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mutLBSgeneDB |
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| Gene summary for RAF1 |
 Gene summary |
| Basic gene Info. | Gene symbol | RAF1 |
| Gene name | Raf-1 proto-oncogene, serine/threonine kinase | |
| Synonyms | CMD1NN|CRAF|NS5|Raf-1|c-Raf | |
| Cytomap | UCSC genome browser: 3p25 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002880.3, | |
| Description | C-Raf proto-oncogene, serine/threonine kinaseOncogene RAF1RAF proto-oncogene serine/threonine-protein kinaseproto-oncogene c-RAFraf proto-oncogene serine/threonine protein kinasev-raf-1 murine leukemia viral oncogene homolog 1 | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 164760 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000132155 | ||
| HPRD : 01265 | ||
| Vega : OTTHUMG00000129789 | ||
| Protein | UniProt: P04049 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RAF1 | |
| BioGPS: 5894 | ||
| Pathway | NCI Pathway Interaction Database: RAF1 | |
| KEGG: RAF1 | ||
| REACTOME: RAF1 | ||
| Pathway Commons: RAF1 | ||
| Context | iHOP: RAF1 | |
| ligand binding site mutation search in PubMed: RAF1 | ||
| UCL Cancer Institute: RAF1 | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0000186 | activation of MAPKK activity | 10644344 | GO:0008285 | negative regulation of cell proliferation | 9765203 | GO:0031333 | negative regulation of protein complex assembly | 19667065 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 19667065 | GO:0043066 | negative regulation of apoptotic process | 19667065 |
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| Ligand binding site mutations for RAF1 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | G123 | I122V | BRCA | 1 | C184 | D186N | COAD | 1 | C165 | R164Q | COAD | 1 | T421,W423 | Q422R | GBM | 1 | I419 | I419V | UCEC | 1 | K375 | I376L | UCEC | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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| Protein structure related information for RAF1 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | I419 | I419V | -1.4139436 | C165 | R164Q | -1.0325975 | K375 | I376L | -0.91161421 | C184 | D186N | -0.60258782 | G123 | I122V | -0.58432839 | T421 | Q422R | -0.48161538 | W423 | Q422R | -0.48161538 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for RAF1 from PDB |
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| Differential gene expression and gene-gene network for RAF1 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for RAF1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0028326 | Noonan Syndrome | 21 | Biomarker, GeneticVariation |
| umls:C0017638 | Glioma | 10 | Biomarker, GeneticVariation |
| umls:C0007131 | Carcinoma, Non-Small-Cell Lung | 8 | Biomarker |
| umls:C0175704 | LEOPARD Syndrome | 6 | Biomarker, GeneticVariation |
| umls:C0007194 | Cardiomyopathy, Hypertrophic | 6 | Biomarker, GeneticVariation |
| umls:C0024121 | Lung Neoplasms | 4 | Biomarker |
| umls:C1458155 | Breast Neoplasms | 3 | Biomarker, Therapeutic |
| umls:C0023903 | Liver Neoplasms | 3 | Biomarker |
| umls:C0007193 | Cardiomyopathy, Dilated | 1 | Biomarker |
| umls:C0022665 | Kidney Neoplasms | 1 | Biomarker |
| umls:C0020429 | Hyperalgesia | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for RAF1 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|investigational | DB00398 | Sorafenib | Small molecule |  |
| Investigational | DB04973 | LErafAON | Biotech |  |
| Investigational | DB05190 | XL281 | Small molecule |  |
| Investigational | DB05268 | iCo-007 | Small molecule |  |
| Approved | DB08896 | Regorafenib | Small molecule |  |
| Approved | DB08912 | Dabrafenib | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of RAF1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 1faq | A | C165 C184 | ZN | ZINC(2+) | 1far | A | C165 C184 | CA | CALCIUM(2+) | 1c1y | B | G123 | CA | CALCIUM(2+) | 1gua | B | G123 | CA | CALCIUM(2+) | 3kuc | B | G123 | SM5 | (1E)-5-(1-PIPERIDIN-4-YL-3-PYRIDIN-4-YL-1H-PYRAZOL-4-YL)-2,3-DIHYDRO-1H-INDEN-1-ONE OXIME | 3omv | B | K375 I419 T421 | SM5 | (1E)-5-(1-PIPERIDIN-4-YL-3-PYRIDIN-4-YL-1H-PYRAZOL-4-YL)-2,3-DIHYDRO-1H-INDEN-1-ONE OXIME | 3omv | A | K375 T421 W423 |
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| Conservation information for LBS of RAF1 |
| Multiple alignments for P04049 in multiple species |
| LBS | AA sequence | # species | Species | A373 | WHGDVAVKILK | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C152 | LKLAFCDICQK | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C155 | AFCDICQKFLL | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C165 | LNGFRCQTCGY | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C168 | FRCQTCGYKFH | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C176 | KFHEHCSTKVP | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C184 | KVPTMCVDWSN | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | C424 | IVTQWCEGSSL | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | D486 | TVKIGDFGLAT | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | E125 | SLIGEELQVDF | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | F475 | KSNNIFLHEGL | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | G123 | AASLIGEELQV | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | H139 | VPLTTHNFARK | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | H173 | CGYKFHEHCST | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | I355 | MLSTRIGSGSF | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | I419 | KDNLAIVTQWC | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | K375 | GDVAVKILKVV | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | K431 | GSSLYKHLHVQ | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | L406 | RHVNILLFMGY | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | N472 | RDMKSNNIFLH | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | S428 | WCEGSSLYKHL | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | T421 | NLAIVTQWCEG | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | V363 | GSFGTVYKGKW | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | W423 | AIVTQWCEGSS | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus |
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