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Pediatric Disease Annotations & Medicines



   li-fraumeni syndrome
  

Disease ID 31
Disease li-fraumeni syndrome
Definition
Tumor suppressor genes located on the short arm of human chromosome 17 and coding for the phosphoprotein p53.
Synonym
gene p53
gene, p53
gene, tp53
genes p 053
genes tp 053
genes, p53
genes, tp53
lfs1
p a 053 genes
p53
p53 gene
p53 genes
p53 oncogene
p53 tumor suppressor
p53 tumor suppressor gene
tp a 053 genes
tp53
tp53 gene
tp53 genes
transformation-related protein 53
trp53
tumor protein p53
tumor protein p53 (li-fraumeni syndrome) gene
tumor suppressor p53
Orphanet
OMIM
DOID
UMLS
C0079419
MeSH
Comorbidity
UMLS | Disease | Sentences' Count(Total Sentences:21)
C0006142  |  breast cancer  |  6
C0024623  |  gastric cancer  |  2
C0151779  |  cutaneous melanoma  |  1
C1261473  |  sarcoma  |  1
C0023418  |  leukemia  |  1
C0023448  |  lymphocytic leukemia  |  1
C0206180  |  anaplastic large cell lymphoma  |  1
C0029463  |  osteosarcoma  |  1
C0025149  |  medulloblastoma  |  1
C0024302  |  large cell lymphoma  |  1
C0029463  |  osteosarcomas  |  1
C0004114  |  astrocytomas  |  1
C0025202  |  melanoma  |  1
C0023449  |  acute lymphocytic leukemia  |  1
C0346109  |  peritoneal mesothelioma  |  1
C0281267  |  bilateral breast cancer  |  1
C0024299  |  lymphoma  |  1
C0346109  |  malignant peritoneal mesothelioma  |  1
C0684249  |  carcinoma of the lung  |  1
C0242379  |  lung cancer  |  1
C0025202  |  melanomas  |  1
Curated Gene
Entrez_id | Symbol | Resource(Total Genes:4)
TP53  |  7157  |  OMIM;ORPHANET;GHR;UniProtKB-KW
CHEK2  |  11200  |  ORPHANET;GHR;UniProtKB-KW
CDKN2A  |  1029  |  UniProtKB-KW
MDM2  |  4193  |  ORPHANET
Inferring Gene
Entrez_id | Symbol | Resource(Total Genes:2)
4193  |  MDM2  |  infer
7157  |  TP53  |  infer
Text Mined Gene
Entrez_id | Symbol | Score | Resource(Total Genes:92)
10928  |  RALBP1  |  DISEASES
10598  |  AHSA1  |  DISEASES
7443  |  VRK1  |  DISEASES
140733  |  MACROD2  |  DISEASES
2553  |  GABPB1  |  DISEASES
657  |  BMPR1A  |  DISEASES
4292  |  MLH1  |  DISEASES
4436  |  MSH2  |  DISEASES
2956  |  MSH6  |  DISEASES
1026  |  CDKN1A  |  DISEASES
22933  |  SIRT2  |  DISEASES
83667  |  SESN2  |  DISEASES
3845  |  KRAS  |  DISEASES
1643  |  DDB2  |  DISEASES
1019  |  CDK4  |  DISEASES
4659  |  PPP1R12A  |  DISEASES
79728  |  PALB2  |  DISEASES
999  |  CDH1  |  DISEASES
57045  |  TWSG1  |  DISEASES
6598  |  SMARCB1  |  DISEASES
51742  |  ARID4B  |  DISEASES
2622  |  GAS8  |  DISEASES
7157  |  TP53  |  DISEASES
2064  |  ERBB2  |  DISEASES
1956  |  EGFR  |  DISEASES
4863  |  NPAT  |  DISEASES
472  |  ATM  |  DISEASES
57630  |  SH3RF1  |  DISEASES
50940  |  PDE11A  |  DISEASES
843  |  CASP10  |  DISEASES
64798  |  DEPTOR  |  DISEASES
7486  |  WRN  |  DISEASES
54949  |  SDHAF2  |  DISEASES
143501  |  C11orf40  |  DISEASES
80709  |  AKNA  |  DISEASES
148979  |  GLIS1  |  DISEASES
4034  |  LRCH4  |  DISEASES
3265  |  HRAS  |  DISEASES
10221  |  TRIB1  |  DISEASES
9844  |  ELMO1  |  DISEASES
3234  |  HOXD8  |  DISEASES
11145  |  PLA2G16  |  DISEASES
995  |  CDC25C  |  DISEASES
5745  |  PTH1R  |  DISEASES
55135  |  WRAP53  |  DISEASES
84260  |  TCHP  |  DISEASES
6794  |  STK11  |  DISEASES
3665  |  IRF7  |  DISEASES
10320  |  IKZF1  |  DISEASES
144608  |  C12orf60  |  DISEASES
4221  |  MEN1  |  DISEASES
4089  |  SMAD4  |  DISEASES
8445  |  DYRK2  |  DISEASES
23405  |  DICER1  |  DISEASES
2624  |  GATA2  |  DISEASES
8295  |  TRRAP  |  DISEASES
1635  |  DCTD  |  DISEASES
4763  |  NF1  |  DISEASES
7516  |  XRCC2  |  DISEASES
8804  |  CREG1  |  DISEASES
1647  |  GADD45A  |  DISEASES
5728  |  PTEN  |  DISEASES
4595  |  MUTYH  |  DISEASES
7507  |  XPA  |  DISEASES
22852  |  ANKRD26  |  DISEASES
4609  |  MYC  |  DISEASES
2131  |  EXT1  |  DISEASES
164312  |  LRRN4  |  DISEASES
84991  |  RBM17  |  DISEASES
675  |  BRCA2  |  DISEASES
11200  |  CHEK2  |  DISEASES
7187  |  TRAF3  |  DISEASES
6996  |  TDG  |  DISEASES
145270  |  PRIMA1  |  DISEASES
29117  |  BRD7  |  DISEASES
57504  |  MTA3  |  DISEASES
28996  |  HIPK2  |  DISEASES
1111  |  CHEK1  |  DISEASES
11052  |  CPSF6  |  DISEASES
3481  |  IGF2  |  DISEASES
1029  |  CDKN2A  |  DISEASES
11105  |  PRDM7  |  DISEASES
86  |  ACTL6A  |  DISEASES
79718  |  TBL1XR1  |  DISEASES
5378  |  PMS1  |  DISEASES
5985  |  RFC5  |  DISEASES
4193  |  MDM2  |  DISEASES
79813  |  EHMT1  |  DISEASES
672  |  BRCA1  |  DISEASES
23022  |  PALLD  |  DISEASES
63970  |  TP53AIP1  |  DISEASES
5820  |  PVT1  |  DISEASES
Locus
Symbol | Locus(Total Locus:3)
CHEK2  |  22q12.1
TP53  |  17p13.1
MDM2  |  12q15
Disease ID 31
Disease li-fraumeni syndrome
Integrated Phenotype
HPO | Name(Total Integrated Phenotypes:12)
HP:0002664  |  Neoplasm
HP:0002665  |  Lymphoma
HP:0002669  |  Osteosarcoma
HP:0002448  |  Progressive encephalopathy
HP:0004375  |  Neoplasm of the nervous system
HP:0100242  |  Sarcoma
HP:0100273  |  Neoplasm of the colon
HP:0002861  |  Melanoma
HP:0008069  |  Neoplasm of the skin
HP:0002894  |  Neoplasm of the pancreas
HP:0003002  |  Breast carcinoma
HP:0100641  |  Neoplasm of the adrenal cortex
Text Mined Phenotype
HPO | Name | Sentences' Count(Total Phenotypes:16)
HP:0002664  |  Neoplasia  |  7
HP:0003002  |  Breast carcinoma  |  6
HP:0012126  |  Gastric cancer  |  2
HP:0006721  |  Acute lymphocytic leukemia  |  1
HP:0030731  |  Carcinoma  |  1
HP:0100242  |  Sarcoma  |  1
HP:0002861  |  Melanoma  |  1
HP:0002885  |  Medulloblastoma  |  1
HP:0012056  |  Cutaneous melanoma  |  1
HP:0030392  |  Choroid plexus carcinoma  |  1
HP:0100003  |  Peritoneal mesothelioma  |  1
HP:0001909  |  Leukemia  |  1
HP:0030692  |  Brain tumor  |  1
HP:0002665  |  Lymphoma  |  1
HP:0002669  |  Osteosarcoma  |  1
HP:0009733  |  Glioma  |  1
Disease ID 31
Disease li-fraumeni syndrome
Manually Symptom
UMLS  | Name(Total Manually Symptoms:9)
C2697415  |  choroid plexus carcinoma
C0678222  |  breast cancer
C0431109  |  carcinoma of the choroid plexus
C0334616  |  malignant triton tumor
C0152013  |  lung adenocarcinoma
C0035412  |  rhabdomyosarcoma
C0023827  |  liposarcoma
C0023467  |  acute myelogenous leukemia
C0004114  |  astrocytomas
Text Mined Symptom
UMLS | Name | Sentences' Count(Total Symptoms:3)
C0006142  |  breast cancer  |  6
C0431109  |  choroid plexus carcinoma  |  1
C0004114  |  astrocytomas  |  1
Manually Genotype(Total Text Mining Genotypes:0)
(Waiting for update.)
All Snps(Total Genotypes:41)
snpId pubmedId geneId geneSymbol diseaseId sourceId sentence score Year geneSymbol_dbSNP CHROMOSOME POS REF ALT
rs1042522162580054193MDM2umls:C0085390BeFreeImpact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome.0.1338970742006TP53177676154GT,C
rs1042522218142244193MDM2umls:C0085390BeFreePrevious studies have highlighted the contribution of the common functional polymorphisms p53 p.Arg72Pro and MDM2 309SNP to the risk of both common cancers and Li-Fraumeni syndrome.0.1338970742011TP53177676154GT,C
rs1042522162580057157TP53umls:C0085390BeFreeImpact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome.0.368546792006TP53177676154GT,C
rs11540652NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674220CT
rs11540654162580054193MDM2umls:C0085390BeFreeImpact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome.0.1338970742006TP53177676040CT,G,A
rs11540654162580057157TP53umls:C0085390BeFreeImpact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome.0.368546792006TP53177676040CT,G,A
rs11540654218142244193MDM2umls:C0085390BeFreePrevious studies have highlighted the contribution of the common functional polymorphisms p53 p.Arg72Pro and MDM2 309SNP to the risk of both common cancers and Li-Fraumeni syndrome.0.1338970742011TP53177676040CT,G,A
rs121912651193783217157TP53umls:C0085390BeFreeHere, we report a family with LFS harboring a germline TP53 mutation (R248W) located in the functional domain of the protein that binds to the minor groove of the DNA.0.368546792009TP53177674221GA
rs121912651NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674221GA
rs121912651174272347157TP53umls:C0085390BeFreeWe report a patient with composite neuroblastoma (NB), adrenocortical tumor (ACT), and Li-Fraumeni syndrome (LFS) with germline TP53 R248W mutation.0.368546792008TP53177674221GA
rs121912660NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177673781CG,A
rs121912663159932737157TP53umls:C0085390BeFreeThree families (4.4%) had a diagnosis of Li-Fraumeni syndrome and germline mutations in TP53 (Lys292Ile, Pro278Ser and Pro278Thr).0.368546792005TP53177673745TA
rs121912664259457457157TP53umls:C0085390BeFreeIn Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome.0.368546792015TP53177670699CT,G,A
rs121912664206050957157TP53umls:C0085390BeFreeMutation of Arg337 to histidine in the tetramerization domain of p53 is most frequently observed in Li-Fraumeni syndrome.0.368546792010TP53177670699CT,G,A
rs121912664211920607157TP53umls:C0085390BeFreeThe current findings demonstrated compellingly that the TP53 R337H mutation is associated not only with ACT but also with CPC and, to a lesser extent, with osteosarcoma, both of which are core-component tumors of the Li-Fraumeni syndrome.0.368546792011TP53177670699CT,G,A
rs121912664182487857157TP53umls:C0085390BeFreeThese findings indicate that R337H may be a low penetrance mutant which predisposes to multiple cancers and occurs in the population of Southern Brazil at a frequency 10-20 times higher than other TP53 mutants commonly associated with LFS.0.368546792008TP53177670699CT,G,A
rs121912664NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177670699CT,G,A
rs121912664232595017157TP53umls:C0085390BeFreeWe compared the CNV profiles of controls, and LFS individuals carrying either p.R337H or DNA binding domain (DBD) TP53 mutations by high resolution array-CGH.0.368546792012TP53177670699CT,G,A
rs121912666159771747157TP53umls:C0085390BeFreeThe TP53 germ line mutation c.659A>C (p.Y220S) was identified in stored DNA from related patients with Li-Fraumeni syndrome (LFS) who died after developing clinically aggressive tumors.0.368546792005TP53177674872TG,C
rs121913499193404323417IDH1umls:C0085390BeFreeSelective acquisition of IDH1 R132C mutations in astrocytomas associated with Li-Fraumeni syndrome.0.0002714422009IDH12208248389GT,A
rs149633775NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177673773GA,T
rs28934574NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177673776GC,A
rs28934575NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674230CT,A
rs28934576214849317157TP53umls:C0085390BeFreePatient 1 with LFS and TP53(R273H) developed a rhabdomyosarcoma twice at the ages of 18 months and 21 years.0.368546792011TP53177673802CT,A
rs371524413NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177675145CT
rs375338359NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177670684CG,T
rs397514495NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177675070CT,A
rs397516436NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674894GA
rs55819519NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177673751CT
rs55819519204550257157TP53umls:C0085390BeFreeOne index case with glioblastoma multiforme (GBM) diagnosed at age 54 and had a family history comprised of a paternal aunt with GBM at age 55, carried the p53 R158H mutation, which is predicted to be functional and has previously been implicated as a cause of Li-Fraumeni syndrome.0.368546792010TP53177673751CT
rs587778720NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674893CT
rs587780073NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674262TC
rs587782596NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177675071GA
rs587782705NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177675157GA
rs730882004NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674254TC
rs730882005NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674250CT
rs730882025NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674885CT
rs760043106NA7157TP53umls:C0085390CLINVARNA0.36854679NATP53177674947AG
rs80357039175417427157TP53umls:C0085390BeFreeWithin a series of BRCA1 and BRCA2 mutation-negative families, a germline TP53 13398 G>A (Arg213Gln) mutation was identified, which was selected for mutation analysis in this gene because of a family history consistent with Li-Fraumeni syndrome (LFS).0.368546792008BRCA11743094680TC
rs8035703917541742675BRCA2umls:C0085390BeFreeWithin a series of BRCA1 and BRCA2 mutation-negative families, a germline TP53 13398 G>A (Arg213Gln) mutation was identified, which was selected for mutation analysis in this gene because of a family history consistent with Li-Fraumeni syndrome (LFS).0.0043530012008BRCA11743094680TC
rs8035703917541742672BRCA1umls:C0085390BeFreeWithin a series of BRCA1 and BRCA2 mutation-negative families, a germline TP53 13398 G>A (Arg213Gln) mutation was identified, which was selected for mutation analysis in this gene because of a family history consistent with Li-Fraumeni syndrome (LFS).0.0019000932008BRCA11743094680TC
GWASdb Annotation(Total Genotypes:5)
Chr Pos SNP_Id RefGene EnsemblGene ENCODE_Factor ENCODE_TFBS Chromosome_interaction GTEx_eQTL SNP_TFBS_affinity_GWAS3D SNP_miRNA_target_affinity_PolymiRTS SNP_splicing_effect_Skippy SNP_splicing_effect_MutPred_Splice SNP_ns_protein_effect_dbNSFP SNP_syn_effect_Silva SNP_phosphorylation_effect_PhosSNP PhastCons_score PhyloP_score GERP++_RS Segway_state Ancestral_allele ESP_AF ESP_AFR ESP_AFR ESP_EUR TG_ASN TG_AMR TG_AFR TG_EUR Type Consequence bStatistic EncH3K27Ac EncH3K4Me1 EncH3K4Me3 EncNucleo OMIM Clinvar
177571752rs78378222NM_001126115,TP53NM_001126116,TP53NM_001126117,TP53NM_000546,TP53NM_001126112,TP53NM_001126113,TP53NM_001126114,TP53ENST00000413465,ENSG00000141510ENST00000269305,ENSG00000141510ENST00000504937,ENSG00000141510ENST00000510385,ENSG00000141510ENST00000504290,ENSG00000141510ENST00000420246,ENSG00000141510ENST00000455263,ENSG00000141510ENST00000445888,ENSG00000141510ENST00000396473,ENSG00000141510NANAchr17,7570001,7580000,chr20,9950001,9960000,5,Hi-Cchr17,7570001,7580000,chr11,101940001,101950000,5,Hi-Cchr17,7570001,7580000,chrX,75640001,75650000,7,Hi-Cchr17,7570001,7580000,chr17,5020001,5030000,8,Hi-Cchr17,7570001,7580000,chrX,23400001,23410000,7,Hi-CNALM58,2.454LM114,14.4256LM119,3.0932LM194,2.4655LM203,2.5212hsa-miR-382-5p,-0.169000NANANANANA
177577407rs12951053NM_001126115,TP53NM_001126116,TP53NM_001126117,TP53NM_000546,TP53NM_001126112,TP53NM_001126113,TP53NM_001126114,TP53ENST00000413465,ENSG00000141510ENST00000269305,ENSG00000141510ENST00000504937,ENSG00000141510ENST00000510385,ENSG00000141510ENST00000504290,ENSG00000141510ENST00000420246,ENSG00000141510ENST00000455263,ENSG00000141510ENST00000445888,ENSG00000141510ENST00000396473,ENSG00000141510ENST00000419024,ENSG00000141510ENST00000359597,ENSG00000141510ENST00000509690,ENSG00000141510ENST00000514944,ENSG00000141510ENST00000505014,ENSG00000141510ENST00000414315,ENSG00000141510MCV-1NAchr17,7570001,7580000,chr20,9950001,9960000,5,Hi-Cchr17,7570001,7580000,chr11,101940001,101950000,5,Hi-Cchr17,7570001,7580000,chrX,75640001,75650000,7,Hi-Cchr17,7570001,7580000,chr17,5020001,5030000,8,Hi-Cchr17,7570001,7580000,chrX,23400001,23410000,7,Hi-CNAAro80-primary,11.5793Cep3-primary,6.1847Homez_1063,4.8876Mcm1-primary,1.8559Sfl1-DBD-primary,6.4512
177578115rs1625895NM_001126115,TP53NM_001126116,TP53NM_001126117,TP53NM_000546,TP53NM_001126112,TP53NM_001126113,TP53NM_001126114,TP53ENST00000413465,ENSG00000141510ENST00000269305,ENSG00000141510ENST00000504937,ENSG00000141510ENST00000510385,ENSG00000141510ENST00000504290,ENSG00000141510ENST00000420246,ENSG00000141510ENST00000455263,ENSG00000141510ENST00000445888,ENSG00000141510ENST00000396473,ENSG00000141510ENST00000419024,ENSG00000141510ENST00000359597,ENSG00000141510ENST00000509690,ENSG00000141510ENST00000514944,ENSG00000141510ENST00000505014,ENSG00000141510ENST00000414315,ENSG00000141510ENST00000508793,ENSG00000141510ENST00000503591,ENSG00000141510MCV-1NAchr17,7570001,7580000,chr20,9950001,9960000,5,Hi-Cchr17,7570001,7580000,chr11,101940001,101950000,5,Hi-Cchr17,7570001,7580000,chrX,75640001,75650000,7,Hi-Cchr17,7570001,7580000,chr17,5020001,5030000,8,Hi-Cchr17,7570001,7580000,chrX,23400001,23410000,7,Hi-CNAAft1-primary,2.5885Aro80-primary,1.6057Asg1-DBD-primary,1.2704
177579472rs1042522NM_001126115,TP53NM_001126116,TP53NM_001126117,TP53NM_000546,TP53NM_001126112,TP53NM_001126113,TP53NM_001126114,TP53ENST00000413465,ENSG00000141510ENST00000269305,ENSG00000141510ENST00000504937,ENSG00000141510ENST00000510385,ENSG00000141510ENST00000504290,ENSG00000141510ENST00000420246,ENSG00000141510ENST00000455263,ENSG00000141510ENST00000445888,ENSG00000141510ENST00000396473,ENSG00000141510ENST00000419024,ENSG00000141510ENST00000359597,ENSG00000141510ENST00000509690,ENSG00000141510ENST00000514944,ENSG00000141510ENST00000505014,ENSG00000141510ENST00000414315,ENSG00000141510ENST00000508793,ENSG00000141510ENST00000503591,ENSG00000141510MCV-2NAchr17,7570001,7580000,chr20,9950001,9960000,5,Hi-Cchr17,7570001,7580000,chr11,101940001,101950000,5,Hi-Cchr17,7570001,7580000,chrX,75640001,75650000,7,Hi-Cchr17,7570001,7580000,chr17,5020001,5030000,8,Hi-Cchr17,7570001,7580000,chrX,23400001,23410000,7,Hi-CNAAsg1-DBD-primary,1.4376Asg1-DBD-primary,8.3677Ceh-22,1.3486
177581228rs8078476NM_000546,TP53NM_001126112,TP53NM_001126113,TP53NM_001126114,TP53ENST00000413465,ENSG00000141510ENST00000269305,ENSG00000141510ENST00000420246,ENSG00000141510ENST00000455263,ENSG00000141510ENST00000445888,ENSG00000141510ENST00000396473,ENSG00000141510ENST00000419024,ENSG00000141510ENST00000359597,ENSG00000141510ENST00000509690,ENSG00000141510ENST00000514944,ENSG00000141510ENST00000505014,ENSG00000141510ENST00000414315,ENSG00000141510ENST00000508793,ENSG00000141510ENST00000503591,ENSG00000141510MCV-2NAchr17,7580001,7590000,chr22,26120001,26130000,61,Hi-CNACutl1_3494,10.2991Gln3-primary,4.1041Mbp1-primary,1.5057Meis1_2335,2.1845Mig3-primary,1.2896NANANANANANA0.000-0.114
GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)
Mapped by lexical matching(Total Items:1)
HP ID HP Name MP ID MP Name Annotation
HP:0100273Neoplasm of the colonMP:0000495abnormal colon morphology;HP:0100641Neoplasm of the adrenal cortex
Mapped by homologous gene(Total Items:1)
HP ID HP Name MP ID MP Name Annotation
HP:0002861MelanomaMP:0001648abnormal apoptosis;HP:0002665Lymphoma
Chemical(Total Drugs:0)
(Waiting for update.)
FDA approved drug and dosage information(Total Drugs:0)
(Waiting for update.)
FDA labeling changes(Total Drugs:0)
(Waiting for update.)