ClinVar Miner

Variants in gene NPHP4

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Gene type:

If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign not provided total
103 98 1105 757 144 47 1958

Condition and significance breakdown #

Total conditions: 56
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Condition pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Nephronophthisis 80 29 679 631 76 2 1493
not provided 21 12 344 81 83 0 502
Nephronophthisis 4; Senior-Loken syndrome 4 8 37 364 42 0 1 451
Inborn genetic diseases 0 0 265 28 0 0 293
NPHP4-related disorder 4 3 90 132 3 1 232
Nephronophthisis 4 27 18 126 18 35 0 219
Senior-Loken syndrome 4 6 2 108 18 33 0 167
not specified 0 0 11 27 61 0 94
Kidney disorder 1 1 9 10 5 0 26
Retinal dystrophy 1 2 18 0 0 0 21
Thyroid cancer, nonmedullary, 1 0 0 0 0 0 17 17
Ovarian serous cystadenocarcinoma 0 0 0 0 0 9 9
Malignant tumor of esophagus 0 0 0 0 0 7 7
Bardet-Biedl syndrome 0 0 5 0 0 0 5
Acute myeloid leukemia 0 0 0 0 0 4 4
Lung cancer 0 0 0 0 0 4 4
Melanoma 0 0 0 0 0 4 4
Sarcoma 0 0 0 0 0 4 4
Cervical cancer 0 0 0 0 0 3 3
Gastric cancer 0 0 0 0 0 3 3
Uterine corpus endometrial carcinoma 0 0 0 0 0 3 3
Autosomal recessive NPHP4-related disorders 0 2 0 0 0 0 2
Cholangiocarcinoma 0 0 0 0 0 2 2
Chronic lymphocytic leukemia/small lymphocytic lymphoma 0 0 0 0 0 2 2
Familial cancer of breast 0 0 0 0 0 2 2
Hepatocellular carcinoma 0 0 0 0 0 2 2
Leber congenital amaurosis 0 0 2 0 0 0 2
Lymphoma 0 0 0 0 0 2 2
Nephronophthisis 4; Senior-Loken syndrome 4; Focal segmental glomerulosclerosis 0 0 2 0 0 0 2
Nonpapillary renal cell carcinoma 0 0 0 0 0 2 2
Optic atrophy 0 0 2 0 0 0 2
Retinitis pigmentosa 0 2 0 0 0 0 2
Uterine carcinosarcoma 0 0 0 0 0 2 2
Atypical hemolytic-uremic syndrome 0 0 0 1 0 0 1
Autosomal. recessive NPHP4-related disorders 1 0 0 0 0 0 1
CHARGE syndrome 0 0 1 0 0 0 1
Cholestasis 0 0 1 0 0 0 1
Clear cell carcinoma of kidney 0 0 0 0 0 1 1
Colon adenocarcinoma 0 0 0 0 0 1 1
Colorectal cancer 0 0 0 0 0 1 1
Congenital anomaly of kidney and urinary tract 0 1 0 0 0 0 1
Cystic renal disease 1 0 0 0 0 0 1
Familial pancreatic carcinoma 0 0 0 0 0 1 1
Familial prostate cancer 0 0 0 0 0 1 1
Focal segmental glomerulosclerosis 0 0 0 0 1 0 1
Incidental Discovery 0 1 0 0 0 0 1
Infantile nephronophthisis 1 0 0 0 0 0 1
Infertility disorder; Cerebello-oculo-renal syndrome (nephronophthisis, oculomotor apraxia and cerebellar abnormalities) 0 1 0 0 0 0 1
Lynch syndrome 1 0 0 0 0 1 0 1
Mesothelioma 0 0 0 0 0 1 1
Ovarian cancer 0 0 0 0 0 1 1
Papillary renal cell carcinoma type 1 0 0 0 0 0 1 1
Renal dysplasia and retinal aplasia; Nephronophthisis; focal and segmental glomerulosclerosis 0 0 1 0 0 0 1
Senior-Loken syndrome 4; Nephronophthisis; Ciliopathy 0 0 0 0 0 1 1
Thymoma 0 0 0 0 0 1 1
Uveal melanoma 0 0 0 0 0 1 1

Submitter and significance breakdown #

Total submitters: 72
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Labcorp Genetics (formerly Invitae), Labcorp 80 26 677 637 76 0 1496
Fulgent Genetics, Fulgent Genetics 8 35 361 40 0 0 444
Eurofins Ntd Llc (ga) 7 1 283 15 28 0 334
Ambry Genetics 0 0 265 28 0 0 293
PreventionGenetics, part of Exact Sciences 4 3 88 141 30 0 266
Illumina Laboratory Services, Illumina 1 0 111 26 34 0 159
GeneDx 6 5 43 1 59 0 114
Mayo Clinic Laboratories, Mayo Clinic 0 1 39 32 26 0 98
Breakthrough Genomics, Breakthrough Genomics 0 0 13 14 59 0 86
Dr. Peter K. Rogan Lab, Western University 0 0 0 0 0 42 42
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 8 19 10 0 37
CeGaT Center for Human Genetics Tuebingen 2 0 6 21 5 0 34
Clinical Genetics, Academic Medical Center 0 0 6 5 17 0 28
Genome Diagnostics Laboratory, The Hospital for Sick Children 1 1 9 11 6 0 28
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 1 11 13 0 25
Department of Pathology and Laboratory Medicine, Sinai Health System 0 1 16 1 1 0 19
Genetic Services Laboratory, University of Chicago 1 0 10 5 1 0 17
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg 1 0 16 0 0 0 17
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 3 3 6 2 1 0 14
Gharavi Laboratory, Columbia University 4 3 5 0 0 0 12
Genome-Nilou Lab 0 0 0 0 11 0 11
Revvity Omics, Revvity 3 1 6 0 0 0 10
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 1 7 1 0 9
Sydney Genome Diagnostics, Children's Hospital Westmead 4 2 3 0 0 0 9
Baylor Genetics 0 1 7 0 0 0 8
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 3 0 5 0 8
OMIM 8 0 0 0 0 0 8
Blueprint Genetics 0 2 5 0 0 0 7
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 4 0 2 0 0 0 6
3billion 1 2 1 1 0 0 5
AiLife Diagnostics, AiLife Diagnostics 0 0 5 0 0 0 5
MVZ Medizinische Genetik Mainz 2 2 1 0 0 0 5
Mendelics 0 0 1 1 3 0 5
Neuberg Centre For Genomic Medicine, NCGM 0 2 3 0 0 0 5
SN ONGC Dept of Genetics and Molecular biology Vision Research Foundation 0 0 5 0 0 0 5
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 2 2 0 0 0 0 4
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 0 1 0 3 0 4
Molecular Biology Laboratory, Fundació Puigvert 3 1 0 0 0 0 4
Precision Medicine Center, Zhengzhou University 2 1 1 0 0 0 4
Variantyx, Inc. 1 3 0 0 0 0 4
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 2 0 0 1 0 3
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 3 0 0 3
Clinical Genomics Laboratory, Stanford Medicine 0 0 3 0 0 0 3
Daryl Scott Lab, Baylor College of Medicine 0 0 3 0 0 0 3
Dasa 1 0 0 1 1 0 3
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 1 0 2 0 0 0 3
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 3 3
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 1 1 1 0 0 0 3
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 1 2 0 0 0 0 3
Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals 2 0 0 0 0 0 2
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center 0 1 1 0 0 0 2
GeneReviews 0 0 0 0 0 2 2
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 2 0 0 0 2
Molecular Diagnostics Laboratory, Seoul National University Hospital 0 0 2 0 0 0 2
Ocular Genomics Institute, Massachusetts Eye and Ear 0 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 1 0 0 0 2
Bionano Laboratories 1 0 0 0 0 0 1
Center for Human Genetics and Genomic Medicine, Uniklinik Rwth Aachen 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 1 0 0 0 0 0 1
Clinical Genetics Laboratory, Skane University Hospital Lund 0 1 0 0 0 0 1
Dubai Health Genomic Medicine Center, Dubai Health 0 0 1 0 0 0 1
Eurofins-Biomnis 0 1 0 0 0 0 1
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 1 0 0 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 0 1 0 0 0 1
Human Molecular Genetics Lab, PMAS-arid Agriculture University Rawalpindi 1 0 0 0 0 0 1
Laboratory of Genetics, Children's Clinical University Hospital Latvia 0 0 0 1 0 0 1
Leeds Institute of Medical Research, University of Leeds 0 1 0 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 1 0 0 0 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 1 0 0 0 0 1
Tolun Lab, Human Genetics Laboratory, Bogazici University 0 0 1 0 0 0 1
Yale Center for Mendelian Genomics, Yale University 0 1 0 0 0 0 1

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