ClinVar Miner

Variants studied for complex hereditary spastic paraplegia

Included ClinVar conditions (73):
Minimum submission review status: Collection method:
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Gene type:
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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 affects not provided total
904 472 4237 4389 587 1 123 10255

Gene and significance breakdown #

Total genes and gene combinations: 85
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign affects not provided total
SPG11 391 103 1198 1257 69 1 93 2893
TECPR2 72 32 220 845 54 0 3 1170
PNPLA6 63 27 492 533 69 0 3 1123
ATP13A2 40 19 372 369 46 0 1 829
ALDH18A1 23 12 268 151 17 0 3 467
ZFYVE26 29 155 214 20 49 0 1 444
KIF1C 13 7 155 183 41 0 0 390
TFG 4 2 164 135 16 0 1 320
CCT5 1 1 148 82 39 0 0 263
MAG 5 3 101 112 18 0 0 237
DDHD2 26 9 100 87 12 0 0 229
AMPD2 5 3 91 90 16 0 1 203
IBA57 14 7 86 69 9 0 0 182
NT5C2 18 9 40 68 8 0 1 140
ENTPD1 9 2 59 57 9 0 1 135
VPS37A 1 0 67 50 15 0 0 133
C19orf12 6 3 61 39 5 0 1 111
PI4KA 17 12 23 32 26 0 0 107
SPART 8 3 73 12 5 0 1 100
AMPD2, LOC126805822 1 3 31 40 8 0 0 82
KIDINS220 7 7 37 4 3 0 2 60
BSCL2, HNRNPUL2-BSCL2 4 1 33 10 4 0 4 53
ARL6IP1 4 1 15 22 6 0 0 48
LOC130056973, SPG11 6 0 16 25 0 0 2 48
KIF1C, LOC126862473 0 1 14 18 5 0 0 38
L1CAM 10 9 15 2 1 0 0 37
KIF1C, LOC126862472 2 0 8 20 6 0 0 36
GBA2 14 10 12 1 1 0 1 34
CAPN1 19 5 6 0 4 0 0 33
HACE1 14 2 9 0 6 0 0 31
CNNM2, NT5C2 1 0 14 12 2 0 0 29
GPT2 10 6 16 0 0 0 0 29
LOC130056519, TECPR2 2 0 10 12 0 0 0 23
LOC130056971, SPG11 5 0 10 7 0 0 1 21
B4GALNT1 11 4 4 0 1 0 1 19
LOC130063377, PNPLA6 0 0 7 6 0 0 0 13
AMPD2, LOC129931109 0 0 4 7 1 0 0 11
ERLIN2 7 1 3 0 0 0 0 11
MTRFR 8 1 2 0 0 0 0 10
GJC2 3 1 2 1 0 0 2 9
ABHD16A 6 1 1 0 0 0 0 8
ARL6IP1, LOC130058582 0 0 2 5 1 0 0 8
DSTYK 2 1 3 0 2 0 0 8
ATP13A2, LOC129929540 0 0 4 3 0 0 0 7
MCOLN1, PNPLA6 0 0 1 1 6 0 0 7
RNF170 4 3 1 0 0 0 0 7
C19orf12, LOC130064129 0 0 4 2 0 0 0 6
KLC2 1 0 1 0 3 0 0 5
​intergenic 4 0 0 0 0 0 0 4
CAPN1, LOC126861236 1 0 0 0 3 0 0 4
GPT2, LOC130058930 0 1 2 0 0 0 0 3
ARF1, C1orf35, GJC2, GUK1, IBA57, MRPL55, OBSCN, WNT3A 1 0 1 0 0 0 0 2
LOC130056974, SPG11 0 1 1 0 0 0 0 2
PAH 2 0 0 0 0 0 0 2
ADAM9, ADGRA2, ADRB3, ASH2L, BAG4, BRF2, DDHD2, EIF4EBP1, ERLIN2, FGFR1, GOT1L1, HTRA4, LETM2, LINC03042, LSM1, NSD3, PLEKHA2, PLPBP, PLPP5, RAB11FIP1, STAR, TACC1, TM2D2 0 0 1 0 0 0 0 1
ADAM9, DDHD2, FGFR1, HTRA4, LETM2, LINC03042, NSD3, PLEKHA2, PLPP5, TACC1, TM2D2 0 0 1 0 0 0 0 1
AGXT, KIF1A, MAB21L4 0 1 0 0 0 0 0 1
AHCYL1, AKNAD1, ALX3, AMIGO1, AMPD2, ATXN7L2, CD53, CELSR2, CFAP276, CLCC1, CSF1, CYB561D1, DRAM2, EEIG2, ELAPOR1, EPS8L3, FNDC7, GNAI3, GNAT2, GPR61, GPSM2, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, HENMT1, KCNA10, KCNA2, KCNA3, KCNC4, LAMTOR5, LRIF1, MIR197, MYBPHL, NBPF4, NBPF6, PROK1, PRPF38B, PSMA5, PSRC1, RBM15, SARS1, SLC16A4, SLC25A24, SLC6A17, SORT1, STRIP1, STXBP3, SYPL2, TAF13, TMEM167B, UBL4B, WDR47 1 0 0 0 0 0 0 1
ALDH18A1, ENTPD1, TCTN3 1 0 0 0 0 0 0 1
ALKBH6, APLP1, ARHGAP33, ATP4A, CAPNS1, CD22, CEBPA, CEBPG, CEP89, CHST8, CLIP3, COX6B1, COX7A1, DMKN, ETV2, FAAP24, FAM187B, FFAR1, FFAR2, FFAR3, FXYD1, FXYD3, FXYD5, FXYD7, GAPDHS, GARRE1, GPATCH1, GPI, GPR42, GRAMD1A, HAMP, HAUS5, HCST, HPN, HSPB6, IGFLR1, KCTD15, KIRREL2, KMT2B, KRTDAP, LGI4, LIN37, LRFN3, LRP3, LSM14A, LSR, MAG, NFKBID, NPHS1, NUDT19, OVOL3, PDCD2L, PEPD, POLR2I, PRODH2, PROSER3, PSENEN, RBM42, RGS9BP, RHPN2, SBSN, SCGB2B2, SCN1B, SDHAF1, SLC7A10, SLC7A9, SYNE4, TBCB, TDRD12, THAP8, TMEM147, TYROBP, U2AF1L4, UBA2, UPK1A, USF2, WDR62, WDR88, WTIP, ZBTB32, ZNF181, ZNF30, ZNF302, ZNF599, ZNF792 0 0 1 0 0 0 0 1
AMPD2, GNAT2 0 0 1 0 0 0 0 1
ANKRD9, LOC130056519, TECPR2 0 0 1 0 0 0 0 1
ARHGEF18, MCOLN1, PEX11G, PNPLA6, SAXO5, ZNF358 0 0 1 0 0 0 0 1
ARL6IP1, LOC130058581, LOC130058582 0 0 1 0 0 0 0 1
ASAH1, ATP6V1B2, CNOT7, CSGALNACT1, FGF20, FGL1, INTS10, LPL, LZTS1, MICU3, MTMR7, MTUS1, NAT1, NAT2, PCM1, PDGFRL, PSD3, SH2D4A, SLC18A1, SLC7A2, VPS37A, ZDHHC2 0 0 1 0 0 0 0 1
B2M, PATL2, SPG11, TRIM69 0 0 1 0 0 0 0 1
BSCL2, GNG3, HNRNPUL2-BSCL2 0 0 1 0 0 0 0 1
C17orf107, CAMTA2, CHRNE, ENO3, GP1BA, INCA1, KIF1C, PFN1, RNF167, SLC25A11, SPAG7 0 0 1 0 0 0 0 1
CNNM2, LOC130004629, NT5C2 1 0 0 0 0 0 0 1
EEF1A2 0 1 0 0 0 0 0 1
EIF3J, SPG11 0 0 1 0 0 0 0 1
ENTPD1, LOC130004411 0 0 1 0 0 0 0 1
GFAP 1 0 0 0 0 0 0 1
GRID2, LNCPRESS2, LOC123477787, LOC126807111 0 0 1 0 0 0 0 1
HACE1, LOC113121301 0 0 0 0 1 0 0 1
LOC130009569, SPART 0 0 1 0 0 0 0 1
LOC130056972, LOC130056973, SPG11 1 0 0 0 0 0 0 1
MT-ATP6 1 0 0 0 0 0 0 1
MT-TK 0 1 0 0 0 0 0 1
PATL2, SPG11 1 0 0 0 0 0 0 1
PRKN 0 1 0 0 0 0 0 1
SON 1 0 0 0 0 0 0 1
SORL1 1 0 0 0 0 0 0 1
SQSTM1 1 0 0 0 0 0 0 1
USP8 0 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 137
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign affects not provided total
Labcorp Genetics (formerly Invitae), Labcorp 578 122 3374 4231 410 0 0 8715
Illumina Laboratory Services, Illumina 0 1 514 54 79 0 0 648
Genome-Nilou Lab 54 18 173 39 173 0 0 457
Natera, Inc. 2 1 103 58 26 0 0 190
Fulgent Genetics, Fulgent Genetics 15 9 104 38 5 0 0 171
OMIM 157 0 1 0 0 0 0 158
Baylor Genetics 17 7 82 0 0 0 0 106
GeneReviews 15 0 0 0 0 0 88 103
Myriad Genetics, Inc. 0 99 1 0 0 0 0 100
Paris Brain Institute, Inserm - ICM 80 0 0 0 0 0 0 80
Counsyl 2 39 24 0 1 0 0 66
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 10 7 38 1 0 0 0 56
Neuberg Centre For Genomic Medicine, NCGM 10 15 29 0 0 0 0 54
Revvity Omics, Revvity 9 13 29 0 0 0 0 51
PreventionGenetics, part of Exact Sciences 0 3 3 32 6 0 0 44
Institute of Human Genetics, University of Leipzig Medical Center 9 11 15 1 1 0 0 37
3billion 10 13 5 1 0 0 0 29
Mendelics 20 1 0 1 2 0 0 24
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 0 22 22
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 3 6 12 0 0 0 0 21
Centre for Mendelian Genomics, University Medical Centre Ljubljana 2 7 10 0 1 0 0 20
Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) 17 2 0 0 0 0 0 19
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 11 7 0 0 0 0 0 18
New York Genome Center 1 0 17 0 0 0 0 18
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 0 0 13 4 0 0 17
Solve-RD Consortium 0 17 0 0 0 0 0 17
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 5 9 0 0 14
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 12 2 0 0 0 0 0 14
Genomic Research Center, Shahid Beheshti University of Medical Sciences 6 0 8 0 0 0 0 14
Juno Genomics, Hangzhou Juno Genomics, Inc 6 2 6 0 0 0 0 14
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 7 3 3 0 1 0 0 14
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 5 8 0 0 13
GenomeConnect, ClinGen 0 0 0 0 0 0 11 11
Genomics England Pilot Project, Genomics England 2 9 0 0 0 0 0 11
Centogene AG - the Rare Disease Company 0 6 3 0 0 0 0 9
Undiagnosed Diseases Network, NIH 7 1 1 0 0 0 0 9
SIB Swiss Institute of Bioinformatics 5 4 0 0 0 0 0 9
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 1 4 3 0 0 8
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 1 5 2 0 0 8
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital 0 0 7 0 1 0 0 8
Department of Biochemistry, Faculty of Medicine, University of Khartoum 8 0 0 0 0 0 0 8
Molecular Genetics, Royal Melbourne Hospital 1 4 3 0 0 0 0 8
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 3 1 4 0 0 0 0 8
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 2 2 3 0 0 0 0 7
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 7 0 0 0 0 7
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 3 2 1 0 0 0 0 6
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 1 3 2 0 0 0 0 6
Athena Diagnostics 0 0 0 0 5 0 0 5
Mayo Clinic Laboratories, Mayo Clinic 0 0 4 0 1 0 0 5
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 2 0 3 0 0 0 0 5
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 1 3 1 0 0 0 0 5
Department of Rehabilitation Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea 4 1 0 0 0 0 0 5
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology 1 2 2 0 0 0 0 5
Section for Clinical Neurogenetics, University of Tübingen 3 2 0 0 0 0 0 5
DASA 3 2 0 0 0 0 0 5
University of Science and Technology Houari Boumediene, Laboratory of Molecular and Cellular Biology (LBCM) 4 0 1 0 0 0 0 5
Neurogenomics Lab, Neuroscience Institute, University Of Cape Town 2 0 3 0 0 0 0 5
MVZ Medizinische Genetik Mainz 1 1 3 0 0 0 0 5
Institute of Human Genetics, Cologne University 3 1 0 0 0 0 0 4
MGZ Medical Genetics Center 0 3 1 0 0 0 0 4
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 2 0 2 0 0 0 0 4
Knight Diagnostic Laboratories, Oregon Health and Sciences University 1 1 2 0 0 0 0 4
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 1 3 0 0 0 0 0 4
Genetics and Molecular Pathology, SA Pathology 0 1 3 0 0 0 0 4
Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia 3 0 1 0 0 0 0 4
Lifecell International Pvt. Ltd 3 1 0 0 0 0 0 4
GenomeConnect - Brain Gene Registry 0 0 0 0 0 0 4 4
Progenie Molecular 2 0 2 0 0 0 0 4
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 1 2 0 0 0 0 0 3
Service de Génétique Moléculaire, Hôpital Robert Debré 0 1 2 0 0 0 0 3
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 1 2 0 0 0 0 0 3
Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University 1 1 1 0 0 0 0 3
Molecular Genetics Lab, CHRU Brest 2 0 1 0 0 0 0 3
Kids Neuroscience Centre, Sydney Children's Hospitals Network 0 3 0 0 0 0 0 3
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 1 0 2 0 0 0 0 3
Institute of Human Genetics, University of Goettingen 1 1 0 0 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 2 0 0 0 0 0 0 2
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 1 1 0 0 0 0 2
Clinical Genomics Laboratory, Washington University in St. Louis 1 1 0 0 0 0 0 2
Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen 0 1 1 0 0 0 0 2
Tgen's Center For Rare Childhood Disorders, Translational Genomics Research Institute (TGEN) 1 1 0 0 0 0 0 2
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 2 0 0 0 0 2
Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology 0 2 0 0 0 0 0 2
Institute of Human Genetics, University Hospital of Duesseldorf 1 1 0 0 0 0 0 2
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 2 0 0 0 0 0 2
Laboratory of Medical Genetics, University of Torino 0 2 0 0 0 0 0 2
Breda Genetics srl 0 1 1 0 0 0 0 2
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 0 2 0 0 0 0 2
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 2 0 0 0 0 0 0 2
Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology 1 1 0 0 0 0 0 2
Institute of Immunology and Genetics Kaiserslautern 0 0 2 0 0 0 0 2
Department of Neurology, The Affiliated Hospital of Zunyi Medical University 2 0 0 0 0 0 0 2
Next Generation Genetic Polyclinic 0 1 1 0 0 0 0 2
Igenomix - Part of Vitrolife Group, Igenomix 0 2 0 0 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 1 0 0 0 0 0 1
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 0 1 0 0 0 0 1
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center 0 1 0 0 0 0 0 1
Faculty of Science, Laboratory of Drosophila Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 1 0 0 0 0 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 0 1 0 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 1 0 0 0 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 1 0 0 0 0 0 1
Paisan-Ruiz Laboratory, Icahn School of Medicine at Mount Sinai 1 0 0 0 0 0 0 1
Institute of Human Genetics, University of Wuerzburg 1 0 0 0 0 0 0 1
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues 0 1 0 0 0 0 0 1
Aziz Sancar Institute of Experimental Medicine, Department of Genetics, Istanbul University 1 0 0 0 0 0 0 1
Ege University Pediatric Genetics, Ege University 0 1 0 0 0 0 0 1
TIDEX, University of British Columbia 0 1 0 0 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 1 0 0 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 1 0 0 0 0 0 1
Dr. Alfred Bastarche Laboratory, Dr. Georges L. Dumont University Hospital Centre 0 0 1 0 0 0 0 1
Pathology and Clinical Laboratory Medicine, King Fahad Medical City 1 0 0 0 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 0 1 0 0 0 0 1
Department of Neurology, The Third Xiangya Hospital, Central South University 1 0 0 0 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 1 0 0 0 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 1 0 0 0 0 1
Genesis Genoma Lab, Genesis Genoma Lab 0 0 0 1 0 0 0 1
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris 1 0 0 0 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 1 0 0 0 0 0 1
Dr Sami Ulus Medical Genetics Department, Dr Sami Ulus Training and Research Hospital for Maternity and Children's Health and Diseases 1 0 0 0 0 0 0 1
Dr. med. U. Finckh, Human Genetics, Eurofins MVZ 0 0 1 0 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 0 1 0 0 0 0 1
Yunnan Provincial Key Laboratory of Clinical Virology, Institution of Basic and Clinical Medicine of Yunnan Province, The First People's Hospital of Yunnan Province 0 0 0 0 0 1 0 1
Suma Genomics 0 1 0 0 0 0 0 1
Provincial Medical Genetics Program of British Columbia, University of British Columbia 0 1 0 0 0 0 0 1
Henan Neurodevelopment Engineering Research Center for Children, Children's Hospital Affiliated to Zhengzhou University 0 1 0 0 0 0 0 1
Palindrome, Gene Kavoshgaran Aria 1 0 0 0 0 0 0 1
Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences 1 0 0 0 0 0 0 1
Pediatric/Medical Genetics, Ministry of Health, Qatif Central Hospital 0 0 1 0 0 0 0 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 0 1 0 0 0 0 0 1
Payam Genetics Center, General Welfare Department of North Khorasan Province 1 0 0 0 0 0 0 1
Breakthrough Genomics, Breakthrough Genomics 1 0 0 0 0 0 0 1
Laboratory of Human Molecular Genetics, Federal University of Alagoas 1 0 0 0 0 0 0 1
Tetreault Lab, University of Montreal Hospital Research Centre (CRCHUM) 0 1 0 0 0 0 0 1
DECIPHERD-UDD, Universidad del Desarrollo 0 0 1 0 0 0 0 1
Razi Pathobiology & Medical Genetics 1 0 0 0 0 0 0 1
Dr.Nikuei Genetic Center 0 1 0 0 0 0 0 1

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