ArticleNature communications2025
Exome analysis links kidney malformations to developmental disorders and reveals causal genes.
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Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 9 papers.
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9citing papers in PubMed
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Who cites it
9 citing papers in PubMed.
- Integrated bioinformatics and clinical validation of oxidative stress-associated genes in atrial fibrillation and chronic kidney disease.Experimental and therapeutic medicine · 2026Article
- Genetic architecture of MRI-derived cervical spinal cord morphology reveals sensory-motor axis and systemic disease associations.Nature communications · 2026Article
- Association between intellectual disability and autism spectrum disorder with kidney failure.Pediatric nephrology (Berlin, Germany) · 2026Article
- The inactive X chromosome as a female protector in autism and beyond.Nature genetics · 2026Review
- Vitamin D Deficiency Activates Gdnf-Ret-pErk1/2 Signal and Induces Kidney Malformations in Mice.International journal of molecular sciences · 2026Article
- Dose-Dependent and Non-Autonomous Signaling in CAKUT: A Lineage-Specific Framework from Conditional Knockout Studies.Biomolecules · 2026Review
- Genetics of CAKUT.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2026Article
- The Developmental Landscape of Children With Uveal Coloboma and Its Relationship With Clinical Phenotype and Genetics.American journal of ophthalmology · 2026Article
- From Genes to Malformations: Molecular Mechanisms Driving the Pathogenesis of Congenital Anomalies of the Kidney and Urinary Tract.International journal of molecular sciences · 2025Review
Corrections and comments
- Erratum issued
Authors and funding
108 authors.
Hila Milo Rasouly *Division of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA. Hila.MiloRasouly@columbia.edu.ORCID http://orcid.org/0000-0002-0770-2190
Sarath Babu Krishna Murthy *Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Natalie VenaDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Gundula PovysilGenomic & Bioinformatics Analysis Resource (GenBAR), Columbia University Medical Center, New York, NY, USA.
Andrew BeenkenDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Miguel VerbitskyDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-7066-0552
Shirlee ShrilDivision of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
Iris LekkerkerkerDepartment of Genetics, University Medical Center Utrecht, Utrecht, Netherlands.
Sandy YangCenter for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Atlas KhanDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-6651-2725
David FaselCenter for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Janewit WongboonsinRenal Division, Department of Internal Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.ORCID http://orcid.org/0000-0002-0010-8228
Jeremiah MartinoDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Juntao KeDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Naama ElefantCenter for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Nikita TomarCenter for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Ofek HarnofCenter for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0009-0004-0939-9318
Sergey KisselevDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Shiraz BhedaCenter for Precision Medicine and Genomics, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Sivan Reytan-MironDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Tze Y LimDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Anna Jamry-DziurlaDepartment of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland.
Francesca LuganiIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Giannina Gaslini, Genoa, Italy.
Jun Y ZhangDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-4996-8699
Maddalena MarasaDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-0712-2329
Victoria KolupaevaDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Emily E GroopmanDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Gina JinDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-7633-474X
Iman GhavamiDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Kelsey O StevensDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Arielle C CoughlinDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Byum Hee KilDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Debanjana ChatterjeeDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Drew BradburyDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Jason ZhengDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Karla MehlDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Maria MorbanDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Rachel ReingoldDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Stacy PivaDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Xueru MuDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Adele MitrottiDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-7037-7773
Agnieszka SzmigielskaDepartment of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-1085-4160
Aleksandra GliwińskaDepartment of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland.
Andrea RanghinoNephrology, Dialysis and Renal Transplantation Unit, Azienda Ospedaliera Universitaria delle Marche, Ancona, Italy.
Andrew S BombackDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Andrzej BadenskiDepartment of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland.ORCID http://orcid.org/0000-0001-6947-005X
Anna Latos-BielenskaDepartment of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland.
Valentina CaponeDivision of Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.
Anna Materna-KirylukDepartment of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland.
Antonio AmorosoDepartment of Medical Sciences, University of Turin, Turin, Italy.ORCID http://orcid.org/0000-0002-9437-9407
Claudia IzziClinical Genetics Unit, Department of Molecular and Translational Medicine, University of Brescia and Spedali Civili, Brescia, Italy.
Claudio La ScolaPediatric Nephrology, Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
David Jonathan CohenDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Domenico SantoroDivision of Nephrology, University of Messina, Messina, Italy.ORCID http://orcid.org/0000-0002-4279-6559
Dorota DrozdzDepartment of Pediatric Nephrology and Hypertension, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland.ORCID http://orcid.org/0000-0002-1281-1164
Enrico FiaccadoriNephrology Unit, Parma University Hospital, Parma, Italy.
Fangming LinDivision of Pediatric Nephrology, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-0858-5472
Francesco ScolariDivision of Nephrology, Spedali Civili and University, Brescia, Italy.
Francesco TondoloNephrology, Dialysis and Kidney Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
Gaetano La MannaNephrology, Dialysis and Kidney Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.ORCID http://orcid.org/0000-0001-5473-8551
Gerald B AppelDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Gian Marco GhiggeriIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Giannina Gaslini, Genoa, Italy.ORCID http://orcid.org/0000-0003-3659-9062
Gianluigi ZazaNephrology, Dialysis and Transplantation Unit, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata, Italy.
Giovanni MontiniDivision of Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.ORCID http://orcid.org/0000-0002-7350-4475
Giuseppe MasnataDepartment of Complex Diseases and Pediatric Nephrology, ARNAS Brotzu Hospital, Cagliari, Italy.ORCID http://orcid.org/0000-0001-5136-3563
Grażyna KrzemienDepartment of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland.
Isabella PisaniNephrology Unit, Parma University Hospital, Parma, Italy.
Jai RadhakrishnanDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Katarzyna ZachwiejaDepartment of Pediatric Nephrology and Hypertension, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland.
Loreto GesualdoDivision of Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy.
Luigi BianconeDivision of Nephrology, Dialysis and Transplantation, Department of Medical Sciences, University of Torino, Torino, Italy.
Davide MeneghessoDivision of Nephrology, Hospital University of Padova, Padova, Italy.
Malgorzata Mizerska-WasiakDepartment of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland.
Marcin TkaczykDepartment of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland.
Marcin ZaniewDepartment of Pediatrics, University of Zielona Góra, Zielona Góra, Poland.
Maria K Borszewska-KornackaDepartment of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland.
Maria SzczepanskaDepartment of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland.ORCID http://orcid.org/0000-0001-5336-261X
Marijan SaragaUniversity of Split, School of Medicine, Split, Croatia.
Maya K RaoDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Monica BodriaPrimary Care Unit, Distretto Sud-Est, Parma, Italy.
Monika MiklaszewskaDepartment of Pediatric Nephrology and Hypertension, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland.
Natalie S UyDivision of Nephrology, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
Olga BaraldiDepartment of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, Bologna, Italy.
Omar BjanidDepartment of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland.
Pasquale EspositoDepartment of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy.
Pasquale ZamboliDivision of Nephrology, AORN San Giuseppe Moscati, Avellino, Italy.
Pierluigi MarzuilloDepartment of Woman, Child and of General and Specialized Surgery, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy.ORCID http://orcid.org/0000-0003-4682-0170
Pietro A CanettaDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-1130-5486
Przemyslaw SikoraDepartment of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland.
Rik WestlandDepartment of Pediatric Nephrology, Emma Children's Hospital-Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.ORCID http://orcid.org/0000-0003-4960-4078
Russell J CrewDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.
Shumyle AlamDivision of Urology, El Paso Children Hospital, El Paso, TX, USA.
Stefano GuarinoDepartment of Woman, Child and of General and Specialized Surgery, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy.
Susanna NegrisoloDepartment of Women's and Children's Health, University of Padova, Padua, Italy.
Thomas HaysDivision of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-3705-8973
Shrikant ManeDepartment of Genetics, Yale University School of Medicine, New Haven, CT, USA.
Valeria GrandinettiNephrology, Dialysis and Kidney Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
Velibor TasicUniversity Children's Hospital, Faculty of Medicine, Skopje, North Macedonia.ORCID http://orcid.org/0000-0002-3377-1245
Vladimir J LozanovskiUniversity Children's Hospital, Faculty of Medicine, Skopje, North Macedonia.ORCID http://orcid.org/0000-0002-7332-3973
Yasar CaliskanDivision of Nephrology, Saint Louis University, St. Louis, MO, USA.ORCID http://orcid.org/0000-0003-3816-8047
David GoldsteinGenomic & Bioinformatics Analysis Resource (GenBAR), Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-1111-2820
Richard P LiftonRockefeller University, New York, NY, USA.
Iuliana Ionita-LazaDepartment of Biostatistics, Columbia University, New York, NY, USA.
Krzysztof KirylukDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-5047-6715
Albertien M van EerdeDepartment of Genetics, University Medical Center Utrecht, Utrecht, Netherlands.ORCID http://orcid.org/0000-0001-5953-5956
Friedhelm HildebrandtDivision of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7130-0030
Simone Sanna-CherchiDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-6185-948X
Ali G GharaviDivision of Nephrology, Department of Medicine, Columbia University Medical Center, New York, NY, USA. ag2239@cumc.columbia.edu.ORCID http://orcid.org/0000-0003-2801-233X
Funding
Viral Sequencing CoreU19AI067854 · NIAID · DUKE UNIVERSITY · PI BHARDWAJ, NINA · 2006 to 2011
$290.5MVirus biology scientific research support componentUM1AI100645 · NIAID · DUKE UNIVERSITY · PI MCMICHAEL, ANDREW JAMES · 2012 to 2018
$204.7MClinical and Translational Science AwardUL1TR001873 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI REILLY, MUREDACH P · 2016 to 2025
$99.0MVASCULAR FACTORS AND MILD COGNITIVE IMPAIRMENT AND ALZHEIMER'S DISEASEP01AG007232 · NIA · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI MANLY, JENNIFER JAIE · 1989 to 2008
$21.7MTranscriptional Regulation of Urothelial Differentiation During Homeostasis and Repair in Response to Urinary Tract InfectionU54DK104309 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI JONATHAN M. BARASCH, ALI G GHARAVI · 2014 to 2026
$17.7MEpidemiology of Biomarkers of Risk and Progression in LOADR01AG037212 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI MAYEUX, RICHARD P, SCHUPF, NICOLE · 2010 to 2015
$10.1MGenetic Epidemiology of Cerebrovascular Factors in Alzheimer's DiseaseRF1AG054023 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI MAYEUX, RICHARD P · 2016 to 2018
$8.9MGenetics of Renal HypodyslasiaR01DK080099 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI GHARAVI, ALI G · 2008 to 2023
$6.3MGenomics of mammalian posterior urethral valvesR01DK115574 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI SANNA-CHERCHI, SIMONE · 2017 to 2021
$2.9MGenetics of Congenital Obstructive UropathyR01DK103184 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI SANNA-CHERCHI, SIMONE · 2014 to 2018
$2.3MHigh Performance Computing Instrumentation for the Yale Center for Genome AnalysisS10OD030363 · OD · YALE UNIVERSITY · PI MANE, SHRIKANT M · 2022 to 2022
$1.2MPredictive utility of polygenic risk scores for chronic kidney disease.K25DK128563 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI KHAN, ATLAS · 2021 to 2025
$846kNCATS NIH HHS UL1 TR001873NIAID NIH HHS U19 AI067854NIAID NIH HHS UM1 AI100645NIA NIH HHS P01 AG007232NIA NIH HHS R01 AG037212NIA NIH HHS RF1 AG054023NIDDK NIH HHS K01 DK132495NIDDK NIH HHS K08 DK132511NIDDK NIH HHS K25 DK128563NIDDK NIH HHS P20 DK116191NIDDK NIH HHS R01 DK080099NIDDK NIH HHS R01 DK103184NIDDK NIH HHS R01 DK115574NIDDK NIH HHS R56 DK138164NIDDK NIH HHS U54 DK104309NIH HHS S10 OD030363U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) 5K01DK132495U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) 5R01DK080099-13U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) 5U54DK104309-10U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) 1S10OD030363-01A1Wellcome Trust
Abstract
Congenital anomalies of the kidneys and urinary tract (CAKUT) are developmental disorders that commonly cause pediatric chronic kidney disease and mortality. We examine here rare coding variants in 248 CAKUT trios and 1742 singleton CAKUT cases and compare them to 22,258 controls. Diagnostic and candidate diagnostic variants are detected in 14.1% of cases. We find a significant enrichment of rare damaging variants in constrained genes expressed during kidney development and in genes associated with other developmental disorders, suggesting phenotype expansion. Consistent with these data, 18% of CAKUT patients with diagnostic variants have neurodevelopmental or cardiac phenotypes. We identify 40 candidate genes, including CELSR1, SSBP2, XPO1, NR6A1, and ARID3A. Two are confirmed as CAKUT genes: ARID3A and NR6A1. This study suggests that many yet-unidentified syndromes would be discoverable with larger cohorts and cross-phenotype analysis, leading to clarification of the genetic and phenotypic spectrum of developmental disorders.
Indexed as
Developmental DisabilitiesExomeKidneyUrogenital AbnormalitiesVesico-Ureteral RefluxChildChild, PreschoolDNA-Binding ProteinsExome SequencingFemaleGenetic Predisposition to DiseaseHumansMalePhenotypeTranscription FactorsDNA-Binding ProteinsTranscription Factors
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