ClinVar Miner

Variants studied for bone neoplasm

Included ClinVar conditions (92):
Minimum submission review status: Collection method:
Minimum conflict level:
Gene type:
ClinVar version:

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 risk factor other not provided total
633 342 949 322 210 2 1 11 2385

Gene and significance breakdown #

Total genes and gene combinations: 124
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign risk factor other not provided total
CEBPA 17 5 283 106 11 0 0 0 420
EXT1 218 11 92 25 21 0 0 0 360
EXT2 95 2 94 48 40 0 0 1 257
MPL 37 10 43 91 14 1 0 0 180
ANTXR2 14 7 103 15 29 0 0 0 167
MTAP 2 0 64 3 56 0 0 0 125
AIP 14 49 20 19 17 0 0 0 104
CASR 12 0 41 8 15 0 0 0 76
TP53 9 63 4 0 0 0 0 0 73
NF1 25 3 27 0 0 0 0 0 55
CHEK2 9 1 33 0 0 0 0 0 43
THPO 6 1 25 6 5 0 0 0 42
FLT3 11 26 0 0 0 0 0 1 37
PTPN11 27 4 3 1 0 0 0 0 35
ABL1 2 26 0 0 0 0 0 1 28
CDH23 6 1 15 0 0 0 0 0 22
KIT 3 3 11 0 0 0 0 1 18
NSDHL 12 4 0 0 1 0 0 0 17
NRAS 3 15 0 0 0 0 0 0 15
RUNX1 1 7 7 0 0 0 0 0 15
HRAS, LRRC56 0 13 0 0 0 0 0 0 13
SF3B1 0 13 0 0 0 0 0 0 13
GATA1 11 0 0 0 0 0 0 0 11
KRAS 7 6 1 0 0 0 0 0 11
DNMT3A 6 4 0 0 0 0 0 0 10
GATA2 0 2 8 0 0 0 0 0 10
INSL6, JAK2 3 4 3 0 0 0 0 2 10
NPM1 6 4 0 0 0 0 0 0 10
GNAS 7 0 2 0 0 0 0 0 9
NSD1 4 1 4 0 0 0 0 0 9
TERT 1 1 7 0 0 0 0 0 9
IDH2 6 2 0 0 0 0 0 0 8
IDH1 6 0 1 0 0 0 0 0 7
JAK3 0 7 0 0 0 0 0 0 7
RB1 2 0 4 0 0 0 0 0 6
C10orf105, CDH23 1 0 4 0 0 0 0 0 5
DDX41 3 2 0 0 0 0 0 0 5
ELMO2 3 1 1 0 1 0 0 0 5
TSC2 0 0 4 0 0 0 1 0 5
USP8 5 0 0 0 0 0 0 0 5
BRCA2 0 0 4 0 0 0 0 0 4
CBL 3 2 1 0 0 0 0 0 4
CTNNB1 0 4 0 0 0 0 0 0 4
MIR181A1HG 4 0 0 0 0 0 0 0 4
U2AF1 0 4 0 0 0 0 0 0 4
ARHGAP26 3 0 0 0 0 0 0 0 3
ETV6 3 0 0 0 0 0 0 0 3
MEN1 1 2 0 0 0 0 0 0 3
SH2B3 2 0 1 0 0 0 0 0 3
TSC1 0 0 3 0 0 0 0 0 3
APC 1 0 1 0 0 0 0 0 2
ASXL1 1 0 1 0 0 0 0 0 2
BCR 0 0 0 0 0 0 0 2 2
CALR 2 0 0 0 0 0 0 0 2
CBFA2T3 2 0 0 0 0 0 0 0 2
CSF3R 0 2 0 0 0 0 0 0 2
CTCF 0 2 0 0 0 0 0 0 2
ERCC2 0 1 0 0 0 0 0 1 2
FGFR3 0 2 0 0 0 0 0 0 2
GNAI2 1 0 1 0 0 0 0 0 2
GPR101 2 0 2 0 0 0 0 0 2
JAK1 0 2 0 0 0 0 0 0 2
LOC110806263, TERT 0 0 2 0 0 0 0 0 2
MN1 0 2 0 0 0 0 0 0 2
PTCH1 0 0 2 0 0 0 0 0 2
RECQL4 1 1 0 0 0 0 0 0 2
SETD2 0 2 0 0 0 0 0 0 2
TMEM127 0 0 2 0 0 0 0 0 2
WT1 0 1 1 0 0 0 0 0 2
​intergenic 1 0 0 0 0 0 0 0 1
ACP3 0 0 1 0 0 0 0 0 1
AKT1 0 1 0 0 0 0 0 0 1
ALK 0 0 1 0 0 0 0 0 1
ALX4 0 0 1 0 0 0 0 0 1
ATG2B, BDKRB1, BDKRB2, C14orf132, GSKIP, LOC107984703, LOC112272571, TCL1A, TUNAR 0 1 0 0 0 0 0 0 1
ATRX 1 0 0 0 0 0 0 0 1
BCR, LOC107963955 0 0 0 0 0 0 0 1 1
BMPR1A 0 0 1 0 0 0 0 0 1
BRAF 0 1 0 0 0 0 0 0 1
BRCA1 0 0 1 0 0 0 0 0 1
CBFB 0 0 1 0 0 0 0 0 1
CDKN2A 0 0 1 0 0 0 0 0 1
CEBPA, GPATCH1, LRP3, RHPN2, SLC7A10, WDR88 0 0 1 0 0 0 0 0 1
CORO7, CORO7-PAM16 0 0 1 0 0 0 0 0 1
CSF1R 0 1 0 0 0 0 0 0 1
CUX2, SH2B3 1 0 0 0 0 0 0 0 1
DHFR, MSH3 0 0 1 0 0 0 0 0 1
DNAJC21 1 0 0 0 0 0 0 0 1
EPOR 0 1 0 0 0 0 0 0 1
ERBB3 0 1 0 0 0 1 0 0 1
ETV6, FLT3 0 1 0 0 0 0 0 0 1
FLT3, MYO18A 0 1 0 0 0 0 0 0 1
KDM5A, NUP98 1 0 0 0 0 0 0 0 1
KMT2A, MLLT6 1 0 0 0 0 0 0 0 1
KMT2A, SEPTIN9 1 0 0 0 0 0 0 0 1
KMT2D 0 1 0 0 0 0 0 0 1
LOC100507346, PTCH1 0 0 1 0 0 0 0 0 1
LOC107303340, VHL 1 0 0 0 0 0 0 0 1
LPP 0 0 1 0 0 0 0 0 1
LRP2 0 1 0 0 0 0 0 0 1
MDGA1 0 0 1 0 0 0 0 0 1
MFSD11, SRSF2 0 1 0 0 0 0 0 0 1
MLLT10 0 0 1 0 0 0 0 0 1
MT-ND6 0 0 1 0 0 0 0 0 1
PAX5 0 0 1 0 0 0 0 0 1
PCF11 0 0 1 0 0 0 0 0 1
PDGFRB 1 0 0 0 0 0 0 0 1
PHOX2B 0 0 1 0 0 0 0 0 1
PMS2 0 1 0 0 0 0 0 0 1
PTEN 1 0 0 0 0 0 0 0 1
RAD21 0 1 0 0 0 0 0 0 1
RASAL3 0 0 1 0 0 0 0 0 1
RTEL1, RTEL1-TNFRSF6B 1 0 0 0 0 0 0 0 1
SETBP1 0 0 0 0 0 0 0 1 1
SF3B2 0 1 0 0 0 0 0 0 1
SLC9A2 0 0 1 0 0 0 0 0 1
SMARCA4 0 0 1 0 0 0 0 0 1
SOX3 0 0 1 0 0 0 0 0 1
SRC 1 1 0 0 0 0 0 0 1
STK11 0 0 1 0 0 0 0 0 1
SUFU 0 0 1 0 0 0 0 0 1
SUZ12 0 1 0 0 0 0 0 0 1
TEK 0 1 0 0 0 0 0 0 1
TGM6 1 0 0 0 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 72
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign risk factor other not provided total
Invitae 326 21 416 208 50 0 0 0 1021
Illumina Clinical Services Laboratory,Illumina 0 0 321 106 168 0 0 0 595
Database of Curated Mutations (DoCM) 30 211 0 0 0 0 0 5 245
Fulgent Genetics,Fulgent Genetics 58 4 120 1 0 0 0 0 183
OMIM 132 0 0 0 0 2 0 0 134
GeneReviews 19 48 5 9 3 0 0 0 84
Baylor Genetics 12 5 23 0 0 0 0 0 40
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital 5 3 30 1 0 0 0 0 39
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia 14 11 0 0 0 0 0 0 25
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 15 1 0 0 0 0 0 0 16
Mendelics 0 1 6 1 4 0 0 0 12
Genetic Services Laboratory, University of Chicago 7 4 0 0 0 0 0 0 11
Centre for Mendelian Genomics,University Medical Centre Ljubljana 3 1 7 0 0 0 0 0 11
NIHR Bioresource Rare Diseases, University of Cambridge 4 7 0 0 0 0 0 0 10
McDonnell Genome Institute,Washington University in St. Louis 2 0 7 0 0 0 0 0 9
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 3 0 4 0 0 0 0 0 7
Service de Biochimie Médicale et Biologie Moléculaire, CHU Clermont-Ferrand 7 0 0 0 0 0 0 0 7
Fujian Institute of Hematology,Fujian Medical University 6 0 0 0 0 0 0 0 6
Institute of Human Genetics, Klinikum rechts der Isar 5 0 0 0 0 0 0 0 5
Bone Marrow Failure laboratory,Queen Mary University London 2 3 0 0 0 0 0 0 5
Johns Hopkins Genomics, Johns Hopkins University 0 1 4 0 0 0 0 0 5
Genome Sciences Centre,British Columbia Cancer Agency 0 3 1 0 0 0 0 0 4
Aziz Sancar Institute of Experimental Medicine,Istanbul University 2 2 0 0 0 0 0 0 4
Baylor-Hopkins Center for Mendelian Genomics,Johns Hopkins University 2 1 1 0 0 0 0 0 4
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 3 0 1 0 0 0 0 0 4
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 1 2 1 0 0 0 0 0 4
Génétique des Maladies du Développement, Hospices Civils de Lyon 1 3 0 0 0 0 0 0 4
Pathology and Clinical Laboratory Medicine,King Fahad Medical City 3 1 0 0 0 0 0 0 4
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 3 0 0 0 0 0 3
Laboratory of Molecular Diagnostics and Monitoring of CML and Ph+ Leukemias, Institute of Hematology and Blood Transfusion 0 0 0 0 0 0 0 3 3
Institute of Human Genetics, University of Leipzig Medical Center 1 1 1 0 0 0 0 0 3
GenomeConnect, ClinGen 0 0 0 0 0 0 0 3 3
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 1 1 1 0 0 0 0 0 3
Integrated Genetics/Laboratory Corporation of America 1 1 0 0 0 0 0 0 2
Division of Human Genetics,Children's Hospital of Philadelphia 0 0 2 0 0 0 0 0 2
Korbonits Lab,Queen Mary University of London 0 1 1 0 0 0 0 0 2
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 2 0 0 0 0 0 0 0 2
Department of Genetics,Sultan Qaboos University Hospital, Oman 0 1 1 0 0 0 0 0 2
Knight Cancer Institute, Oregon Health and Science University 0 2 0 0 0 0 0 0 2
Breda Genetics srl 2 0 0 0 0 0 0 0 2
Molecular Haematology Laboratory,NSW Health Pathology 2 0 0 0 0 0 0 0 2
Godley laboratory, The University of Chicago 2 0 0 0 0 0 0 0 2
Department of Cell Biology,School of Life Sciences, Central South University 2 0 0 0 0 0 0 0 2
Hematopathology,The University of Texas M.D. Anderson Cancer Center 2 0 0 0 0 0 0 0 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 1 0 0 0 0 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 1 0 0 0 1
Centogene AG - the Rare Disease Company 1 0 0 0 0 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 1 0 0 0 0 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 1 0 0 0 0 0 0 0 1
Service de Génétique Moléculaire,Hôpital Robert Debré 0 0 1 0 0 0 0 0 1
INSERM UMR 1170,INSERM 0 1 0 0 0 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 0 0 1
Center of Genomic medicine, Geneva,University Hospital of Geneva 1 0 0 0 0 0 0 0 1
Diagnostics Division,Centre for DNA Fingerprinting and Diagnostics 0 1 0 0 0 0 0 0 1
Department of Medical Genetics, Zhongshan School of Medicine and Center for Genome Research, Sun Yat-Sen University 1 0 0 0 0 0 0 0 1
Donald Williams Parsons Laboratory,Baylor College of Medicine 0 0 0 0 0 0 1 0 1
GenePathDx,Causeway Health Care Private Ltd 1 0 0 0 0 0 0 0 1
Undiagnosed Diseases Network,NIH 1 0 0 0 0 0 0 0 1
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 1 0 0 0 0 0 0 0 1
Clinical Genetics Department,Hospital Sant Joan de Deu 1 0 0 0 0 0 0 0 1
Center for Precision Medicine,Vanderbilt University Medical Center 1 0 0 0 0 0 0 0 1
Medical Genetics Lab,Policlinico S. Orsola.Malpighi 1 0 0 0 0 0 0 0 1
Pediatric Leukemia/Lymphoma,Memorial Sloan Kettering Cancer Center 1 0 0 0 0 0 0 0 1
Laboratory Oncology Unit, Dr.B.R.A. Institute Rotary Cancer Hospital,All India Institute of Medical Sciences 0 0 1 0 0 0 0 0 1
Al Jalila Children's Genomics Center,Al Jalila Childrens Speciality Hospital 1 0 0 0 0 0 0 0 1
Genetics Institute, Tel Aviv Sourasky Medical Center 0 0 1 0 0 0 0 0 1
Clinical Genomics Program, Stanford Medicine 0 1 0 0 0 0 0 0 1
Pediatrics Genetics, Post Graduate Institute of Medical Education and Research 0 1 0 0 0 0 0 0 1
Department of Laboratory Medicine, Fuzhou Second Hospital Affiliated to Xiamen University 1 0 0 0 0 0 0 0 1
UOSD Laboratory of Genetics & Genomics of Rare Diseases,Istituto Giannina Gaslini 0 0 1 0 0 0 0 0 1
Malcovati Lab, University of Pavia 0 0 1 0 0 0 0 0 1
Department of Pediatrics,Inha University Hospital, Inha University College of Medicine 0 1 0 0 0 0 0 0 1

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