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Zellers M, Solanki K, Retterer K, Murphy KM, Kelly MA, Les Kirchner H, Bucaloiu ID, Mirshahi T, Moore B, Chang AR. Genotype-first analysis in an unselected health system-based population reveals variable phenotypic severity of COL4A5 variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.04.24308453. [PMID: 38883771 PMCID: PMC11177927 DOI: 10.1101/2024.06.04.24308453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Introduction Our knowledge of X-linked Alport Syndrome [AS] comes mostly from selected cohorts with more severe disease. Methods We examined the phenotypic spectrum of X-linked AS in males and females with a genotype-based approach using data from the Geisinger MyCode DiscovEHR study, an unselected health system-based cohort with exome sequencing and electronic health record data. Patients with COL4A5 variants reported as pathogenic (P) or likely pathogenic (LP) in ClinVar, or protein-truncating variants (PTVs), were each matched with up to 5 controls without COL4A3/4/5 variants by sociodemographics, diabetes diagnosis, and year of first outpatient encounter. AS-related phenotypes included dipstick hematuria, bilateral sensorineural hearing loss (BSHL), proteinuria, decreased eGFR, and ESKD. Results Out of 170,856 patients, there were 30 hemizygous males (mean age 52.4 [SD 19.8] years) and 56 heterozygous females (mean age 58.5 [SD 19.4]) with a COL4A5 P/LP variant, including 48 with the hypomorphic variant p.Gly624Asp. Overall, penetrance (having any AS phenotypic feature) was highest for non-p.Gly624Asp P/LP variants (males: 89%, females: 86%), intermediate for p.Gly624Asp (males: 77%, females: 69%), compared to controls (males: 32%; females: 50%). The proportion with ESKD was highest for males with P/LP variants (41%), intermediate for males with p.Gly624Asp (15%) and females with P/LP variants (10%), compared to controls (males: 3%, females 2%). Only 33% of males and 11% of females had a known diagnosis of Alport syndrome or thin basement membrane disease. Only 47% of individuals with COL4A5 had completed albuminuria screening, and a minority were taking renin-angiotensin aldosterone system (RAAS) inhibitors. Conclusion In an unselected cohort, we show increased risks of AS-related phenotypes in men and women compared to matched controls, while showing a wider spectrum of severity than has been described previously and variability by genotype. Future studies are needed to determine whether early genetic diagnosis can improve outcomes in Alport Syndrome.
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Affiliation(s)
| | | | | | | | - Melissa A Kelly
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
- Department of Genomic Health, Geisinger, Danville, PA
| | - H Les Kirchner
- Department of Population Health Sciences, Geisinger, Danville, PA
| | - Ion Dan Bucaloiu
- Department of Nephrology, Geisinger, Danville, PA
- Department of Population Health Sciences, Geisinger, Danville, PA
| | | | - Bryn Moore
- Department of Genomic Health, Geisinger, Danville, PA
| | - Alexander R Chang
- Department of Nephrology, Geisinger, Danville, PA
- Department of Population Health Sciences, Geisinger, Danville, PA
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Lujinschi ȘN, Sorohan BM, Obrișcă B, Vrabie A, Lupușoru G, Achim C, Andronesi AG, Covic A, Ismail G. Genotype-Phenotype Correlations in Alport Syndrome-A Single-Center Experience. Genes (Basel) 2024; 15:593. [PMID: 38790222 PMCID: PMC11121304 DOI: 10.3390/genes15050593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Alport syndrome (AS) is a common and heterogeneous genetic kidney disease, that often leads to end-stage kidney disease (ESKD). METHODS This is a single-center, retrospective study that included 36 adults with type IV collagen (COL4) mutations. Our main scope was to describe how genetic features influence renal survival. RESULTS A total of 24 different mutations were identified, of which eight had not been previously described. Mutations affecting each of the type IV collagen α chains were equally prevalent (33.3%). Most of the patients had pathogenic variants (61.1%). Most patients had a family history of kidney disease (71%). The most prevalent clinical picture was nephritic syndrome (64%). One-third of the subjects had extrarenal manifestations, 41.6% of patients had ESKD at referral, and another 8.3% developed ESKD during follow-up. The median renal survival was 42 years (95% CI, 29.98-54.01). The COL4A4 group displayed better renal survival than the COL4A3 group (p = 0.027). Patients with missense variants had higher renal survival (p = 0.023). Hearing loss was associated with lower renal survival (p < 0.001). CONCLUSIONS Patients with COL4A4 variants and those with missense mutations had significantly better renal survival, whereas those with COL4A3 variants and those with hearing loss had worse prognoses.
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Affiliation(s)
- Ștefan Nicolaie Lujinschi
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Bogdan Marian Sorohan
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Bogdan Obrișcă
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Alexandra Vrabie
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Gabriela Lupușoru
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Camelia Achim
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andreea Gabriella Andronesi
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andreea Covic
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Nephrology Depatment, Dialysis and Renal Transplant Center, “Dr. C. I. Parhon” Clinical Hospital, 700503 Iasi, Romania
| | - Gener Ismail
- Department of Nephrology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (B.M.S.); (B.O.); (A.V.); (G.L.); (C.A.); (A.G.A.); (G.I.)
- Department of Nephrology, Fundeni Clinical Institute, 022328 Bucharest, Romania
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Riedhammer KM, Simmendinger H, Tasic V, Putnik J, Abazi-Emini N, Stajic N, Berutti R, Weidenbusch M, Patzer L, Lungu A, Milosevski-Lomic G, Günthner R, Braunisch MC, Ćomić J, Hoefele J. Is there a dominant-negative effect in individuals with heterozygous disease-causing variants in COL4A3/COL4A4? Clin Genet 2024; 105:406-414. [PMID: 38214412 DOI: 10.1111/cge.14471] [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: 10/29/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024]
Abstract
Alport syndrome (AS) shows a broad phenotypic spectrum ranging from isolated microscopic hematuria (MH) to end-stage kidney disease (ESKD). Monoallelic disease-causing variants in COL4A3/COL4A4 have been associated with autosomal dominant AS (ADAS) and biallelic variants with autosomal recessive AS (ARAS). The aim of this study was to analyze clinical and genetic data regarding a possible genotype-phenotype correlation in individuals with disease-causing variants in COL4A3/COL4A4. Eighty-nine individuals carrying at least one COL4A3/COL4A4 variant classified as (likely) pathogenic according to the American College of Medical Genetics guidelines and current amendments were recruited. Clinical data concerning the prevalence and age of first reported manifestation of MH, proteinuria, ESKD, and extrarenal manifestations were collected. Individuals with monoallelic non-truncating variants reported a significantly higher prevalence and earlier diagnosis of MH and proteinuria than individuals with monoallelic truncating variants. Individuals with biallelic variants were more severely affected than those with monoallelic variants. Those with biallelic truncating variants were more severely affected than those with compound heterozygous non-truncating/truncating variants or individuals with biallelic non-truncating variants. In this study an association of heterozygous non-truncating COL4A3/COL4A4 variants with a more severe phenotype in comparison to truncating variants could be shown indicating a potential dominant-negative effect as an explanation for this observation. The results for individuals with ARAS support the, still scarce, data in the literature.
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Affiliation(s)
- Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Hannes Simmendinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Macedonia
| | - Jovana Putnik
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Nora Abazi-Emini
- Medical Faculty of Skopje, University Children's Hospital, Macedonia
| | - Natasa Stajic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Marc Weidenbusch
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Ludwig-Maximilians University, Munich, Germany
| | - Ludwig Patzer
- Department of Pediatric Nephrology, Children's Hospital St. Elisabeth and St. Barbara, Halle/Saale, Germany
| | - Adrian Lungu
- Pediatric Nephrology Department, Fundeni Clinical Institute, Bucharest, Romania
| | - Gordana Milosevski-Lomic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Roman Günthner
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Matthias C Braunisch
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Jasmina Ćomić
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
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Zeni L, Mescia F, Toso D, Dordoni C, Mazza C, Savoldi G, Econimo L, Cortinovis R, Fisogni S, Alberici F, Scolari F, Izzi C. Clinical Significance of the Cystic Phenotype in Alport Syndrome. Am J Kidney Dis 2024:S0272-6386(24)00681-4. [PMID: 38514012 DOI: 10.1053/j.ajkd.2024.02.005] [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: 09/21/2023] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024]
Abstract
RATIONALE & OBJECTIVE Alport syndrome (AS) is the most common genetic glomerular disease caused by mutations that affect type IV collagen. However, the clinical characteristics and significance of AS with kidney cysts are not well defined. This study investigated the prevalence and clinical significance of cystic kidney phenotype in AS. STUDY DESIGN Retrospective cohort study. SETTING & PARTICIPANTS One hundred-eight patients with AS and a comparison cohort of 79 patients with IgA nephropathy (IgAN). Clinical, genetic, and imaging data were collected from medical records. EXPOSURE Cystic kidney phenotype evaluated by ultrasonography and defined as the presence of≥3 cysts in each kidney; demographic characteristics and estimated glomerular filtration rate (eGFR) at disease onset. OUTCOME Cystic kidney phenotype in the AS and IgAN cohorts; time to chronic kidney disease (CKD) stage 3b and longitudinal changes in eGFR in the AS cohort. ANALYTICAL APPROACH Logistic regression analysis to test independent strengths of associations of clinical/demographic features with the binary outcome of cystic phenotype. Survival analysis for the outcome of reaching CKD stage 3b and linear mixed models for changes in eGFR over time in the AS cohort. RESULTS We studied 108 patients with AS; 76 (70%) had a genetic diagnosis. Autosomal dominant AS was prevalent, accounting for 68% of patients with a genetic diagnosis. Cystic kidney phenotype was observed in 38% of patients with AS and was associated with normal-sized kidneys in all but 3 patients, who showed increased total kidney volume, mimicking autosomal dominant polycystic kidney disease. The prevalence of cystic kidney phenotype was significantly higher in patients with AS when compared with the group of patients with IgAN (42% vs 19%; P=0.002). Patients with the cystic kidney phenotype were older and had more marked reduction in eGFR than patients without cystic changes. Among patients with AS, the cystic phenotype was associated with older age and a faster decline eGFR. LIMITATIONS Retrospective, single-center study. CONCLUSIONS Cystic kidney phenotype is a common finding in AS. The cystic kidney phenotype is a common finding in AS, suggesting a possible role in cystogenesis for the genetic variants that cause this disease. PLAIN-LANGUAGE SUMMARY Hematuria is the classic renal presentation of Alport syndrome (AS), a hereditary glomerulopathy caused by pathogenic variants of the COL4A3-5 genes. An atypical kidney cystic phenotype has been rarely reported in individuals with these variants. To determine the prevalence of kidney cysts, we performed abdominal ultrasonography in a large group of patients with AS and a comparison group of patients with another glomerular kidney disease, IgA nephropathy (IgAN). Multiple kidney cysts, usually with normal kidney volume, were found in 38% of patients with AS. A few patients' kidney volumes were large enough to mimic a different hereditary cystic kidney disease, autosomal dominant polycystic kidney disease. The overall prevalence of kidney cysts in AS was more than double that observed in the well-matched comparison group with IgAN. These findings emphasize the high prevalence of cystic kidney phenotype in AS, suggesting a likely association between the genetic variants that cause this disease and the development of kidney cysts.
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Affiliation(s)
- Letizia Zeni
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili
| | - Federica Mescia
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Diego Toso
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Chiara Dordoni
- Clinical Genetics Unit, Department of Obstetrics and Gynaecology, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili
| | - Cinzia Mazza
- Medical Genetics Laboratory, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili
| | - Gianfranco Savoldi
- Medical Genetics Laboratory, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili
| | - Laura Econimo
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili
| | - Roberta Cortinovis
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili
| | - Simona Fisogni
- Section of Pathology, Department of Molecular and Translational Medicine, ASST-Spedali Civili, University of Brescia, Brescia, Italy
| | - Federico Alberici
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Claudia Izzi
- Clinical Genetics Unit, Department of Obstetrics and Gynaecology, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili; Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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Wu J, Cui Y, Liu T, Gu C, Ma X, Yu C, Cai Y, Shu J, Wang W, Cai C. Whole exome sequencing approach for identification of the molecular etiology in pediatric patients with hematuria. Clin Chim Acta 2024; 554:117795. [PMID: 38262496 DOI: 10.1016/j.cca.2024.117795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/25/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Hematuria is a common condition in clinical practice of pediatric patients. It is related to a wide spectrum of disorders and has high heterogeneity both clinically and genetically, which contributes to challenges of diagnosis and lead many pediatric patients with hematuria not to receive accurate diagnosis and early management. METHODS In this single center study, 42 children with hematuria were included in Tianjin Children's Hospital between 2019 and 2020. We analyzed the clinical information and performed WES (Whole exome sequencing) for all cases. Then the classification of identified variants was performed according to the American College of Medical Genetics and Genomics (ACMG) guidelines for interpreting sequence variants. For the fragment deletion, qPCR was performed to validate and confirm the inherited pattern. RESULTS For the 42 patients, 16 cases had gross hematuria and 26 had microscopic hematuria. Molecular genetic causes were uncovered in 9 (21.4%) children, including 7 with Alport syndrome (AS), one with polycystic nephropathy and one with lipoprotein glomerulopathy. The genetic causes for other patients were not related with hematuria. CONCLUSIONS WES is a rapid and effective way to evaluate patients with hematuria. The analysis of genotype-phenotype correlations of patients with AS indicated that severe variants were associated with early kidney failure. Secondary findings were not rare in Chinese children, thus the clinician should pay more attention to the clinical interpretation of sequencing results and properly interaction with patients and their family.
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Affiliation(s)
- Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Yaqiong Cui
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Tao Liu
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Chunyu Gu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Ximeng Ma
- Basic Medical College, Tianjin Medical University, Tianjin 30070, China
| | - Changshun Yu
- Tianjin KingMed Center for Clinical Laboratory Co. Ltd., Tianjin 300392, China
| | - Yingzi Cai
- Department of Medicine,Tianjin University, Tianjin 300110, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
| | - Wenhong Wang
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
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Mitrotti A, Di Bari I, Giliberti M, Franzin R, Conserva F, Chiusolo A, Gigante M, Accetturo M, Cafiero C, Ricciato L, Stea ED, Forleo C, Gallone A, Rossini M, Fiorentino M, Castellano G, Pontrelli P, Gesualdo L. What Is Hidden in Patients with Unknown Nephropathy? Genetic Screening Could Be the Missing Link in Kidney Transplantation Diagnosis and Management. Int J Mol Sci 2024; 25:1436. [PMID: 38338714 PMCID: PMC10855929 DOI: 10.3390/ijms25031436] [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: 12/21/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Between 15-20% of patients with end stage renal disease (ESRD) do not know the cause of the primary kidney disease and can develop complications after kidney transplantation. We performed a genetic screening in 300 patients with kidney transplantation, or undiagnosed primary renal disease, in order to identify the primary disease cause and discriminate between overlapping phenotypes. We used a custom-made panel for next-generation sequencing (Agilent technology, Santa Clara, CA, USA), including genes associated with Fabry disease, podocytopaties, complement-mediated nephropathies and Alport syndrome-related diseases. We detected candidate diagnostic variants in genes associated with nephrotic syndrome and Focal Segmental Glomerulosclerosis (FSGS) in 29 out of 300 patients, solving about 10% of the probands. We also identified the same genetic cause of the disease (PAX2: c.1266dupC) in three family members with different clinical diagnoses. Interestingly we also found one female patient carrying a novel missense variant, c.1259C>A (p.Thr420Lys), in the GLA gene not previously associated with Fabry disease, which is in silico defined as a likely pathogenic and destabilizing, and associated with a mild alteration in GLA enzymatic activity. The identification of the specific genetic background may provide an opportunity to evaluate the risk of recurrence of the primary disease, especially among patient candidates living with a donor kidney transplant.
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Affiliation(s)
- Adele Mitrotti
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Ighli Di Bari
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Marica Giliberti
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Rossana Franzin
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Francesca Conserva
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Anna Chiusolo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Maddalena Gigante
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Matteo Accetturo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Cesira Cafiero
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Luisa Ricciato
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Emma Diletta Stea
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Cinzia Forleo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Anna Gallone
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Michele Rossini
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Marco Fiorentino
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Giuseppe Castellano
- Department of Clinical Sciences and Community Health, University of Milano, 20122 Milano, Italy;
- Fondazione IRCCS Cà Grande Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Paola Pontrelli
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Loreto Gesualdo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
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Mahrous NN, Jamous YF, Almatrafi AM, Fallatah DI, Theyab A, Alanati BH, Alsagaby SA, Alenazi MK, Khan MI, Hawsawi YM. A Current Landscape on Alport Syndrome Cases: Characterization, Therapy and Management Perspectives. Biomedicines 2023; 11:2762. [PMID: 37893135 PMCID: PMC10604007 DOI: 10.3390/biomedicines11102762] [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: 09/09/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Alport syndrome (AS) is a rare genetic disorder categorized by the progressive loss of kidney function, sensorineural hearing loss and eye abnormalities. It occurs due to mutations in three genes that encode for the alpha chains of type IV collagen. Globally, the disease is classified based on the pattern of inheritance into X-linked AS (XLAS), which is caused by pathogenic variants in COL4A5, representing 80% of AS. Autosomal recessive AS (ARAS), caused by mutations in either COL4A3 or COL4A4, represents 15% of AS. Autosomal dominant AS (ADAS) is rare and has been recorded in 5% of all cases due to mutations in COL4A3 or COL4A4. This review provides updated knowledge about AS including its clinical and genetic characteristics in addition to available therapies that only slow the progression of the disease. It also focuses on reported cases in Saudi Arabia and their prevalence. Moreover, we shed light on advances in genetic technologies like gene editing using CRISPR/Cas9 technology, the need for an early diagnosis of AS and managing the progression of the disease. Eventually, we provide a few recommendations for disease management, particularly in regions like Saudi Arabia where consanguineous marriages increase the risk.
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Affiliation(s)
- Nahed N. Mahrous
- Department of Biological Sciences, College of Science, University of Hafr Al-Batin, Hafr Al-Batin 39524, Saudi Arabia;
| | - Yahya F. Jamous
- The National Center of Vaccines and Bioprocessing, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia;
| | - Ahmad M. Almatrafi
- Department of Biological Sciences, College of Science, Taibah University, Madinah 42353, Saudi Arabia;
| | - Deema I. Fallatah
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Abdulrahman Theyab
- Department of Laboratory and Blood Bank, Security Forces Hospital, Makkah 11481, Saudi Arabia;
- Department of Biochemistry & Molecular Medicine, College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Bayan H. Alanati
- Center for Synthetic Microbiology, Bioinformatics Core Facility, University of Marburg, 35032 Marburg, Germany;
| | - Suliman A. Alsagaby
- Department of Medicinal Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia;
| | - Munifa K. Alenazi
- Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 40047, Jeddah 21499, Saudi Arabia; (M.K.A.); (M.I.K.)
| | - Mohammed I. Khan
- Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 40047, Jeddah 21499, Saudi Arabia; (M.K.A.); (M.I.K.)
| | - Yousef M. Hawsawi
- Department of Biochemistry & Molecular Medicine, College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
- Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 40047, Jeddah 21499, Saudi Arabia; (M.K.A.); (M.I.K.)
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Solanki KV, Hu Y, Moore BS, Abedi V, Avula V, Mirshahi T, Strande NT, Bucaloiu ID, Chang AR. The Phenotypic Spectrum of COL4A3 Heterozygotes. Kidney Int Rep 2023; 8:2088-2099. [PMID: 37849993 PMCID: PMC10577321 DOI: 10.1016/j.ekir.2023.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/17/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction The penetrance and phenotypic spectrum of autosomal dominant Alport Syndrome (ADAS), affecting 1 in 106, remains understudied. Methods Using data from 174,418 participants in the Geisinger MyCode/DiscovEHR study, an unselected health system-based cohort with whole exome sequencing, we identified 403 participants who were heterozygous for likely pathogenic COL4A3 variants. Phenotypic data was evaluated using International Classification of Diseases (ICD) codes, laboratory data, and chart review. To evaluate the phenotypic spectrum of genetically-determined ADAS, we matched COL4A3 heterozygotes 1:5 to nonheterozygotes using propensity scores by demographics, hypertension, diabetes, and nephrolithiasis. Results COL4A3 heterozygotes were at significantly increased risks of hematuria, decreased estimated glomerular filtration rate (eGFR), albuminuria, and kidney failure (P < 0.05 for all comparisons) but not bilateral sensorineural hearing loss (P = 0.9). Phenotypic severity was more severe for collagenous domain glycine missense variants than protein truncating variants (PTVs). For example, patients with Gly695Arg (n = 161) had markedly increased risk of dipstick hematuria (odds ratio [OR] 9.50; 95% confidence interval [CI]: 6.32, 14.28) and kidney failure (OR 7.02; 95% CI: 3.48, 14.16) whereas those with PTVs (n = 119) had moderately increased risks of dipstick hematuria (OR 1.64; 95% CI: 1.03, 2.59) and kidney failure (OR 3.44; 95% CI: 1.28, 9.22). Less than a third of patients had albuminuria screening completed, and fewer than 1 of 3 were taking inhibitors of the renin-angiotensin-aldosterone system. Conclusion This study demonstrates a wide spectrum of phenotypic severity in ADAS due to COL4A3 with phenotypic variability by genotype. Future studies are needed to evaluate the impact of earlier diagnosis, appropriate evaluation, and treatment of ADAS.
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Affiliation(s)
- Kaushal V Solanki
- Center for Kidney Health Research, Geisinger, Danville, Pennsylvania, USA
| | - Yirui Hu
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania, USA
| | - Bryn S Moore
- Department of Genomic Health, Geisinger, Danville, Pennsylvania, USA
| | - Vida Abedi
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, USA; Road, Tarrytown, New York, USA
| | - Venkatesh Avula
- Department of Genomic Health, Geisinger, Danville, Pennsylvania, USA
| | - Tooraj Mirshahi
- Department of Genomic Health, Geisinger, Danville, Pennsylvania, USA
| | - Natasha T Strande
- Department of Genomic Health, Geisinger, Danville, Pennsylvania, USA
- Autism and Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Ion D Bucaloiu
- Department of Nephrology, Geisinger, Danville, Pennsylvania, USA
| | - Alexander R Chang
- Center for Kidney Health Research, Geisinger, Danville, Pennsylvania, USA
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania, USA
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Levy M, Bazak L, Lev-El N, Greenberg R, Kropach N, Basel-Salmon L, Maya I. Potential Founder Variants in COL4A4 Identified in Bukharian Jews Linked to Autosomal Dominant and Autosomal Recessive Alport Syndrome. Genes (Basel) 2023; 14:1854. [PMID: 37895203 PMCID: PMC10606019 DOI: 10.3390/genes14101854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Alport syndrome is a hereditary disorder caused by pathogenic variants in the COL4A gene, which can be inherited in an autosomal recessive, dominant, or X-linked pattern. In the Bukharian Jewish population, no founder pathogenic variant has been reported in COL4A4. METHODS The cohort included 38 patients from 22 Bukharian Jewish families with suspected Alport syndrome who were referred the nephrogenetics clinic between 2012 and 2022. The study collected demographic, clinical, and genetic data from electronic medical records, which were used to evaluate the molecular basis of the disease using Sanger sequencing, and next-generation sequencing. RESULTS Molecular diagnosis was confirmed in 20/38 patients, with each patient having at least one of the three disease-causing COL4A4 variants detected: c.338G A (p.Gly1008Arg), and c.871-6T>C. In addition, two patients were obligate carriers. Overall, there were 17 heterozygotes, 2 compound heterozygotes, and 3 homozygotes. Each variant was detected in more than one unrelated family. All patients had hematuria with/without proteinuria at referral, and the youngest patient with proteinuria (age 5 years) was homozygous for the c.338G>A variant. End-stage renal disease was diagnosed in two patients at the age of 38 years, a compound heterozygote for c.338G>A and c.871-6T>C. Hearing deterioration was detected in three patients, the youngest aged 40 years, all of whom were heterozygous for c.338G>A. CONCLUSION This study unveils three novel disease-causing variants, c.3022G>A, c.871-6T>C, and c.338G>A, in the COL4A4 gene that are recurrent among Jews of Bukharian ancestry, and cause Alport syndrome in both dominant and recessive autosomal inheritance patterns.
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Affiliation(s)
- Michal Levy
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
| | - Lily Bazak
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Noa Lev-El
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Rotem Greenberg
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Nesia Kropach
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva 4920235, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Felsenstein Medical Research Center, Petach Tikva 4920235, Israel
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
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Shanks J, Butler G, Cheng D, Jayasinghe K, Quinlan C. Clinical and diagnostic utility of genomic sequencing for children referred to a Kidney Genomics Clinic with microscopic haematuria. Pediatr Nephrol 2023; 38:2623-2630. [PMID: 36715773 DOI: 10.1007/s00467-022-05846-1] [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: 09/04/2022] [Revised: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Microscopic haematuria in children is associated with the risk of progression to chronic kidney disease. Genetic disease is an important potential aetiology. Genomic sequencing presents the most effective diagnostic route for these conditions, but access remains inequitable internationally. METHODS We conducted a retrospective review of the electronic medical records of a Kidney Genomics Clinic (KGC) from January 2016 to December 2021. RESULTS Sixty patients were referred to the KGC with haematuria over this period. Forty-three percent of patients had analysis of a limited haematuria panel (COL4A1, COL4A3, COL4A4, COL4A5, MYH9) with 58% receiving a genetic diagnosis. Forty-two percent of referred patients had further analysis of genes implicated in the development of kidney disease, and 36% received a diagnosis. Eight percent of patients underwent cascade testing for a known familial variant, and all received a diagnosis. Children with the highest levels of haematuria (> 500 × 106/L red blood cells) had the highest diagnostic yield (67%). Proteinuria, defined as a urinary protein to creatinine ratio > 20, increased the diagnostic yield from 31 to 65%. Importantly, negative genetic analysis can still have significant clinical utility for patients by altering surveillance and further management; the genetic result had clinical utility in 60% of patients. CONCLUSIONS Our KGC review highlights the substantial clinical utility and diagnostic yield of genomic analysis for microscopic haematuria in paediatric patients. Whilst the management of variants of uncertain significance can be challenging, a multidisciplinary team including genetic counselling can help ensure these patients are followed up meaningfully. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Josiah Shanks
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia.
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia.
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia.
| | - Grainne Butler
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Daryl Cheng
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia
| | - Kushani Jayasinghe
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia
| | - Catherine Quinlan
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
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Ponleitner M, Allmer DM, Hecking M, Gatterer C, Graf S, Smogavec M, Laccone F, Rommer PS, Sunder-Plassmann G. Phenotyping of a novel COL4A4 and novel GLA variant in a patient presenting with microhematuria and mildly impaired kidney function: a case report. Front Genet 2023; 14:1211858. [PMID: 37323669 PMCID: PMC10267447 DOI: 10.3389/fgene.2023.1211858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
We describe the case of a 44-year-old male patient with a longstanding history of microhematuria and mildly impaired kidney function (CKD G2A1). The family history disclosed three females who also had microhematuria. Genetic testing by whole exome sequencing revealed two novel variants in COL4A4 (NM_000092.5: c.1181G>T, NP_000083.3: p.Gly394Val, heterozygous, likely pathogenic; Alport syndrome, OMIM# 141200, 203780) and GLA (NM_000169.3: c.460A>G, NP_000160.1: p.Ile154Val, hemizygous, variant of uncertain significance; Fabry disease, OMIM# 301500), respectively. Extensive phenotyping revealed no biochemical or clinical evidence for the presence of Fabry disease. Thus, the GLA c.460A>G, p.Ile154Val, is to be classified as a benign variant, whereas the COL4A4 c.1181G>T, p.Gly394Val confirms the diagnosis of autosomal dominant Alport syndrome in this patient.
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Affiliation(s)
- Markus Ponleitner
- Department of Neurology, Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Daniela Maria Allmer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Manfred Hecking
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Constantin Gatterer
- Division of Cardiology, Department of Medicine II, Medical University of Vienna, Vienna, Austria
| | - Senta Graf
- Division of Cardiology, Department of Medicine II, Medical University of Vienna, Vienna, Austria
| | - Mateja Smogavec
- Institute for Human Genetics, Medical University of Vienna, Vienna, Austria
| | - Franco Laccone
- Institute for Human Genetics, Medical University of Vienna, Vienna, Austria
| | - Paulus Stefan Rommer
- Department of Neurology, Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Gere Sunder-Plassmann
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
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12
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Prasad B, Sharma A, Lanktree MB, Goyal K, Dokouhaki P. Kidney Biopsy and Type IV Collagen Gene Sequencing Fail to Explain Hematuria in Loin Pain Hematuria Syndrome. Kidney Int Rep 2023; 8:1013-1021. [PMID: 37180518 PMCID: PMC10166728 DOI: 10.1016/j.ekir.2023.02.1075] [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: 11/08/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Loin pain hematuria syndrome (LPHS) is a rare clinical syndrome with a reported prevalence of 1 in 10,000. The syndrome is characterized by severe pain localized to the kidney in the absence of identifiable urinary tract disease. Because of an inadequate understanding of the pathophysiology of the disease, the goal of management has been limited to symptomatic pain management. Through detailed phenotype and genotype assessment we sought to identify possible underlying etiologies. Methods We completed a chart review, ultrasound imaging, kidney biopsy, and type IV collagen (COL4A3, COL4A4, and COL4A5) gene sequencing in 14 patients with loin pain hematuria recruited from a single center. Results Red blood cells and red cell casts were observed within the tubules in 10 of 14 patients. The glomerular basement membrane (GBM) was normal in 11 patients and thickened in 1 patient. Staining for IgA kappa was present in 1 patient. C3 deposition without any inflammation was present in 7 patients. Arteriolar hyalinosis was present in 4 patients and endothelial cell injury was present in 6 patients. No pathogenic COL4A3, COL4A4, or COL4A5 variants were identified. Conclusion Conventional histopathology and genetic testing for type IV collagen variants failed to identify the cause of hematuria in 14 patients with LPHS.
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Affiliation(s)
- Bhanu Prasad
- Section of Nephrology, Department of Medicine, Regina General Hospital, Regina, Saskatchewan, Canada
- College of Medicine, University of Saskatchewan, Regina, Saskatchewan, Canada
| | - Aditi Sharma
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Mathew B Lanktree
- Division of Nephrology, St. Joseph’s Healthcare Hamilton, McMaster University, Hamilton, Ontario, Canada
| | - Kunal Goyal
- Department of Radiology, Regina General Hospital, Regina, Saskatchewan, Canada
| | - Pouneh Dokouhaki
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Solanki KV, Hu Y, Moore BS, Abedi V, Avula V, Mirshahi T, Strande NT, Bucaloiu ID, Chang AR. The Phenotypic Spectrum of COL4A3 Heterozygotes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.11.23288298. [PMID: 37163122 PMCID: PMC10168410 DOI: 10.1101/2023.04.11.23288298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Most data on Alport Syndrome (AS) due to COL4A3 are limited to families with autosomal recessive AS or severe manifestations such as focal segmental glomerulosclerosis (FSGS). Using data from 174,418 participants in the Geisinger MyCode/DiscovEHR study, an unselected health system-based cohort with whole exome sequencing, we identified 403 participants (0.2%) who were heterozygous for likely pathogenic COL4A3 variants. Phenotypic data was evaluated using International Classification of Diseases (ICD) codes, laboratory data, and chart review. To evaluate the phenotypic spectrum of genetically-determined autosomal dominant AS, we matched COL4A3 heterozygotes 1:5 to non-heterozygotes using propensity scores by demographics, hypertension, diabetes, and nephrolithiasis. COL4A3 heterozygotes were at significantly increased risks of hematuria, decreased estimated glomerular filtration rate (eGFR), albuminuria, and end-stage kidney disease (ESKD) (p<0.05 for all comparisons) but not bilateral sensorineural hearing loss (p=0.9). Phenotypic severity tended to be more severe among patients with glycine missense variants located within the collagenous domain. For example, patients with Gly695Arg (n=161) had markedly increased risk of dipstick hematuria (OR 9.47, 95% CI: 6.30, 14.22) and ESKD diagnosis (OR 7.01, 95% CI: 3.48, 14.12) whereas those with PTVs (n=119) had moderately increased risks of dipstick hematuria (OR 1.63, 95% CI: 1.03, 2.58) and ESKD diagnosis (OR 3.43, 95% CI: 1.28, 9.19). Less than a third of patients had albuminuria screening completed, and fewer than 1/3 were taking inhibitors of the renin-angiotensin-aldosterone system (RAASi). Future studies are needed to evaluate the impact of earlier diagnosis, appropriate evaluation, and treatment of ADAS.
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Affiliation(s)
| | - Yirui Hu
- Department of Population Health Sciences, Geisinger, Danville, PA
| | - Bryn S Moore
- Department of Genomic Health, Geisinger, Danville, PA
| | - Vida Abedi
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | | | | | - Natasha T Strande
- Department of Genomic Health, Geisinger, Danville, PA
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | | | - Alexander R Chang
- Center for Kidney Health Research, Geisinger, Danville, PA
- Department of Population Health Sciences, Geisinger, Danville, PA
- Regeneron Genetics Center, Sawmill Road, Tarrytown, NY
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Groen In 't Woud S, Rood IM, Steenbergen E, Willemsen B, Dijkman HB, van Geel M, Schoots J, Wetzels JFM, Lugtenberg D, Deegens JKJ, Bongers EMHF. Kidney Disease Associated With Mono-allelic COL4A3 and COL4A4 Variants: A Case Series of 17 Families. Kidney Med 2023; 5:100607. [PMID: 36925663 PMCID: PMC10011433 DOI: 10.1016/j.xkme.2023.100607] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rationale & Objective Mono-allelic variants in COL4A3 and COL4A4 (COL4A3/COL4A4) have been identified in a spectrum of glomerular basement membrane nephropathies, including thin basement membrane nephropathy and autosomal dominant Alport syndrome. With the increasing use of next generation sequencing, mono-allelic COL4A3/COL4A4 variants are detected more frequently, but phenotypic heterogeneity impedes counseling. We aimed to investigate the phenotypic spectrum, kidney biopsy results, and segregation patterns of patients with mono-allelic COL4A3/COL4A4 variants identified by whole exome sequencing. Study Design Case series. Setting & Participants We evaluated clinical and pathologic characteristics of 17 Dutch index patients with mono-allelic variants in COL4A3/COL4A4 detected by diagnostic whole exome sequencing and 25 affected family members with variants confirmed by Sanger sequencing. Results Eight different mono-allelic COL4A3/COL4A4 variants were identified across members of 11 families, comprising 7 glycine substituted missense variants and 1 frameshift variant. All index patients had microscopic hematuria at clinical presentation (median age 43 years) and 14 had (micro)albuminuria/proteinuria. All family members showed co-segregation of the variant with at least hematuria. At end of follow-up of all 42 individuals (median age 54 years), 16/42 patients had kidney function impairment, of whom 6 had kidney failure. Reports of kidney biopsies of 14 patients described thin basement membrane nephropathy, focal segmental glomerulosclerosis, minimal change lesions, and Alport syndrome. Electron microscopy images of 7 patients showed a significantly thinner glomerular basement membrane compared with images of patients with idiopathic focal segmental glomerulosclerosis and other hereditary glomerular diseases. No genotype-phenotype correlations could be established. Limitations Retrospective design, ascertainment bias toward severe kidney phenotypes, and familial hematuria. Conclusions This study confirms the wide phenotypic spectrum associated with mono-allelic COL4A3/COL4A4 variants, extending from isolated microscopic hematuria to kidney failure with high intra- and interfamilial variability.
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Affiliation(s)
- Sander Groen In 't Woud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilse M Rood
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eric Steenbergen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brigith Willemsen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Henry B Dijkman
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michel van Geel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jeroen Schoots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jack F M Wetzels
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen K J Deegens
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Zhang H, Wang F, Xiao H. Combined Alport syndrome, Klinefelter syndrome and Fanconi syndrome in a Chinese boy. Nephrology (Carlton) 2023; 28:272-275. [PMID: 36878861 DOI: 10.1111/nep.14152] [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: 12/08/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023]
Abstract
Alport syndrome (AS) is a progressive renal disease characterized by hematuria and progressive renal failure. X-linked dominant (XLAS) is the major inheritance form, accounting for almost 80% of the cases, caused by mutations in COL4A5 genes. Klinefelter syndrome (KS) is the most common genetic cause of human male gonadal dysgenesis. AS and KS are both rare disease, there are only three cases of combined AS and KS in the literatures. Fanconi syndrome (FS) caused by AS is also very rare. We report here the first case combined AS, KS and FS in a Chinese boy. We suggest that the severe renal phenotype and FS might be due to the two homozygous COL4A5 variants in our boy, and cases of AS combined KS will be good research objects for X chromosome inactivation.
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Affiliation(s)
- Hongwen Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
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Plevova P, Indrakova J, Savige J, Kuhnova P, Tvrda P, Cerna D, Hilscherova S, Kudrejova M, Polendova D, Jaklova R, Langova M, Jahnova H, Lastuvkova J, Dusek J, Gut J, Vlckova M, Solarova P, Kreckova G, Kantorova E, Soukalova J, Slavkovsky R, Zapletalova J, Tichy T, Thomasova D. A founder COL4A4 pathogenic variant resulting in autosomal recessive Alport syndrome accounts for most genetic kidney failure in Romani people. Front Med (Lausanne) 2023; 10:1096869. [PMID: 36844206 PMCID: PMC9948603 DOI: 10.3389/fmed.2023.1096869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Romani people have a high prevalence of kidney failure. This study examined a Romani cohort for pathogenic variants in the COL4A3, COL4A4, and COL4A5 genes that are affected in Alport syndrome (AS), a common cause of genetic kidney disease, characterized by hematuria, proteinuria, end-stage kidney failure, hearing loss, and eye anomalies. Materials and methods The study included 57 Romani from different families with clinical features that suggested AS who underwent next-generation sequencing (NGS) of the COL4A3, COL4A4, and COL4A5 genes, and 83 family members. Results In total, 27 Romani (19%) had autosomal recessive AS caused by a homozygous pathogenic c.1598G>A, p.Gly533Asp variant in COL4A4 (n = 20) or a homozygous c.415G>C, p.Gly139Arg variant in COL4A3 (n = 7). For p.Gly533Asp, 12 (80%) had macroscopic hematuria, 12 (63%) developed end-stage kidney failure at a median age of 22 years, and 13 (67%) had hearing loss. For p.Gly139Arg, none had macroscopic hematuria (p = 0.023), three (50%) had end-stage kidney failure by a median age of 42 years (p = 0.653), and five (83%) had hearing loss (p = 0.367). The p.Gly533Asp variant was associated with a more severe phenotype than p.Gly139Arg, with an earlier age at end-stage kidney failure and more macroscopic hematuria. Microscopic hematuria was very common in heterozygotes with both p.Gly533Asp (91%) and p.Gly139Arg (92%). Conclusion These two founder variants contribute to the high prevalence of kidney failure in Czech Romani. The estimated population frequency of autosomal recessive AS from these variants and consanguinity by descent is at least 1:11,000 in Czech Romani. This corresponds to a population frequency of autosomal dominant AS from these two variants alone of 1%. Romani with persistent hematuria should be offered genetic testing.
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Affiliation(s)
- Pavlina Plevova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia,Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czechia,*Correspondence: Pavlina Plevova,
| | - Jana Indrakova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Judy Savige
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Royal Melbourne Hospital, Melbourne, Australia
| | - Petra Kuhnova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Petra Tvrda
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Dita Cerna
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Sarka Hilscherova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Monika Kudrejova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Daniela Polendova
- Department of Medical Genetics, Faculty of Medicine in Plzeň, Charles University and University Hospital Plzeň, Plzeň, Czechia
| | - Radka Jaklova
- Department of Medical Genetics, Faculty of Medicine in Plzeň, Charles University and University Hospital Plzeň, Plzeň, Czechia
| | - Martina Langova
- Department of Medical Genetics, Thomayer University Hospital, Prague, Czechia
| | - Helena Jahnova
- Department of Pediatrics, Third Faculty of Medicine, Charles University and University Hospital Královské Vinohrady, Prague, Czechia
| | - Jana Lastuvkova
- Department of Medical Genetics, Krajská zdravotní, a.s., Masaryk Hospital in Ústí nad Labem, Ústí nad Labem, Czechia
| | - Jiri Dusek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Josef Gut
- Department of Pediatrics, Hospital Česká Lípa, Česká Lípa, Czechia
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Pavla Solarova
- Department of Medical Genetics, University Hospital Hradec Králové, Hradec Králové, Czechia
| | | | - Eva Kantorova
- Department of Medical Genetics, Hospital České Budějovice a.s., České Budějovice, Czechia
| | - Jana Soukalova
- Department of Medical Genetics and Genomics, University Hospital Brno, Brno, Czechia
| | - Rastislav Slavkovsky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Jana Zapletalova
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Tomas Tichy
- Institute of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Dana Thomasova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
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Abstract
Hundreds of different genetic causes of chronic kidney disease are now recognized, and while individually rare, taken together they are significant contributors to both adult and pediatric diseases. Traditional genetics approaches relied heavily on the identification of large families with multiple affected members and have been fundamental to the identification of genetic kidney diseases. With the increased utilization of massively parallel sequencing and improvements to genotype imputation, we can analyze rare variants in large cohorts of unrelated individuals, leading to personalized care for patients and significant research advancements. This review evaluates the contribution of rare disorders to patient care and the study of genetic kidney diseases and highlights key advancements that utilize new techniques to improve our ability to identify new gene-disease associations.
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Affiliation(s)
- Mark D Elliott
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA;
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA;
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA;
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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Novel and Founder Pathogenic Variants in X-Linked Alport Syndrome Families in Greece. Genes (Basel) 2022; 13:genes13122203. [PMID: 36553470 PMCID: PMC9778032 DOI: 10.3390/genes13122203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Alport syndrome (AS) is the most frequent monogenic inherited glomerulopathy and is also genetically and clinically heterogeneous. It is caused by semi-dominant pathogenic variants in the X-linked COL4A5 (NM_000495.5) gene or recessive variants in the COL4A3/COL4A4 (NM_000091.4/NM_000092.4) genes. The disease manifests in early childhood with persistent microhematuria and can progress to proteinuria and kidney failure in adolescence or early adulthood if left untreated. On biopsy, pathognomonic features include alternate thinning, thickening and lamellation of the glomerular basement membrane (GBM), in the presence of podocyte foot process effacement. Although previous studies indicate a prevalence of AS of about 1/50,000, a recent publication reported a predicted rate of pathogenic COL4A5 variants of 1/2320. We herewith present 98 patients (40 M/58 F) from 26 Greek families. We are selectively presenting the families segregating the X-linked form of AS with pathogenic variants in the COL4A5 gene. We found 21 different pathogenic variants, 12 novel: eight glycine and one proline substitutions in the collagenous domain, one cysteine substitution in the NC1 domain, two premature termination of translation codons, three splicing variants, one 5-bp insertion/frameshift variant, one indel-frameshift variant and four gross deletions. Notably, patients in six families we describe here and three families we reported previously, carried the COL4A5-p.G624D substitution, a founder defect encountered all over Europe which is hypomorphic with mostly milder symptomatology. Importantly, on several occasions, the correct genetic diagnosis reclassified patients as patients with AS, leading to termination of previous immunosuppressive/cyclosporine A therapy and a switch to angiotensin converting enzyme inhibitors (ACEi). With the understanding that all 98 patients span a wide range of ages from infancy to late adulthood, 15 patients (11 M/4 F) reached kidney failure and 11 (10 M/1 F) received a transplant. The prospects of avoiding lengthy diagnostic investigations and erroneous medications, and the advantage of delaying kidney failure with very early administration of renin-angiotensin-aldosterone system (RAAS) blockade, highlights the importance of timely documentation of AS by genetic diagnosis.
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Gibson JT, de Gooyer M, Huang M, Savige J. A systematic review of pathogenic COL4A5 variants and proteinuria in women and girls with X-linked Alport syndrome. Kidney Int Rep 2022; 7:2454-2461. [DOI: 10.1016/j.ekir.2022.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
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Gibson JT, Sadeghi-Alavijeh O, Gale DP, Rothe H, Savige J. Pathogenicity of missense variants affecting the collagen IV α5 carboxy non-collagenous domain in X-linked Alport syndrome. Sci Rep 2022; 12:11257. [PMID: 35789182 PMCID: PMC9253329 DOI: 10.1038/s41598-022-14928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022] Open
Abstract
X-linked Alport syndrome is a genetic kidney disease caused by pathogenic COL4A5 variants, but little is known of the consequences of missense variants affecting the NC1 domain of the corresponding collagen IV α5 chain. This study examined these variants in a normal (gnomAD) and other databases (LOVD, Clin Var and 100,000 Genomes Project) to determine their pathogenicity and clinical significance. Males with Cys substitutions in the collagen IV α5 NC1 domain reported in LOVD (n = 25) were examined for typical Alport features, including age at kidney failure. All NC1 variants in LOVD (n = 86) were then assessed for structural damage using an online computational tool, Missense3D. Variants in the ClinVar, gnomAD and 100,000 Genomes Project databases were also examined for structural effects. Predicted damage associated with NC1 substitutions was then correlated with the level of conservation of the affected residues. Cys substitutions in males were associated with the typical features of X-linked Alport syndrome, with a median age at kidney failure of 31 years. NC1 substitutions predicted to cause structural damage were overrepresented in LOVD (p < 0.001), and those affecting Cys residues or 'buried' Gly residues were more common than expected (both p < 0.001). Most NC1 substitutions in gnomAD (88%) were predicted to be structurally-neutral. Substitutions affecting conserved residues resulted in more structural damage than those affecting non-conserved residues (p < 0.001). Many pathogenic missense variants affecting the collagen IV α5 NC1 domain have their effect through molecular structural damage and 3D modelling is a useful tool in their assessment.
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Affiliation(s)
- Joel T Gibson
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Omid Sadeghi-Alavijeh
- Department of Renal Medicine, University College London, London, UK
- Genomics England, Queen Mary University of London, London, UK
| | - Daniel P Gale
- Department of Renal Medicine, University College London, London, UK
- Genomics England, Queen Mary University of London, London, UK
| | - Hansjörg Rothe
- Centre for Nephrology and Metabolic Disorders, 02943, Weisswasser, Germany
| | - Judy Savige
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Parkville, VIC, 3050, Australia.
- Genomics England, Queen Mary University of London, London, UK.
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Savige J, Huang M, Croos Dabrera MS, Shukla K, Gibson J. Genotype-Phenotype Correlations for Pathogenic COL4A3–COL4A5 Variants in X-Linked, Autosomal Recessive, and Autosomal Dominant Alport Syndrome. Front Med (Lausanne) 2022; 9:865034. [PMID: 35602506 PMCID: PMC9120524 DOI: 10.3389/fmed.2022.865034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/24/2022] [Indexed: 12/28/2022] Open
Abstract
Alport syndrome is inherited as an X-linked (XL), autosomal recessive (AR), or autosomal dominant (AD) disease, where pathogenic COL4A3 – COL4A5 variants affect the basement membrane collagen IV α3α4α5 network. About 50% of pathogenic variants in each gene (major rearrangements and large deletions in 15%, truncating variants in 20%, splicing changes in 15%) are associated with “severe” disease with earlier onset kidney failure, and hearing loss and ocular abnormalities in males with XL inheritance and in males and females with AR disease. Severe variants are also associated with early proteinuria which is itself a risk factor for kidney failure. The other half of pathogenic variants are missense changes which are mainly Gly substitutions. These are generally associated with later onset kidney failure, hearing loss, and less often with major ocular abnormalities. Further determinants of severity for missense variants for XL disease in males, and in AD disease, include Gly versus non-Gly substitutions; increased distance from a non-collagenous interruption or terminus; and Gly substitutions with a more (Arg, Glu, Asp, Val, and Trp) or less disruptive (Ala, Ser, and Cys) residue. Understanding genotype-phenotype correlations in Alport syndrome is important because they help predict the likely age at kidney failure, and the need for early and aggressive management with renin-angiotensin system blockade and other therapies. Genotype-phenotype correlations also help standardize patients with Alport syndrome undergoing trials of clinical treatment. It is unclear whether severe variants predispose more often to kidney cysts or coincidental IgA glomerulonephritis which are recognized increasingly in COL4A3-, COL4A4 - and COL4A5-associated disease.
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