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Zhang J, Wang Y, Zhao Y, Liu F. A new atypical splice mutation in PKD2 leading to autosomal dominant polycystic kidney disease in a Chinese family. Singapore Med J 2024; 65:229-234. [PMID: 34749493 PMCID: PMC11132625 DOI: 10.11622/smedj.2021162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 07/25/2021] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Autosomal dominant polycystic kidney disease (ADPKD) is a very common hereditary renal disorder. Mutations in PKD1 and PKD2 , identified as disease-causing genes, account for 85% and 15% of the ADPKD cases, respectively. METHODS In this study, the mutation analysis of polycystic kidney disease (PKD) genes was performed in a Chinese family with suspected ADPKD using targeted clinical exome sequencing (CES). The candidate pathogenic variants were further tested by using Sanger sequencing and validated for co-segregation. In addition, reverse transcription-polymerase chain reaction (RT-PCR) was performed to test for abnormal splicing and assess its potential pathogenicity. RESULTS A novel atypical splicing mutation that belongs to unclassified variants (UCVs), IVS6+5G>C, was identified in three family members by CES and was shown to co-segregate only with the affected individuals. The RT-PCR revealed the abnormal splicing of exon 6, which thus caused truncating mutation. These findings suggested that the atypical splice site alteration, IVS6+5G>C, in the PKD2 gene was the potential pathogenic mutation leading to ADPKD in this Chinese family. CONCLUSION The data available in this study provided strong evidence that IVS6+5G>C is the potential pathogenic mutation for ADPKD. In addition, our findings emphasised the significance of functional analysis of UCVs and genotype-phenotype correlation in ADPKD.
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Affiliation(s)
- Junlin Zhang
- Division of Nephrology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yiting Wang
- Division of Nephrology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yingwang Zhao
- Joy Orient Translational Medicine Research Center Co Ltd, Beijing, China
| | - Fang Liu
- Division of Nephrology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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Nigro E, Amicone M, D'Arco D, Sellitti G, De Marco O, Guarino M, Riccio E, Pisani A, Daniele A. Molecular Diagnosis and Identification of Novel Pathogenic Variants in a Large Cohort of Italian Patients Affected by Polycystic Kidney Diseases. Genes (Basel) 2023; 14:1236. [PMID: 37372416 DOI: 10.3390/genes14061236] [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: 04/11/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Polycystic Kidney Diseases (PKDs) consist of a genetically and phenotypically heterogeneous group of inherited disorders characterized by numerous renal cysts. PKDs include autosomal dominant ADPKD, autosomal recessive ARPKD and atypical forms. Here, we analyzed 255 Italian patients using an NGS panel of 63 genes, plus Sanger sequencing of exon 1 of the PKD1 gene and MPLA (PKD1, PKD2 and PKHD1) analysis. Overall, 167 patients bore pathogenic/likely pathogenic variants in dominant genes, and 5 patients in recessive genes. Four patients were carriers of one pathogenic/likely pathogenic recessive variant. A total of 24 patients had a VUS variant in dominant genes, 8 patients in recessive genes and 15 patients were carriers of one VUS variant in recessive genes. Finally, in 32 patients we could not reveal any variant. Regarding the global diagnostic status, 69% of total patients bore pathogenic/likely pathogenic variants, 18.4% VUS variants and in 12.6% of patients we could not find any. PKD1 and PKD2 resulted to be the most mutated genes; additional genes were UMOD and GANAB. Among recessive genes, PKHD1 was the most mutated gene. An analysis of eGFR values showed that patients with truncating variants had a more severe phenotype. In conclusion, our study confirmed the high degree of genetic complexity at the basis of PKDs and highlighted the crucial role of molecular characterization in patients with suspicious clinical diagnosis. An accurate and early molecular diagnosis is essential to adopt the appropriate therapeutic protocol and represents a predictive factor for family members.
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Affiliation(s)
- Ersilia Nigro
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche, Farmaceutiche, Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Amicone
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Daniela D'Arco
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gina Sellitti
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Oriana De Marco
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Maria Guarino
- Gastroenterology and Hepatology Unit, Department of Clinical Medicine and Surgery, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy
| | - Eleonora Riccio
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Antonio Pisani
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Aurora Daniele
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi "Federico II", Via Pansini 5, 80131 Napoli, Italy
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Autosomal dominant polycystic kidney disease (ADPKD) in Tunisia: From molecular genetics to the development of prognostic tools. Gene X 2022; 817:146174. [PMID: 35031424 DOI: 10.1016/j.gene.2021.146174] [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: 10/06/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
A high prevalence of genetic kidney disease in Tunisia has been detected, and their study provides very important clinical and genetic information. Autosomal dominant polycystic kidney disease (ADPKD) is one of the main causes of morbidity and mortality associated with the kidneys in Tunisia. We present here clinical and genetic characteristics of a cohort of Tunisian patients with ADPKD. Nineteen Tunisian patients with ADPKD, among 4 familial cases and 11 sporadic cases, and 50 Healthy individuals were included in this cohort. Genetic studies of PKD1/2 were carried on using Sanger sequencing and MLPA. In our study, the mean age at diagnosis was 47 ± 18 years. In addition, 84.21% of cases present a family history of ADPKD. Overall, 57.89% of the affected individuals had HTA and 26.31% patients had hematuria. 15.78 % of the patient has extra-renal cysts i.e. one patient with splenic cysts and two patients had liver cysts. 57.89 % of patients were diagnosed with various extra-renal clinical presentations i.e. myopia, hernia, deafness, intracranial aneurysm, respiratory distress, hyperthyroidism, urinary tract infection and lower back pains. The PKD1 genotype showed earlier onset of ESRD compared to PKD2 genotype (43 vs. 55 years old). Six mutations have been detected in PKD1 gene. Among them, three were novels e.g. c.688 T>G, p.C230G and c.690C>G, p.C230W among exon 5 and c.8522A>G, p.N2841S among exon 23. In addition, thirteen single nucleotides polymorphisms have been reported in PKD1 gene. Among them, eleven previously reported in heterozygous state and two novel single nucleotides polymorphisms in heterozygous and homozygous state and predicted to be probable polymorphisms by computational tools: c.496C>T, p.L166= among the exon 4, and c.10165G>C and p.E3389Gln among the exon 31. Only three single nucleotides polymorphisms previously reported in ADPKD database have been identified in PKD2 gene. The description and analysis of our cohort can help in rapid and reliable diagnosis for early management of patients in Tunisia. Indeed, predictive genetic testing can facilitate donor evaluation and increase living related kidney transplantation.
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Raj S, Singh RG, Das P. Mutational screening of PKD1 and PKD2 in Indian ADPKD patients identified 95 genetic variants. Mutat Res 2020; 821:111718. [PMID: 32823016 DOI: 10.1016/j.mrfmmm.2020.111718] [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: 07/25/2019] [Revised: 05/01/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mutation screening of autosomal dominant polycystic kidney disease (ADPKD) cases imply the major involvement of PKD1 mutations in 85% of patients while rest of the cases harbor mutation in PKD2, DNAJB11 and GANAB. This essentially indicates that individual's genotype holds the key for disease susceptibility and its severity. METHODS For finding genetic variability underlying the disease pathophysiology, 84 Indian ADPKD cases, 31 family members (12 susceptible) and 122 age matched control were screened for PKD1 and PKD2 using Sanger sequencing, PCR-RFLP and ARMS-PCR. RESULTS Genetic screening of Indian ADPKD cases revealed total 67 variants in PKD1 and 28 variants in PKD2. Among the identified variants in PKD1 and PKD2 genes, 35.79% were novel variants and 64.2% recurrent. Further, subcategorization of PKD1 variants showed 14 truncation/frameshift, 21 nonsynonymous, 25 synonymous and 7 intronic variants. Moreover, we observed 40 families with PKD1 pathogenic variants, 7 families with PKD2 pathogenic variants, 9 families with PKD1 & PKD2 pathogenic variants, and 26 families with PKD1/PKD2/PKD1-PKD2 non-pathogenic genetic variants. CONCLUSION Present study represented genetic background of Indian ADPKD cases which will be helpful in disease management as well as finding the genetically matched donor for kidney transplant.
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Affiliation(s)
- Sonam Raj
- Banaras Hindu University, Varanasi, 221005, India.
| | - Rana Gopal Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Parimal Das
- Centre for Genetic Disorders, Banaras Hindu University, Varanasi, 221005, India.
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Bitarafan F, Garshasbi M. Molecular genetic analysis of polycystic kidney disease 1 and polycystic kidney disease 2 mutations in pedigrees with autosomal dominant polycystic kidney disease. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2019; 24:44. [PMID: 31160911 PMCID: PMC6540774 DOI: 10.4103/jrms.jrms_835_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/08/2019] [Accepted: 02/25/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Dysfunction of polycystin-1 or polycystin-2, the proteins encoded by polycystic kidney disease 1 (PKD1) and PKD2, respectively, are the cause of autosomal dominant PKD (ADPKD). This genetically heterogeneous monogenic disorder is the most common inherited kidney disease. The disease manifests are progressive cyst growth, renal enlargement, and renal failure, due to abnormal proliferation of kidney tubular epithelium. MATERIALS AND METHODS In this study, mutation analysis of PKD1 and PKD2 genes in nine Iranian families was performed using next-generation sequencing. All patients met the diagnostic criteria of ADPKD. RESULTS Mutations were found in all 9 families in PKD1 gene, comprising 2 novel and 7 previously reported mutations. No mutation in PKD2 was identified. CONCLUSION Finding more mutations and expanding the spectrum of PKD1 and PKD2 mutations can increase the diagnostic value of molecular testing in the screening of ADPKD patients.
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Affiliation(s)
- Fatemeh Bitarafan
- Department of Cellular and Molecular Biology, North Tehran Branch, Islamic Azad University, Teheran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Teheran, Iran
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Hafizi A, Khatami SR, Galehdari H, Shariati G, Saberi AH, Hamid M. Exon sequencing of PKD1 gene in an Iranian patient with autosomal-dominant polycystic kidney disease. IRANIAN BIOMEDICAL JOURNAL 2015; 18:143-50. [PMID: 24842140 PMCID: PMC4048478 DOI: 10.6091/ibj.1317.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Introduction: Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic kidney disorders with the incidence of 1 in 1,000 births. ADPKD is genetically heterogeneous with two genes identified: PKD1 (16p13.3, 46 exons) and PKD2 (4q21, 15 exons). Eighty five percent of the patients with ADPKD have at least one mutation in the PKD1 gene. Genetic studies have demonstrated an important allelic variability among patients, but very few data are known about the genetic variation among Iranian populations. Methods: In this study, exon direct sequencing of PKD1 was performed in a seven-year old boy with ADPKD and in his parents. The patient’s father was ADPKD who was affected without any kidney dysfunction, and the patient’s mother was congenitally missing one kidney. Results: Molecular genetic testing found a mutation in all three members of this family. It was a missense mutation GTG>ATG at position 3057 in exon 25 of PKD1. On the other hand, two novel missense mutations were reported just in the 7-year-old boy: ACA>GCA found in exon 15 at codon 2241 and CAC>AAC found in exon 38 at codon 3710. For checking the pathogenicity of these mutations, exons 15, 25, and 38 of 50 unrelated normal cases were sequenced. Conclusion: our findings suggested that GTG>ATG is a polymorphism with high frequency (60%) as well as ACA>GCA and CAC>AAC are polymorphisms with frequencies of 14% and 22%, respectively in the population of Southwest Iran.
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Affiliation(s)
- Atousa Hafizi
- Dept. of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
| | - Saeid Reza Khatami
- Dept. of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
| | - Hamid Galehdari
- Dept. of Genetics, Faculty of Science, Shahid Chamran University, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetic Laboratory, Ahvaz, Iran.,Dept. of Medical Genetics, Jundishapur University of Medical Science, Ahvaz, Iran
| | - Ali Hossein Saberi
- Narges Medical Genetic Laboratory, Ahvaz, Iran.,Dept. of Medical Genetics, Jundishapur University of Medical Science, Ahvaz, Iran
| | - Mohammad Hamid
- Research Center of Biotechnology, Pasteur Institute of Iran, Tehran, Iran
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Yu C, Yang Y, Zou L, Hu Z, Li J, Liu Y, Ma Y, Ma M, Su D, Zhang S. Identification of novel mutations in Chinese Hans with autosomal dominant polycystic kidney disease. BMC MEDICAL GENETICS 2011; 12:164. [PMID: 22185115 PMCID: PMC3341574 DOI: 10.1186/1471-2350-12-164] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 12/20/2011] [Indexed: 02/05/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disease with an incidence of 1 in 400 to 1000. The disease is genetically heterogeneous, with two genes identified: PKD1 (16p13.3) and PKD2 (4q21). Molecular diagnosis of the disease in at-risk individuals is complicated due to the structural complexity of PKD1 gene and the high diversity of the mutations. This study is the first systematic ADPKD mutation analysis of both PKD1 and PKD2 genes in Chinese patients using denaturing high-performance liquid chromatography (DHPLC). METHODS Both PKD1 and PKD2 genes were mutation screened in each proband from 65 families using DHPLC followed by DNA sequencing. Novel variations found in the probands were checked in their family members available and 100 unrelated normal controls. Then the pathogenic potential of the variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice site alterations using online mutation prediction resources. RESULTS A total of 92 variations were identified, including 27 reported previously. Definitely pathogenic mutations (ten frameshift, ten nonsense, two splicing defects and one duplication) were identified in 28 families, and probably pathogenic mutations were found in an additional six families, giving a total detection level of 52.3% (34/65). About 69% (20/29) of the mutations are first reported with a recurrent mutation rate of 31%. CONCLUSIONS Mutation study of PKD1 and PKD2 genes in Chinese Hans with ADPKD may contribute to a better understanding of the genetic diversity between different ethnic groups and enrich the mutation database. Besides, evaluating the pathogenic potential of novel variations should also facilitate the clinical diagnosis and genetic counseling of the disease.
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Affiliation(s)
- Chaowen Yu
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yuan Yang
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, Chongqing, 400014, P. R. China
| | - Zhangxue Hu
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Jing Li
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yunqiang Liu
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yongxin Ma
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Mingyi Ma
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Dan Su
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Sizhong Zhang
- Department of Medical Genetics, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
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Hoefele J, Mayer K, Scholz M, Klein HG. Novel PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease (ADPKD). Nephrol Dial Transplant 2010; 26:2181-8. [PMID: 21115670 DOI: 10.1093/ndt/gfq720] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic renal disorder with an incidence of 1:1000. Mutations in two genes (PKD1 and PKD2) have been identified as causative. Eighty-five percent of patients with ADPKD carry their mutation in the PKD1 gene. So far, > 500 mutations for PKD1 and > 120 mutations for PKD2, respectively, are known. METHODS In this study, we performed mutation analysis of PKD1 and PKD2 by exon sequencing in patients during routine molecular diagnostics for ADPKD. RESULTS In total, 60 mutations were identified in 93 patients representing a mutation detection efficiency of 64.5%. Fifty-two mutations were identified in PKD1 (86.7%) and 8 in PKD2 (13.3%). These include 41 novel mutations detected in PKD1 and 5 novel mutations in PKD2. Accordingly, our data expand the spectrum of known PKD mutations by 8% for PKD1 (41/513) and 4.2% for PKD2 (5/120). These results are in agreement with the detection ranges of 42%, 63% and 64% for definitive disease-causing mutations, and 78%, 86% and 89% for all identified variants reported in several comprehensive mutation screening reports. CONCLUSIONS The increased number of known mutations will facilitate future studies into genotype-phenotype correlations.
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Affiliation(s)
- Julia Hoefele
- Center for Human Genetics and Laboratory Medicine Dr Klein and Dr Rost, Martinsried, Germany.
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