ClinVar Miner

Variants from St. Jude Molecular Pathology, St. Jude Children's Research Hospital

Location: United States  Primary collection method: clinical testing
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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 total
115 61 1376 46 16 1613

Gene and significance breakdown #

Total genes and gene combinations: 175
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign total
APC 3 0 53 3 1 60
BRCA2 6 1 43 5 1 56
POLE 0 0 54 0 0 54
RECQL4 4 2 42 0 0 48
FANCA 3 2 30 0 0 35
MSH6 1 1 33 0 0 35
ATM 3 1 27 2 0 33
RB1 15 1 16 0 0 32
DICER1 4 0 23 2 1 30
ELP1 2 2 26 0 0 30
ALK 0 0 28 1 0 29
NF1 6 1 21 0 1 29
RET 0 0 27 2 0 29
BLM 2 2 23 0 0 27
BRIP1 2 2 23 0 0 27
MSH2 1 0 24 2 0 27
TSC2 0 0 24 2 0 26
ERCC4 2 1 22 0 0 25
ATM, C11orf65 3 1 19 0 0 23
ANKRD26 0 0 21 0 0 21
MSH3 0 1 20 0 0 21
MUTYH 3 0 18 0 0 21
PMS2 6 1 14 1 0 21
BRCA1 2 1 14 3 0 20
KIF1B 0 0 20 0 0 20
MET 0 0 19 0 1 20
PTCH2 0 0 20 0 0 20
CHEK2 3 4 11 1 0 19
SAMD9L 0 1 18 0 0 19
CDH1 0 0 12 3 3 18
EXT2 0 2 16 0 0 18
POLD1 0 0 18 0 0 18
MLH1 2 0 14 0 1 17
PALB2 2 0 15 0 0 17
PTCH1 0 0 17 0 0 17
SAMD9 0 0 17 0 0 17
SMARCA4 2 1 12 2 0 17
SOS1 0 0 12 2 1 15
TP53 7 3 2 1 2 15
BARD1 0 2 11 0 0 13
BUB1B 0 2 11 0 0 13
LZTR1 0 0 13 0 0 13
NTHL1 1 0 11 1 0 13
TSC1 1 0 12 0 0 13
FH 1 2 9 0 0 12
FLCN 1 1 10 0 0 12
NBN 2 1 7 2 0 12
PDGFRA 0 0 11 1 0 12
AXIN2 0 0 11 0 0 11
FANCG 0 0 11 0 0 11
KIT 1 0 10 0 0 11
SDHA 3 0 8 0 0 11
AOPEP, FANCC 0 1 9 0 0 10
CDKN2A 1 0 9 0 0 10
EPCAM 0 0 9 1 0 10
AIP 0 0 8 1 0 9
BAP1 0 1 8 0 0 9
FANCA, ZNF276 1 0 8 0 0 9
GPR161 0 0 9 0 0 9
POT1 0 3 6 0 0 9
STK11 0 0 9 0 0 9
TERT 0 0 8 1 0 9
CBL 0 2 6 0 0 8
CEBPA 0 1 6 1 0 8
IKZF1 0 0 8 0 0 8
REST 0 0 8 0 0 8
SOS2 0 0 8 0 0 8
TRIM28 1 0 7 0 0 8
DDX41 1 1 5 0 0 7
EXT1 1 0 6 0 0 7
MITF 1 0 6 0 0 7
PAX5 0 1 5 1 0 7
PTPN11 1 1 4 0 1 7
BMPR1A 0 0 6 0 0 6
CDKN1B 0 0 6 0 0 6
GATA2 1 0 5 0 0 6
LOC107982234, WT1 0 1 5 0 0 6
MAP2K2 0 0 6 0 0 6
RAD51C 1 0 5 0 0 6
RAF1 0 0 5 0 1 6
RUNX1 0 0 6 0 0 6
WT1 3 0 3 0 0 6
FANCC 1 0 4 0 0 5
SDHB 0 0 5 0 0 5
SDHD 0 0 5 0 0 5
SLX4 0 1 4 0 0 5
SUFU 1 1 3 0 0 5
BRAF 0 0 3 1 0 4
BRCA1, LOC126862571 1 0 3 0 0 4
CDK4, TSPAN31 0 0 4 0 0 4
CTR9 0 0 4 0 0 4
DKC1 0 0 4 0 0 4
LOC100507346, PTCH1 1 0 2 1 0 4
LOC107303340, VHL 2 0 2 0 0 4
LOC129934333, TMEM127 0 0 4 0 0 4
SHOC2 0 0 4 0 0 4
SPRED1 0 0 4 0 0 4
BUB1B, BUB1B-PAK6 0 0 3 0 0 3
CDC73 0 0 3 0 0 3
CDKN1C 0 0 3 0 0 3
ERCC6 0 0 3 0 0 3
FANCA, LOC112486223 0 0 3 0 0 3
HRAS, LRRC56 0 0 3 0 0 3
LOC130001411, RECQL4 0 0 3 0 0 3
LOC130002133, PTCH1 0 0 3 0 0 3
LOC130062899, STK11 0 0 3 0 0 3
MEN1 0 0 3 0 0 3
NF2 0 0 3 0 0 3
PHOX2B 0 0 3 0 0 3
RAD51D, RAD51L3-RFFL 0 1 2 0 0 3
RRAS 0 0 3 0 0 3
SMARCB1 0 0 3 0 0 3
TMEM127 0 0 3 0 0 3
AMER1 0 0 2 0 0 2
CASP10 0 0 2 0 0 2
CDK4 0 0 2 0 0 2
DHFR, MSH3 0 0 2 0 0 2
ERCC2 0 2 0 0 0 2
ERCC4, LOC130058543 0 0 2 0 0 2
ETV6 0 1 0 0 1 2
FANCA, LOC130059837 0 0 2 0 0 2
FANCM 1 1 0 0 0 2
GREM1 0 0 2 0 0 2
KRAS 0 0 2 0 0 2
LOC105376032, PAX5 0 0 2 0 0 2
LOC110011216, PHOX2B 0 0 2 0 0 2
LOC129390903, RAD51C 0 1 1 0 0 2
LOC129933535, SOS1 0 0 2 0 0 2
LOC130065239, TRIM28 0 0 2 0 0 2
LOC130067016, LZTR1 0 0 2 0 0 2
MAP2K1 0 0 2 0 0 2
MAX 0 0 1 1 0 2
MYH9 0 0 2 0 0 2
PTEN 0 0 2 0 0 2
SDHAF2 0 0 2 0 0 2
SMAD4 0 0 2 0 0 2
VHL 0 0 2 0 0 2
VPS13B 0 0 2 0 0 2
ADA2 0 0 1 0 0 1
AIP, LOC130006206 0 0 1 0 0 1
ANKRD26, LOC130003554 0 0 1 0 0 1
BRAF, LOC126860202 0 0 1 0 0 1
CREBBP 0 0 0 1 0 1
DHX34 0 0 1 0 0 1
DIS3L2 0 0 0 1 0 1
EFL1 0 0 1 0 0 1
ETV6, LOC126861452 0 0 1 0 0 1
FANCD2, LOC107303338 0 0 1 0 0 1
INSL6, JAK2 0 0 1 0 0 1
KIF1B, LOC129388446 0 0 1 0 0 1
LIG4 0 1 0 0 0 1
LOC111811965, MIR4733HG, NF1 0 0 1 0 0 1
LOC126807054, PDGFRA 0 0 1 0 0 1
LOC126860438, NBN 0 0 1 0 0 1
LOC129929542, SDHB 1 0 0 0 0 1
LOC129999303, SMO 0 0 1 0 0 1
LOC130003710, RET 0 0 1 0 0 1
LOC130004614, SUFU 0 0 1 0 0 1
LOC130063193, MAP2K2 0 0 1 0 0 1
LOC130067183, LOC130067184, NF2 1 0 0 0 0 1
MAP2K1, SNAPC5 0 0 0 0 1 1
MYSM1 0 0 1 0 0 1
PIK3CD 0 0 1 0 0 1
PRKAR1A 0 0 1 0 0 1
PRKCD 0 0 1 0 0 1
RAD50 0 0 1 0 0 1
RIT1 0 0 1 0 0 1
SDHC 0 0 1 0 0 1
SH2D1A 0 0 1 0 0 1
SMARCE1 0 0 1 0 0 1
STAT5B 0 0 1 0 0 1
TCIRG1 0 0 1 0 0 1
TERC 0 0 1 0 0 1
WAS 0 0 1 0 0 1
WRN 0 1 0 0 0 1

Condition and significance breakdown #

Total conditions: 205
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Condition pathogenic likely pathogenic uncertain significance likely benign benign total
Familial cancer of breast 3 4 60 0 0 67
Familial adenomatous polyposis 1 1 0 52 3 1 57
Colorectal cancer, susceptibility to, 12 0 0 54 0 0 54
Rothmund-Thomson syndrome type 2 3 1 44 0 0 48
Hereditary breast ovarian cancer syndrome 5 1 28 8 1 43
Medulloblastoma 3 3 37 0 0 43
Gorlin syndrome 1 0 36 1 0 38
Retinoblastoma 15 2 21 0 0 38
Fanconi anemia complementation group A 3 2 30 0 0 35
Lynch syndrome 1 0 26 3 1 31
Noonan syndrome 0 0 22 3 4 29
Breast-ovarian cancer, familial, susceptibility to, 2 4 0 24 0 0 28
Bloom syndrome 2 2 23 0 0 27
Ataxia-telangiectasia syndrome 2 0 21 2 0 25
Familial adenomatous polyposis 4 0 1 22 0 0 23
Fanconi anemia 1 0 21 0 0 22
Lynch syndrome 5 1 1 20 0 0 22
Neurofibromatosis, type 1 3 0 18 0 1 22
Thrombocytopenia 2 0 0 22 0 0 22
Pheochromocytoma 0 0 20 1 0 21
MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIA 0 0 19 1 0 20
Papillary renal cell carcinoma type 1 0 0 18 0 1 19
Predisposition to cancer 3 4 11 1 0 19
Colorectal cancer, susceptibility to, 10 0 0 18 0 0 18
Familial adenomatous polyposis 2 2 0 16 0 0 18
Familial isolated pituitary adenoma 0 0 16 2 0 18
Hereditary diffuse gastric adenocarcinoma 0 0 12 3 3 18
Neuroblastoma, susceptibility to, 3 0 0 18 0 0 18
Rhabdoid tumor predisposition syndrome 2 2 0 14 2 0 18
Wilms tumor 1 3 0 14 0 0 17
Lynch syndrome 4 5 0 11 0 0 16
Pleuropulmonary blastoma 2 0 14 0 0 16
Tuberous sclerosis 2 0 0 16 0 0 16
Colorectal cancer, hereditary nonpolyposis, type 2 2 0 13 0 0 15
Lynch syndrome 1 0 0 15 0 0 15
Breast-ovarian cancer, familial, susceptibility to, 1 1 1 12 0 0 14
DICER1-related tumor predisposition 2 0 9 2 1 14
Noonan syndrome 10 0 0 14 0 0 14
Ataxia-pancytopenia syndrome 0 0 13 0 0 13
Exostoses, multiple, type 2 0 2 11 0 0 13
Familial adenomatous polyposis 3 1 0 11 1 0 13
Microcephaly, normal intelligence and immunodeficiency 2 1 8 2 0 13
Xeroderma pigmentosum, group F 1 0 12 0 0 13
Fanconi anemia complementation group C 1 1 10 0 0 12
Fanconi anemia complementation group Q 0 1 11 0 0 12
MIRAGE syndrome 0 0 12 0 0 12
Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0 0 12 0 0 12
Tuberous sclerosis syndrome 0 0 10 2 0 12
Acute myeloid leukemia 0 1 9 1 0 11
Birt-Hogg-Dube syndrome 1 0 10 0 0 11
Gastrointestinal stromal tumor 0 0 10 1 0 11
Li-Fraumeni syndrome 1 6 3 2 0 0 11
Mosaic variegated aneuploidy syndrome 1 0 1 10 0 0 11
Oligodontia-cancer predisposition syndrome 0 0 11 0 0 11
Hereditary leiomyomatosis and renal cell cancer 0 2 8 0 0 10
Lynch syndrome 8 0 0 9 1 0 10
Fanconi anemia complementation group G 0 0 9 0 0 9
Leukemia, acute lymphoblastic, susceptibility to, 3 0 1 7 1 0 9
Paragangliomas 5 2 0 7 0 0 9
Peutz-Jeghers syndrome 0 0 9 0 0 9
Tumor predisposition syndrome 3 0 3 6 0 0 9
Breast-ovarian cancer, familial, susceptibility to, 3 1 1 6 0 0 8
Craniopharyngioma 1 1 6 0 0 8
Hereditary pheochromocytoma-paraganglioma 1 0 7 0 0 8
Melanoma-pancreatic cancer syndrome 1 0 7 0 0 8
Noonan syndrome 4 0 0 8 0 0 8
Noonan syndrome 9 0 0 8 0 0 8
Wilms tumor 6 0 0 8 0 0 8
Acute lymphoid leukemia 0 0 7 0 0 7
DDX41-related hematologic malignancy predisposition syndrome 1 1 5 0 0 7
Dyskeratosis congenita, autosomal dominant 2 0 0 7 0 0 7
Melanoma, cutaneous malignant, susceptibility to, 8 1 0 6 0 0 7
BAP1-related tumor predisposition syndrome 0 0 6 0 0 6
CBL-related disorder 0 1 5 0 0 6
Exostoses, multiple, type 1 1 0 5 0 0 6
Monosomy 7 myelodysplasia and leukemia syndrome 1 0 1 5 0 0 6
Multiple congenital exostosis 0 0 6 0 0 6
Multiple endocrine neoplasia type 4 0 0 6 0 0 6
Multiple endocrine neoplasia, type 2 0 0 5 1 0 6
Predisposition to Wilms tumor 1 0 5 0 0 6
Tuberous sclerosis 1 1 0 5 0 0 6
Cardiofaciocutaneous syndrome 4 0 0 5 0 0 5
Fanconi anemia complementation group J 1 0 4 0 0 5
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 0 0 5 0 0 5
Monosomy 7 myelodysplasia and leukemia syndrome 2 0 0 5 0 0 5
Mosaic variegated aneuploidy syndrome 0 1 4 0 0 5
Neuroblastoma 0 1 4 0 0 5
Pilocytic astrocytoma 2 1 2 0 0 5
Somatotroph adenoma 0 0 5 0 0 5
Von Hippel-Lindau syndrome 1 0 4 0 0 5
B Lymphoblastic Leukemia/Lymphoma, Not Otherwise Specified 0 0 4 0 0 4
B lymphoblastic leukemia lymphoma with t(12;21)(p13;q22); TEL-AML1 (ETV6-RUNX1) 1 0 3 0 0 4
Dyskeratosis congenita, X-linked 0 0 4 0 0 4
Legius syndrome 0 0 4 0 0 4
Melanoma, cutaneous malignant, susceptibility to, 3 0 0 4 0 0 4
Neuroblastoma, susceptibility to, 2 0 0 4 0 0 4
Neurofibromatosis, type 2 1 0 3 0 0 4
Precursor B-cell acute lymphoblastic leukemia 2 2 0 0 0 4
Beckwith-Wiedemann syndrome 0 0 3 0 0 3
Breast-ovarian cancer, familial, susceptibility to, 4 0 1 2 0 0 3
Costello syndrome 0 0 3 0 0 3
Diffuse intrinsic pontine glioma 1 1 1 0 0 3
Fanconi anemia complementation group P 0 0 3 0 0 3
Generalized juvenile polyposis/juvenile polyposis coli 0 0 3 0 0 3
Hyperparathyroidism 2 with jaw tumors 0 0 3 0 0 3
Juvenile polyposis syndrome 0 0 3 0 0 3
Li-Fraumeni syndrome 0 0 0 1 2 3
Neuroblastoma, susceptibility to, 1 0 0 3 0 0 3
Noonan syndrome 7 0 0 3 0 0 3
Noonan syndrome-like disorder with loose anagen hair 1 0 0 3 0 0 3
Paragangliomas 1 0 0 3 0 0 3
Thrombocytopenia 5 0 1 1 0 1 3
Anaplastic ependymoma 0 0 2 0 0 2
Autoimmune lymphoproliferative syndrome type 2A 0 0 2 0 0 2
Cardiofaciocutaneous syndrome 3 0 0 2 0 0 2
Cockayne syndrome 0 0 2 0 0 2
Cohen syndrome 0 0 2 0 0 2
Congenital fibrosarcoma 1 1 0 0 0 2
Dyskeratosis congenita 0 0 1 1 0 2
Ewing sarcoma 0 1 1 0 0 2
Familial melanoma 0 0 2 0 0 2
GATA2 deficiency with susceptibility to MDS/AML 0 0 2 0 0 2
Glioblastoma 1 1 0 0 0 2
Hereditary mixed polyposis syndrome 0 0 2 0 0 2
Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss 0 0 2 0 0 2
Malignant germ cell tumor of ovary 1 1 0 0 0 2
Multiple endocrine neoplasia, type 1 0 0 2 0 0 2
Myelodysplastic syndrome 1 0 1 0 0 2
Nephroblastoma 0 0 2 0 0 2
Noonan syndrome 1 0 1 1 0 0 2
Optic nerve glioma 2 0 0 0 0 2
Osteopathia striata with cranial sclerosis 0 0 2 0 0 2
Papillary thyroid carcinoma 0 1 1 0 0 2
Paragangliomas 2 0 0 2 0 0 2
Paragangliomas 4 0 0 2 0 0 2
Acute leukemia of ambiguous lineage 1 0 0 0 0 1
Acute monocytic leukemia; Acute monoblastic leukemia 0 0 1 0 0 1
Acute promyelocytic leukemia 0 0 1 0 0 1
Astrocytoma, anaplastic; Pleomorphic xanthoastrocytoma 1 0 0 0 0 1
Atypical teratoid rhabdoid tumor 0 0 1 0 0 1
Autoimmune lymphoproliferative syndrome, type III caused by mutation in PRKCD 0 0 1 0 0 1
B Lymphoblastic Leukemia/Lymphoma with t(9;22)(q34.1;q11.2); BCR-ABL1 0 0 1 0 0 1
B Lymphoblastic Leukemia/Lymphoma with t(v;11q23.3); KMT2A Rearranged 1 0 0 0 0 1
B lymphoblastic leukemia lymphoma with hyperdiploidy 0 0 1 0 0 1
B lymphoblastic leukemia lymphoma, no ICD-O subtype 1 0 0 0 0 1
B-lymphoblastic leukemia/lymphoma with hypodiploidy 0 0 1 0 0 1
Bone marrow failure syndrome 4 0 0 1 0 0 1
Breast-ovarian cancer, familial, susceptibility to, 5 0 0 1 0 0 1
Burkitt lymphoma; Lymphoma 1 0 0 0 0 1
Cardio-facio-cutaneous syndrome 0 0 1 0 0 1
Carney complex, type 1 0 0 1 0 0 1
Cockayne syndrome type 2 0 0 1 0 0 1
Coffin-Siris syndrome 5 0 0 1 0 0 1
Cowden syndrome 1 0 0 1 0 0 1
DHX34-associated thromobocytopenia 0 0 1 0 0 1
Desmoid tumor 1 0 0 0 0 1
Dyskeratosis congenita, autosomal dominant 1 0 0 1 0 0 1
Embryonal rhabdomyosarcoma 0 0 1 0 0 1
Ependymoma 0 0 1 0 0 1
Ewing sarcoma of soft tissue 0 0 1 0 0 1
Familial multiple polyposis syndrome 0 0 1 0 0 1
Fanconi anemia complementation group D2 0 0 1 0 0 1
Fanconi anemia complementation group N 0 0 1 0 0 1
Fumarase deficiency 1 0 0 0 0 1
Ganglioglioma 0 0 1 0 0 1
Gastric adenocarcinoma and proximal polyposis of the stomach 0 0 1 0 0 1
Germinoma 0 0 1 0 0 1
Glioblastoma multiforme 0 1 0 0 0 1
Growth hormone insensitivity with immune dysregulation 1, autosomal recessive 0 0 1 0 0 1
Hepatoblastoma 0 0 1 0 0 1
Hereditary papillary renal cell carcinoma 0 0 1 0 0 1
High grade surface osteosarcoma 1 0 0 0 0 1
Immunodeficiency 14 0 0 1 0 0 1
Increased risk to develop myelodysplastic syndrome, acute myeloid leukemia, or chronic myelomonocytic leukemia 0 0 1 0 0 1
Lymphoma; B lymphoblastic leukemia lymphoma, no ICD-O subtype 1 0 0 0 0 1
Malignant fibrous histiocytoma 0 1 0 0 0 1
Malignant glioma 1 0 0 0 0 1
Mixed Phenotype Acute Leukemia with t(v;11q23.3); KMT2A Rearranged 0 0 1 0 0 1
Mixed Phenotype Acute Leukemia, T/Myeloid, Not Otherwise Specified 0 1 0 0 0 1
Neutropenia, severe congenital, 1, autosomal dominant 0 0 1 0 0 1
Nijmegen breakage syndrome-like disorder 0 0 1 0 0 1
Noonan syndrome 5 0 0 1 0 0 1
Noonan syndrome 8 0 0 1 0 0 1
Osteoblastic osteosarcoma 0 0 1 0 0 1
PTEN hamartoma tumor syndrome 0 0 1 0 0 1
Pancytopenia due to IKZF1 mutations 0 0 1 0 0 1
Paragangliomas 3 0 0 1 0 0 1
Perlman syndrome 0 0 0 1 0 1
Pituitary carcinoma 0 1 0 0 0 1
Predisposition to medulloblastoma 0 0 1 0 0 1
Predisposition to myelodysplastic syndrome 0 0 1 0 0 1
Predisposition to neuroblastoma 0 0 1 0 0 1
Primitive neuroectodermal tumor 0 0 1 0 0 1
Rhabdoid tumor predisposition syndrome 1 0 0 1 0 0 1
Rothmund-Thomson syndrome 0 0 1 0 0 1
Rubinstein-Taybi syndrome due to CREBBP mutations 0 0 0 1 0 1
Schwannomatosis 2 0 0 1 0 0 1
Shwachman-Diamond syndrome 2 0 0 1 0 0 1
Thrombocythemia 3 0 0 1 0 0 1
Uveal melanoma 0 0 1 0 0 1
Vasculitis due to ADA2 deficiency 0 0 1 0 0 1
Wiskott-Aldrich syndrome 0 0 1 0 0 1
X-linked lymphoproliferative disease due to SH2D1A deficiency 0 0 1 0 0 1
Xeroderma pigmentosum, group F; Fanconi anemia complementation group Q 0 0 1 0 0 1
not specified 0 0 1 0 0 1

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