, we identified two novel variants c.597delG (p. Q199Hfs*2) and deletion of the entire exon 13 in AGL in a Chinese GSD III patient. We extend the mutation spectrum of AGL. We suggest that high-throughput sequencing technology can detect and screen pathogenic variant, which is a scientific basis about genetic counseling and clinical diagnosis.
Collapse
Affiliation(s)
- Jing Wang
- Department of Gastroenterology, Tianjin Children's Hospital, 300134, Tianjin, China.,Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China
| | - Yuping Yu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China.,Graduate College of Tianjin Medical University, 300070, Tianjin, China
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China.,Tianjin Pediatric Research Institute, 300134, Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, 300134, Tianjin, China
| | - Xiufang Zhi
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China.,Graduate College of Tianjin Medical University, 300070, Tianjin, China
| | - Ying Zhang
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China.,Graduate College of Tianjin Medical University, 300070, Tianjin, China
| | - Yu Zhao
- Department of Gastroenterology, Tianjin Children's Hospital, 300134, Tianjin, China.,Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), 300134, Tianjin, China. .,Tianjin Pediatric Research Institute, 300134, Tianjin, China. .,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, 300134, Tianjin, China. .,Tianjin Pediatric Research Institute, Tianjin Children's Hospital, No. 238 Longyan Road, Beichen District, 300134, Tianjin, China.
| |
Collapse
|
3
|
Hashmi JA, Safar RA, Afzal S, Albalawi AM, Abdu-Samad F, Iqbal Z, Basit S. Whole exome sequencing identification of a novel insertion mutation in the phospholipase C ε‑1 gene in a family with steroid resistant inherited nephrotic syndrome. Mol Med Rep 2018; 18:5095-5100. [PMID: 30280192 DOI: 10.3892/mmr.2018.9528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/27/2018] [Indexed: 11/05/2022] Open
Abstract
Nephrotic syndrome (NS) represents a heterogeneous group of kidney disorders characterized by excessive proteinuria, hypoalbuminemia and edema. Defects in the filtration barrier of the glomeruli results in the development of NS. The genetic cause of NS remains to be fully elucidated. However, previous studies based on positional cloning of genes mutated in NS have provided limited insight into the pathogenesis of this disease. Mutations in phospholipase C ε‑1 (PLCE1) have been reported as a cause of early onset NS characterized by histology of diffuse mesangial sclerosis. In the present study, the underlying cause of NS in a consanguineous family was identified. Clinical and molecular aspects of a consanguineous Saudi family comprised of five individuals with steroid resistant NS were examined. Seven healthy individuals from the same family were also studied. Whole exome sequencing (WES) was performed to detect the genetic defect underlying NS. WES identified a homozygous novel insertion mutation (c.6272_6273insT) in the PLCE1 gene. Pedigree and segregation analysis confirmed an autosomal recessive inheritance pattern. This mutation may result in a bi‑allelic loss of the C‑terminal Ras‑associating domain in PLCE1 that results in NS. The present study expanded the mutational spectrum of PLCE1 in NS. In addition, the present study provided further evidence that supports the important involvement of PLCE1 in the physiological function of the glomerular filtration barrier.
Collapse
Affiliation(s)
- Jamil Amjad Hashmi
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| | - Ramziah Ahmed Safar
- Department of Nephrology, Madinah Maternity and Children Hospital, Medina 42319, Kingdom of Saudi Arabia
| | - Sibtain Afzal
- Prince Naif Centre for Immunology Research, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh 12372, Kingdom of Saudi Arabia
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| | - Feroz Abdu-Samad
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| | - Zafar Iqbal
- College of Applied Medical Sciences, National Guard Health Affairs, Al‑Ahsa 36428, Kingdom of Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| |
Collapse
|
4
|
Yuan L, Chen L, Liao RX, Lin YY, Jiang Y, Wang O, Li M, Xing XP, Pang QQ, Jiajue R, Xia WB. A Common Mutation and a Novel Mutation in the HPGD Gene in Nine Patients with Primary Hypertrophic Osteoarthropathy. Calcif Tissue Int 2015; 97:336-42. [PMID: 26135126 DOI: 10.1007/s00223-015-0024-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
Primary hypertrophic osteoarthropathy (PHO) is a hereditary bone disease characterized by digital clubbing, periostosis, and pachydermia. The HPGD gene encoding 15-prostaglandin dehydrogenase and SLCO2A1 encoding one type of prostaglandin transporter were found to be responsible for PHO. Mutations of either gene would lead to increased level of prostaglandin E2 (PGE2), which might contribute to the constellation of the symptoms. The aim of the study was to analyze the HPGD gene and the clinical characteristics in nine patients with the diagnosis of PHO. Nine patients, (eight males and one female) including two siblings and seven sporadic cases, were enrolled in the study. Clinical features were summarized, and blood and urine samples were collected. Sanger method was used to sequence the HPGD gene to detect mutations. Urinary PGE2 and prostaglandin metabolite (PGE-M) levels for each patient were measured and compared to the healthy controls. A recurrent c.310_311delCT mutation was identified in all patients, of which six were homozygous, two were heterozygous, and one was compound heterozygous with this mutation and a novel heterozygous missense mutation c.488G>A (p.R163H). The levels of PGE2 in urine were much higher than normal in all patients, along with lower PGE-M levels. In conclusion, nine PHO patients were characterized by typical clinical manifestations including digital clubbing, periostosis, and pachydermia. A common mutation and a novel mutation in HPGD gene were identified to be responsible for the disease, and c.310_311delCT mutation is likely to be a hot-spot mutation site for Asian PHO patients.
Collapse
Affiliation(s)
- Lu Yuan
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Ling Chen
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Ruo-xi Liao
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Yuan-yuan Lin
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
- Department of Endocrinology, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Yan Jiang
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Ou Wang
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Mei Li
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Xiao-Ping Xing
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Qian-Qian Pang
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
- Department of Endocrinology, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Ruizhi Jiajue
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China
| | - Wei-bo Xia
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China.
| |
Collapse
|