eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| li-fraumeni syndrome | ||||
| Disease ID | 19 |
|---|---|
| Disease | li-fraumeni syndrome |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:9) |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:3) |
Manually Genotype(Total Manually Genotypes:2) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| TP53 | NM_000546.5:c.91G>A, NP_000537.3:p.Val31Ile | doi:10.1038/gim.2015.26 | Frequency and spectrum of actionable pathogenic secondary findings in 196 Korean exomes |
| TP53 | - | doi:10.1038/gim.2015.51 | Clinical performance of the CytoScan Dx Assay in diagnosing developmental delay/intellectual disability |
Text Mining Genotype(Total 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 |
| rs1042522 | 16258005 | 4193 | MDM2 | umls:C0085390 | BeFree | Impact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome. | 0.133897074 | 2006 | TP53 | 17 | 7676154 | G | T,C |
| rs1042522 | 21814224 | 4193 | MDM2 | umls:C0085390 | BeFree | Previous 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. | 0.133897074 | 2011 | TP53 | 17 | 7676154 | G | T,C |
| rs1042522 | 16258005 | 7157 | TP53 | umls:C0085390 | BeFree | Impact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome. | 0.36854679 | 2006 | TP53 | 17 | 7676154 | G | T,C |
| rs11540652 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674220 | C | T |
| rs11540654 | 16258005 | 4193 | MDM2 | umls:C0085390 | BeFree | Impact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome. | 0.133897074 | 2006 | TP53 | 17 | 7676040 | C | T,G,A |
| rs11540654 | 16258005 | 7157 | TP53 | umls:C0085390 | BeFree | Impact of the MDM2 SNP309 and p53 Arg72Pro polymorphism on age of tumour onset in Li-Fraumeni syndrome. | 0.36854679 | 2006 | TP53 | 17 | 7676040 | C | T,G,A |
| rs11540654 | 21814224 | 4193 | MDM2 | umls:C0085390 | BeFree | Previous 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. | 0.133897074 | 2011 | TP53 | 17 | 7676040 | C | T,G,A |
| rs121912651 | 19378321 | 7157 | TP53 | umls:C0085390 | BeFree | Here, 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. | 0.36854679 | 2009 | TP53 | 17 | 7674221 | G | A |
| rs121912651 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674221 | G | A |
| rs121912651 | 17427234 | 7157 | TP53 | umls:C0085390 | BeFree | We report a patient with composite neuroblastoma (NB), adrenocortical tumor (ACT), and Li-Fraumeni syndrome (LFS) with germline TP53 R248W mutation. | 0.36854679 | 2008 | TP53 | 17 | 7674221 | G | A |
| rs121912660 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7673781 | C | G,A |
| rs121912663 | 15993273 | 7157 | TP53 | umls:C0085390 | BeFree | Three families (4.4%) had a diagnosis of Li-Fraumeni syndrome and germline mutations in TP53 (Lys292Ile, Pro278Ser and Pro278Thr). | 0.36854679 | 2005 | TP53 | 17 | 7673745 | T | A |
| rs121912664 | 25945745 | 7157 | TP53 | umls:C0085390 | BeFree | In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. | 0.36854679 | 2015 | TP53 | 17 | 7670699 | C | T,G,A |
| rs121912664 | 20605095 | 7157 | TP53 | umls:C0085390 | BeFree | Mutation of Arg337 to histidine in the tetramerization domain of p53 is most frequently observed in Li-Fraumeni syndrome. | 0.36854679 | 2010 | TP53 | 17 | 7670699 | C | T,G,A |
| rs121912664 | 21192060 | 7157 | TP53 | umls:C0085390 | BeFree | The 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. | 0.36854679 | 2011 | TP53 | 17 | 7670699 | C | T,G,A |
| rs121912664 | 18248785 | 7157 | TP53 | umls:C0085390 | BeFree | These 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. | 0.36854679 | 2008 | TP53 | 17 | 7670699 | C | T,G,A |
| rs121912664 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7670699 | C | T,G,A |
| rs121912664 | 23259501 | 7157 | TP53 | umls:C0085390 | BeFree | We 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. | 0.36854679 | 2012 | TP53 | 17 | 7670699 | C | T,G,A |
| rs121912666 | 15977174 | 7157 | TP53 | umls:C0085390 | BeFree | The 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. | 0.36854679 | 2005 | TP53 | 17 | 7674872 | T | G,C |
| rs121913499 | 19340432 | 3417 | IDH1 | umls:C0085390 | BeFree | Selective acquisition of IDH1 R132C mutations in astrocytomas associated with Li-Fraumeni syndrome. | 0.000271442 | 2009 | IDH1 | 2 | 208248389 | G | T,A |
| rs149633775 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7673773 | G | A,T |
| rs28934574 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7673776 | G | C,A |
| rs28934575 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674230 | C | T,A |
| rs28934576 | 21484931 | 7157 | TP53 | umls:C0085390 | BeFree | Patient 1 with LFS and TP53(R273H) developed a rhabdomyosarcoma twice at the ages of 18 months and 21 years. | 0.36854679 | 2011 | TP53 | 17 | 7673802 | C | T,A |
| rs371524413 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7675145 | C | T |
| rs375338359 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7670684 | C | G,T |
| rs397514495 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7675070 | C | T,A |
| rs397516436 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674894 | G | A |
| rs55819519 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7673751 | C | T |
| rs55819519 | 20455025 | 7157 | TP53 | umls:C0085390 | BeFree | One 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. | 0.36854679 | 2010 | TP53 | 17 | 7673751 | C | T |
| rs587778720 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674893 | C | T |
| rs587780073 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674262 | T | C |
| rs587782596 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7675071 | G | A |
| rs587782705 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7675157 | G | A |
| rs730882004 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674254 | T | C |
| rs730882005 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674250 | C | T |
| rs730882025 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674885 | C | T |
| rs760043106 | NA | 7157 | TP53 | umls:C0085390 | CLINVAR | NA | 0.36854679 | NA | TP53 | 17 | 7674947 | A | G |
| rs80357039 | 17541742 | 7157 | TP53 | umls:C0085390 | BeFree | Within 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). | 0.36854679 | 2008 | BRCA1 | 17 | 43094680 | T | C |
| rs80357039 | 17541742 | 675 | BRCA2 | umls:C0085390 | BeFree | Within 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). | 0.004353001 | 2008 | BRCA1 | 17 | 43094680 | T | C |
| rs80357039 | 17541742 | 672 | BRCA1 | umls:C0085390 | BeFree | Within 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). | 0.001900093 | 2008 | BRCA1 | 17 | 43094680 | T | C |
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 |
| 17 | 7571752 | rs78378222 | NM_001126115,TP53 | NM_001126116,TP53 | NM_001126117,TP53 | NM_000546,TP53 | NM_001126112,TP53 | NM_001126113,TP53 | NM_001126114,TP53 | ENST00000413465,ENSG00000141510 | ENST00000269305,ENSG00000141510 | ENST00000504937,ENSG00000141510 | ENST00000510385,ENSG00000141510 | ENST00000504290,ENSG00000141510 | ENST00000420246,ENSG00000141510 | ENST00000455263,ENSG00000141510 | ENST00000445888,ENSG00000141510 | ENST00000396473,ENSG00000141510 | NA | NA | chr17,7570001,7580000,chr20,9950001,9960000,5,Hi-C | chr17,7570001,7580000,chr11,101940001,101950000,5,Hi-C | chr17,7570001,7580000,chrX,75640001,75650000,7,Hi-C | chr17,7570001,7580000,chr17,5020001,5030000,8,Hi-C | chr17,7570001,7580000,chrX,23400001,23410000,7,Hi-C | NA | LM58,2.454 | LM114,14.4256 | LM119,3.0932 | LM194,2.4655 | LM203,2.5212 | hsa-miR-382-5p,-0.169000 | NA | NA | NA | NA | NA |
| 17 | 7577407 | rs12951053 | NM_001126115,TP53 | NM_001126116,TP53 | NM_001126117,TP53 | NM_000546,TP53 | NM_001126112,TP53 | NM_001126113,TP53 | NM_001126114,TP53 | ENST00000413465,ENSG00000141510 | ENST00000269305,ENSG00000141510 | ENST00000504937,ENSG00000141510 | ENST00000510385,ENSG00000141510 | ENST00000504290,ENSG00000141510 | ENST00000420246,ENSG00000141510 | ENST00000455263,ENSG00000141510 | ENST00000445888,ENSG00000141510 | ENST00000396473,ENSG00000141510 | ENST00000419024,ENSG00000141510 | ENST00000359597,ENSG00000141510 | ENST00000509690,ENSG00000141510 | ENST00000514944,ENSG00000141510 | ENST00000505014,ENSG00000141510 | ENST00000414315,ENSG00000141510 | MCV-1 | NA | chr17,7570001,7580000,chr20,9950001,9960000,5,Hi-C | chr17,7570001,7580000,chr11,101940001,101950000,5,Hi-C | chr17,7570001,7580000,chrX,75640001,75650000,7,Hi-C | chr17,7570001,7580000,chr17,5020001,5030000,8,Hi-C | chr17,7570001,7580000,chrX,23400001,23410000,7,Hi-C | NA | Aro80-primary,11.5793 | Cep3-primary,6.1847 | Homez_1063,4.8876 | Mcm1-primary,1.8559 | Sfl1-DBD-primary,6.4512 |
| 17 | 7578115 | rs1625895 | NM_001126115,TP53 | NM_001126116,TP53 | NM_001126117,TP53 | NM_000546,TP53 | NM_001126112,TP53 | NM_001126113,TP53 | NM_001126114,TP53 | ENST00000413465,ENSG00000141510 | ENST00000269305,ENSG00000141510 | ENST00000504937,ENSG00000141510 | ENST00000510385,ENSG00000141510 | ENST00000504290,ENSG00000141510 | ENST00000420246,ENSG00000141510 | ENST00000455263,ENSG00000141510 | ENST00000445888,ENSG00000141510 | ENST00000396473,ENSG00000141510 | ENST00000419024,ENSG00000141510 | ENST00000359597,ENSG00000141510 | ENST00000509690,ENSG00000141510 | ENST00000514944,ENSG00000141510 | ENST00000505014,ENSG00000141510 | ENST00000414315,ENSG00000141510 | ENST00000508793,ENSG00000141510 | ENST00000503591,ENSG00000141510 | MCV-1 | NA | chr17,7570001,7580000,chr20,9950001,9960000,5,Hi-C | chr17,7570001,7580000,chr11,101940001,101950000,5,Hi-C | chr17,7570001,7580000,chrX,75640001,75650000,7,Hi-C | chr17,7570001,7580000,chr17,5020001,5030000,8,Hi-C | chr17,7570001,7580000,chrX,23400001,23410000,7,Hi-C | NA | Aft1-primary,2.5885 | Aro80-primary,1.6057 | Asg1-DBD-primary,1.2704 |
| 17 | 7579472 | rs1042522 | NM_001126115,TP53 | NM_001126116,TP53 | NM_001126117,TP53 | NM_000546,TP53 | NM_001126112,TP53 | NM_001126113,TP53 | NM_001126114,TP53 | ENST00000413465,ENSG00000141510 | ENST00000269305,ENSG00000141510 | ENST00000504937,ENSG00000141510 | ENST00000510385,ENSG00000141510 | ENST00000504290,ENSG00000141510 | ENST00000420246,ENSG00000141510 | ENST00000455263,ENSG00000141510 | ENST00000445888,ENSG00000141510 | ENST00000396473,ENSG00000141510 | ENST00000419024,ENSG00000141510 | ENST00000359597,ENSG00000141510 | ENST00000509690,ENSG00000141510 | ENST00000514944,ENSG00000141510 | ENST00000505014,ENSG00000141510 | ENST00000414315,ENSG00000141510 | ENST00000508793,ENSG00000141510 | ENST00000503591,ENSG00000141510 | MCV-2 | NA | chr17,7570001,7580000,chr20,9950001,9960000,5,Hi-C | chr17,7570001,7580000,chr11,101940001,101950000,5,Hi-C | chr17,7570001,7580000,chrX,75640001,75650000,7,Hi-C | chr17,7570001,7580000,chr17,5020001,5030000,8,Hi-C | chr17,7570001,7580000,chrX,23400001,23410000,7,Hi-C | NA | Asg1-DBD-primary,1.4376 | Asg1-DBD-primary,8.3677 | Ceh-22,1.3486 |
| 17 | 7581228 | rs8078476 | NM_000546,TP53 | NM_001126112,TP53 | NM_001126113,TP53 | NM_001126114,TP53 | ENST00000413465,ENSG00000141510 | ENST00000269305,ENSG00000141510 | ENST00000420246,ENSG00000141510 | ENST00000455263,ENSG00000141510 | ENST00000445888,ENSG00000141510 | ENST00000396473,ENSG00000141510 | ENST00000419024,ENSG00000141510 | ENST00000359597,ENSG00000141510 | ENST00000509690,ENSG00000141510 | ENST00000514944,ENSG00000141510 | ENST00000505014,ENSG00000141510 | ENST00000414315,ENSG00000141510 | ENST00000508793,ENSG00000141510 | ENST00000503591,ENSG00000141510 | MCV-2 | NA | chr17,7580001,7590000,chr22,26120001,26130000,61,Hi-C | NA | Cutl1_3494,10.2991 | Gln3-primary,4.1041 | Mbp1-primary,1.5057 | Meis1_2335,2.1845 | Mig3-primary,1.2896 | NA | NA | NA | NA | NA | NA | 0.000 | -0.114 |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:6) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0004375 | Neoplasm of the nervous system | MP:0010287 | increased reproductive system tumor incidence | greater than the expected number of tumors originating in the reproductive system in a given population in a given time period |
| HP:0008069 | Neoplasm of the skin | MP:0011205 | excessive folding of visceral yolk sac | the appearance of wrinkles or folds on the surface of the visceral yolk sac |
| HP:0003002 | Breast carcinoma | MP:0010367 | increased spindle cell carcinoma incidence | greater than the expected number of a highly malignant variant of squamous cell carcinoma, occurring in a specific population in a given time period; spindle cell carcinoma shows biphasic proliferation of conventional SCC component and malignant spindle s |
| HP:0100641 | Neoplasm of the adrenal cortex | MP:0004097 | abnormal cerebellar cortex morphology | any structural anomaly of the thin mantle of grey matter that covers the surface of each cerebral hemisphere, including the six layers of nerve cells and the nerve pathways that connect them; together, these regions are responsible for the processes of co |
| HP:0002894 | Neoplasm of the pancreas | MP:0008261 | arrest of male meiosis | cessation of the progression of the process of nuclear division that results in sperm with one half the normal chromosome number of the original cell |
| HP:0100273 | Neoplasm of the colon | MP:0008261 | arrest of male meiosis | cessation of the progression of the process of nuclear division that results in sperm with one half the normal chromosome number of the original cell |
Mapped by homologous gene(Total Items:12) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0008069 | Neoplasm of the skin | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0004375 | Neoplasm of the nervous system | MP:0014171 | increased fatty acid oxidation | increased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr |
| HP:0002664 | Neoplasm | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0100273 | Neoplasm of the colon | MP:0014083 | blunted small intestinal villi | abnormal flattening of the surface of the tiny hair-like projections which protrude from the inside of the small intestine and contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; usually due to intestinal d |
| HP:0100641 | Neoplasm of the adrenal cortex | MP:0013886 | increased CD4-negative, CD25-positive NK T cell number | increase in the number of CD4-negative NK T cells expressing the activation marker CD25 |
| HP:0003002 | Breast carcinoma | MP:0020039 | increased bone ossification | increase in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance |
| HP:0002665 | Lymphoma | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0100242 | Sarcoma | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002861 | Melanoma | MP:0012431 | increased lymphoma incidence | greater than the expected number of neoplasms characterized by a proliferation of malignant lymphocytes in lymphoid tissue in a specific population in a given time period |
| HP:0002669 | Osteosarcoma | MP:0020039 | increased bone ossification | increase in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance |
| HP:0002448 | Progressive encephalopathy | MP:0013504 | increased embryonic tissue cell apoptosis | increase in the timing or the number of cells in embryonic tissue undergoing programmed cell death |
| HP:0002894 | Neoplasm of the pancreas | MP:0014126 | increased mammary gland apoptosis | increase in the number of any cells of a mammary gland undergoing programmed cell death |
| Disease ID | 19 |
|---|---|
| Disease | li-fraumeni syndrome |
| Case | (Waiting for update.) |