Atlas of Genetics and Cytogenetics in Oncology and Haematology


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BRAF (v-raf murine sarcoma viral oncogene homolog B1)

Identity

Other namesv-raf murine sarcoma viral oncogene homolog B1
BRAF1
RAFB1
HGNC (Hugo) BRAF
LocusID (NCBI) 673
Location 7q34
Location_base_pair Starts at 140433813 and ends at 140624564 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order Between the NDUFB2 and MRPS33 genes.
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics

DNA/RNA

 
  Diagram of the BRAF gene. Exons are represented by boxes (in scale) transcribed and untranscribed sequences in blue and yellow, with exon numbers on top and number of base pairs at the bottom. Introns are represented by black bars (not in scale) and the number of base pairs indicated. The arrows show the ATG and the stop codons respectively.
Description The BRAF gene is composed of 18 exons spanning in a region of 190284 bp.
Transcription The transcribed mRNA has 2478 bp.
Pseudogene BRAF2 in Xq13.3

Protein

Note The real sequence A31 G32 A33 was erroneously considered R31 P32. As the A33 was missing in previous sequences, some articles have erroneously assigned wrong numbers to coding mutations and amino acids (i.e. V599E mutation instead of V600E).
 
  Diagram of the BRAF protein in scale. Numbers inside the blue boxes indicate the exon from which is translated each part of the protein. The three boxes inside represent the conserved regions of the protein with the ARAF and RAF-1 genes (CR1, CR2 and CR3). With green bars are represented three different domains: RBD (Ras binding domain), CRD (Cysteine-rich domain) and KD (Kinase domain). A conserved glycine motif (G-loop) in exon 11 is indicated with a red bar and the activation segment (AS) in exon 15 with a pink bar. The black arrows indicate the major phosphorylation sites of the protein. C: Carboxyl-terminal; N: Amino-terminal.
Description Amino acids: 766. Molecular Weight: 84436 Daltons. The BRAF gene is a proto-oncogene that belongs to the Serine/Threonine Kinase Family. It is also a member of the RAF Subfamily together with the ARAF and RAF1 genes.
Expression BRAF is expressed in most tissues with high expression in neuronal tissue.
Localisation Cytoplasmic.
Function BRAF is a serine/threonine kinase that belongs to the RAS/RAF/MEK/ERK/MAPK pathway, which is involved in the transduccion of mitogenic signals from the cell membrane to the nucleus. RAS is inactive when binded to GDP, but when it binds to GTP becomes active and promotes phosphorylation and activation of BRAF and the activation of the pathway signal. Several genes have been found to be activated by this pathway, among them, cyclin D1, cyclin D2 and cyclin D3 (self-sufficiency in growth), VEGF (angiogenesis), c-myc (insensitivity to antigrowth signals), b3-integrin (tissue invasion and metastasis) and mdm2 (apoptosis evasion, limitless replicative potential and angiogenesis).
Homology BRAF shares three conserved regions (CR1, CR2 and CR3) with the other two RAF genes: ARAF and RAF1. CR1, which has 131 aa, contains the cysteine-rich domain (CRD) and most of the Ras binding domain (RBD). These two domains bind to RAS-GTP. CR2, which has 16 aa, is rich in serine and threonine residues, including S365 as an inhibitory phosphorylation site. Finally CR3, which has 293 aa and has the kinase domain, contains also the G-loop GXGXXG motif (highly conserved in most of the human kinases), the activation segment and the regulatory phosphorylation sites S446, S447, D448, D449, T599 and S602.

Mutations

Note Single nucleotide polymorphism (SNP) found in BRAF: A1023G (P341P); A1227G (S409S); A1383G (Q461Q); A1797C (T599T); A1929G (G643G); G2272A (G758R).
Germinal No germinal mutations described.
Somatic BRAF presents somatic mutations in different sort of tumors, predominantly in malignant melanoma, sporadic colorectal tumors showing mismatch repair defects in microsatellites (MSI), low-grade ovarian serous carcinoma and thyroid papillary cancer. 80% of these mutations correspond to the hotspot transversion mutation T1799A that causes the amino acidic substitution V600E. The other 20% accounts for a wide variable range of missense mutations and all of them reside in the glycines of the G-loop in the exon 11 or in the activation segment in exon 15 near the V600. The mutation V600E confers transformant activity to the cells because it mimics the phosphorylation of T599 and/or S602 in the activation segment and so BRAF rests constitutively active in a RAS independent manner. Mutations in or NRAS are not concomitant with the BRAF mutation V600E. This mutation has not been found in other tumors like gastric cancer, endometrial cancer, uveal melanoma, biliary tract cancer or hepatocellular carcinoma..

Implicated in

Entity Melanoma
Note BRAF is mutated in 70% of malignant melanomas. The mutation V600E is an early event and alone is insufficient for the development of melanoma as it is present in 80% of primary melanomas and 80% of nevi, which are the first lesions associated with this tumor. No BRAF mutations are associated with uveal melanoma.
 
Diagram with BRAF mutations found in melanoma. The black arrows indicate the mutations. The mutations inside a box are in the same amino acid. The hotspot mutation V600E is in red. Numbers inside the blue boxes indicate the exon from which is translated each part of the protein. The three boxes inside represent the conserved regions of the protein with the ARAF and RAF-1 genes (CR1, CR2 and CR3). A conserved glycine motif (G-loop) in exon 11 is indicated with a red bar and the activation segment (AS) in exon 15 with a pink bar. C: Carboxyl-terminal; N: Amino-terminal.
  
Entity Colorectal cancer
Note BRAF mutation V600E is associated with mismatch repair deficiency (MSI) and found in 40% of the cases while in mismatch repair proficient tumors (MSS) the frequency is around 5%. Gastric and endometrial MSI and MSS tumors do not have BRAF mutations. In sporadic MSI colon cases this mutation is found in proximal colon tumors with MLH1 methylation (80% of cases), while in tumors from the hereditary nonpolyposis colorectal cancer (HNPCC), either with MLH1, MSH2 or MSH6 germline mutations or none, no BRAF mutations are detected. Because of this it has been proposed the use of the BRAF V600E mutation for HNPCC diagnostic as a exclusion criteria for germline mutation in mismatch repair genes.
Prognosis Even though its association with sporadic MSI suggest BRAF as a good prognosis factor, it has been also associated to metastatic colorectal MSS cancers. In this cases, BRAF associates with poor prognosis.
 
Diagram with BRAF mutations found in colorectal cancer. The black arrows indicate the mutations. The mutations inside a box are in the same amino acid. The hotspot mutation V600E is in red. Numbers inside the blue boxes indicate the exon from which is translated each part of the protein. The three boxes inside represent the conserved regions of the protein with the ARAF and RAF-1 genes (CR1, CR2 and CR3). A conserved glycine motif (G-loop) in exon 11 is indicated with a red bar and the activation segment (AS) in exon 15 with a pink bar. C: Carboxyl-terminal; N: Amino-terminal.
  
Entity Ovarian cancer
Note The only BRAF mutation is V600E which is found in 30% of low-grade serous carcinoma and borderline tumors. The mutation seems to occur very early in the development. High-grade tumors do not show BRAF mutations.
  
Entity Thyroid cancer
Note In thyroid papillary cancer the only BRAF mutation present is V600E with a frequency around 50%. The K601E mutation has also been found in some cases of the follicular variant of thyroid cancer.
  
Entity cell lines
 
Mutations of BRAF in cell lines from colorectal cancer, gastric cancer, endometrial cancer, melanoma and thyroid cancer. It is indicated the MSI status and KRAS mutations in the colorectal, gastric and endometrial cell lines. NRAS mutations are indicated in melanoma and thyroid cell lines.
  

Other Solid tumors implicated (Data extracted from papers in the Atlas)

Solid Tumors AmeloblastomID5945 MedulloblastomaID5065 rhab5004

External links

Nomenclature
HGNC (Hugo)BRAF   1097
Cards
AtlasBRAFID828
Entrez_Gene (NCBI)BRAF  673  B-Raf proto-oncogene, serine/threonine kinase
GeneCards (Weizmann)BRAF
Ensembl (Hinxton)ENSG00000157764 [Gene_View]  chr7:140433813-140624564 [Contig_View]  BRAF [Vega]
ICGC DataPortalENSG00000157764
cBioPortalBRAF
AceView (NCBI)BRAF
Genatlas (Paris)BRAF
WikiGenes673
SOURCE (Princeton)NM_004333
Genomic and cartography
GoldenPath (UCSC)BRAF  -  7q34   chr7:140433813-140624564 -  7q34   [Description]    (hg19-Feb_2009)
EnsemblBRAF - 7q34 [CytoView]
Mapping of homologs : NCBIBRAF [Mapview]
OMIM115150   164757   211980   613706   613707   
Gene and transcription
Genbank (Entrez)AA252358 AA834931 AI203435 AK054801 AK094023
RefSeq transcript (Entrez)NM_004333
RefSeq genomic (Entrez)AC_000139 NC_000007 NC_018918 NG_007873 NT_007933 NW_001839073 NW_004929333
Consensus coding sequences : CCDS (NCBI)BRAF
Cluster EST : UnigeneHs.659507 [ NCBI ]
CGAP (NCI)Hs.659507
Alternative Splicing : Fast-db (Paris)GSHG0028642
Alternative Splicing GalleryENSG00000157764
Gene ExpressionBRAF [ NCBI-GEO ]     BRAF [ SEEK ]   BRAF [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP15056 (Uniprot)
NextProtP15056  [Medical]
With graphics : InterProP15056
Splice isoforms : SwissVarP15056 (Swissvar)
Catalytic activity : Enzyme2.7.11.1 [ Enzyme-Expasy ]   2.7.11.12.7.11.1 [ IntEnz-EBI ]   2.7.11.1 [ BRENDA ]   2.7.11.1 [ KEGG ]   
Domaine pattern : Prosite (Expaxy)PROTEIN_KINASE_ATP (PS00107)    PROTEIN_KINASE_DOM (PS50011)    PROTEIN_KINASE_ST (PS00108)    RBD (PS50898)    ZF_DAG_PE_1 (PS00479)    ZF_DAG_PE_2 (PS50081)   
Domains : Interpro (EBI)DAG/PE-bd [organisation]   Kinase-like_dom [organisation]   Prot_Kinase_C-like_PE/DAG-bd [organisation]   Prot_kinase_dom [organisation]   Protein_kinase_ATP_BS [organisation]   Raf-like_ras-bd [organisation]   Ser-Thr/Tyr_kinase_cat_dom [organisation]   Ser/Thr_kinase_AS [organisation]   Ubiquitin-rel_dom [organisation]  
Related proteins : CluSTrP15056
Domain families : Pfam (Sanger)C1_1 (PF00130)    Pkinase_Tyr (PF07714)    RBD (PF02196)   
Domain families : Pfam (NCBI)pfam00130    pfam07714    pfam02196   
Domain families : Smart (EMBL)C1 (SM00109)  RBD (SM00455)  
DMDM Disease mutations673
Blocks (Seattle)P15056
PDB (SRS)1UWH    1UWJ    2FB8    2L05    3C4C    3D4Q    3IDP    3II5    3NY5    3OG7    3PPJ    3PPK    3PRF    3PRI    3PSB    3PSD    3Q4C    3Q96    3SKC    3TV4    3TV6    4DBN    4E26    4E4X    4EHE    4EHG    4FC0    4FK3    4G9C    4G9R    4H58    4JVG    4KSP    4KSQ    4MBJ    4PP7   
PDB (PDBSum)1UWH    1UWJ    2FB8    2L05    3C4C    3D4Q    3IDP    3II5    3NY5    3OG7    3PPJ    3PPK    3PRF    3PRI    3PSB    3PSD    3Q4C    3Q96    3SKC    3TV4    3TV6    4DBN    4E26    4E4X    4EHE    4EHG    4FC0    4FK3    4G9C    4G9R    4H58    4JVG    4KSP    4KSQ    4MBJ    4PP7   
PDB (IMB)1UWH    1UWJ    2FB8    2L05    3C4C    3D4Q    3IDP    3II5    3NY5    3OG7    3PPJ    3PPK    3PRF    3PRI    3PSB    3PSD    3Q4C    3Q96    3SKC    3TV4    3TV6    4DBN    4E26    4E4X    4EHE    4EHG    4FC0    4FK3    4G9C    4G9R    4H58    4JVG    4KSP    4KSQ    4MBJ    4PP7   
PDB (RSDB)1UWH    1UWJ    2FB8    2L05    3C4C    3D4Q    3IDP    3II5    3NY5    3OG7    3PPJ    3PPK    3PRF    3PRI    3PSB    3PSD    3Q4C    3Q96    3SKC    3TV4    3TV6    4DBN    4E26    4E4X    4EHE    4EHG    4FC0    4FK3    4G9C    4G9R    4H58    4JVG    4KSP    4KSQ    4MBJ    4PP7   
Human Protein AtlasENSG00000157764 [gene] [tissue] [antibody] [cell] [cancer]
Peptide AtlasP15056
HPRD01264
IPIIPI00303797   IPI00976947   IPI00945692   IPI00945505   IPI00946013   
Protein Interaction databases
DIP (DOE-UCLA)P15056
IntAct (EBI)P15056
FunCoupENSG00000157764
BioGRIDBRAF
InParanoidP15056
Interologous Interaction database P15056
IntegromeDBBRAF
STRING (EMBL)BRAF
Ontologies - Pathways
Ontology : AmiGOMAPK cascade  activation of MAPKK activity  protein kinase activity  protein serine/threonine kinase activity  MAP kinase kinase kinase activity  calcium ion binding  protein binding  ATP binding  nucleus  cytosol  plasma membrane  protein phosphorylation  small GTPase mediated signal transduction  synaptic transmission  fibroblast growth factor receptor signaling pathway  organ morphogenesis  positive regulation of gene expression  small GTPase binding  mitogen-activated protein kinase kinase binding  positive regulation of peptidyl-serine phosphorylation  identical protein binding  neuron projection  negative regulation of apoptotic process  response to peptide hormone  negative regulation of neuron apoptotic process  protein heterodimerization activity  neurotrophin TRK receptor signaling pathway  protein heterooligomerization  response to cAMP  positive regulation of ERK1 and ERK2 cascade  response to epidermal growth factor  cellular response to calcium ion  
Ontology : EGO-EBIMAPK cascade  activation of MAPKK activity  protein kinase activity  protein serine/threonine kinase activity  MAP kinase kinase kinase activity  calcium ion binding  protein binding  ATP binding  nucleus  cytosol  plasma membrane  protein phosphorylation  small GTPase mediated signal transduction  synaptic transmission  fibroblast growth factor receptor signaling pathway  organ morphogenesis  positive regulation of gene expression  small GTPase binding  mitogen-activated protein kinase kinase binding  positive regulation of peptidyl-serine phosphorylation  identical protein binding  neuron projection  negative regulation of apoptotic process  response to peptide hormone  negative regulation of neuron apoptotic process  protein heterodimerization activity  neurotrophin TRK receptor signaling pathway  protein heterooligomerization  response to cAMP  positive regulation of ERK1 and ERK2 cascade  response to epidermal growth factor  cellular response to calcium ion  
Pathways : KEGGMAPK signaling pathway    ErbB signaling pathway    Rap1 signaling pathway    Chemokine signaling pathway    FoxO signaling pathway    mTOR signaling pathway    Vascular smooth muscle contraction    Focal adhesion    Natural killer cell mediated cytotoxicity    Long-term potentiation    Neurotrophin signaling pathway    Serotonergic synapse    Long-term depression    Regulation of actin cytoskeleton    Insulin signaling pathway    Progesterone-mediated oocyte maturation    Alcoholism    Hepatitis C    Pathways in cancer    Proteoglycans in cancer    Colorectal cancer    Renal cell carcinoma    Pancreatic cancer    Endometrial cancer    Glioma    Prostate cancer    Thyroid cancer    Melanoma    Bladder cancer    Chronic myeloid leukemia    Acute myeloid leukemia    Non-small cell lung cancer   
Protein Interaction DatabaseBRAF
Wikipedia pathwaysBRAF
Gene fusion - rearrangments
Rearrangement : COSMICAGTRAP [1p36.22]  -  BRAF [7q34]  
  [COSF828] [COSF829] 
Rearrangement : COSMICAKAP9 [7q21.2]  -  BRAF [7q34]  
  [COSF1013] [COSF1014] [COSF1017] 
Rearrangement : COSMICBRAF [7q34]  -  AKAP9 [7q21.2]  
  [COSF1015] [COSF1016] 
Rearrangement : COSMICCLCN6 [1p36.22]  -  BRAF [7q34]  
  [COSF1440] [COSF1441] 
Rearrangement : COSMICFAM131B [7q34]  -  BRAF [7q34]  
  [COSF1189] [COSF1190] [COSF1191] [COSF1192] [COSF1193] [COSF1194] [COSF1611] 
Rearrangement : COSMICFCHSD1 [5q31.3]  -  BRAF [7q34]  
  [COSF403] [COSF404] 
Rearrangement : COSMICGNAI1 [7q21.11]  -  BRAF [7q34]  
  [COSF1442] [COSF1443] 
Rearrangement : COSMICKIAA1549 [7q34]  -  BRAF [7q34]  
  [COSF1226] [COSF1227] [COSF1228] [COSF1229] [COSF1283] [COSF1284] [COSF1471] [COSF1472] [COSF1474] 
  [COSF1475] [COSF1476] [COSF1477] [COSF481] [COSF482] [COSF483] [COSF484] [COSF485] 
  [COSF486] [COSF509] [COSF510] [COSF511] [COSF512] [COSF588] 
Rearrangement : COSMICMKRN1 [7q34]  -  BRAF [7q34]  
  [COSF1444] [COSF1445] 
Rearrangement : COSMICRNF130 [5q35.3]  -  BRAF [7q34]  
  [COSF1483] [COSF1484] 
Rearrangement : COSMICSLC45A3 [1q32.1]  -  BRAF [7q34]  
  [COSF871] [COSF872] 
Rearrangement : TICdbFCHSD1 [5q31.3]  -  BRAF [5q32]
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)BRAF
snp3D : Map Gene to Disease673
SNP (GeneSNP Utah)BRAF
SNP : HGBaseBRAF
Genetic variants : HAPMAPBRAF
Exome VariantBRAF
1000_GenomesBRAF 
ICGC programENSG00000157764 
Cancer Gene: CensusBRAF 
Somatic Mutations in Cancer : COSMICBRAF 
CONAN: Copy Number AnalysisBRAF 
Mutations and Diseases : HGMDBRAF
Mutations and Diseases : intOGenBRAF
Genomic VariantsBRAF  BRAF [DGVbeta]
dbVarBRAF
ClinVarBRAF
Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
Diseases
OMIM115150    164757    211980    613706    613707   
MedgenBRAF
GENETestsBRAF
Disease Genetic AssociationBRAF
Huge Navigator BRAF [HugePedia]  BRAF [HugeCancerGEM]
General knowledge
Homologs : HomoloGeneBRAF
Homology/Alignments : Family Browser (UCSC)BRAF
Phylogenetic Trees/Animal Genes : TreeFamBRAF
Chemical/Protein Interactions : CTD673
Chemical/Pharm GKB GenePA25408
Drug Sensitivity BRAF
Clinical trialBRAF
Cancer Resource (Charite)ENSG00000157764
Other databases
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=BRAF
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
CoreMineBRAF
iHOPBRAF
OncoSearchBRAF

Bibliography

Mutations of the BRAF gene in human cancer.
Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA
Nature. 2002 ; 417 (6892) : 949-954.
PMID 12068308
 
BRAF mutation in papillary thyroid carcinoma.
Cohen Y, Xing M, Mambo E, Guo Z, Wu G, Trink B, Beller U, Westra WH, Ladenson PW, Sidransky D
Journal of the National Cancer Institute. 2003 ; 95 (8) : 625-627.
PMID 12697856
 
Raf proteins and cancer: B-Raf is identified as a mutational target.
Mercer KE, Pritchard CA
Biochimica et biophysica acta. 2003 ; 1653 (1) : 25-40.
PMID 12781369
 
BRAF mutations characterize colon but not gastric cancer with mismatch repair deficiency.
Oliveira C, Pinto M, Duval A, Brennetot C, Domingo E, Espˆ‚n E, Armengol M, Yamamoto H, Hamelin R, Seruca R, Schwartz S Jr
Oncogene. 2003 ; 22 (57) : 9192-9196.
PMID 14668801
 
High frequency of BRAF mutations in nevi.
Pollock PM, Harper UL, Hansen KS, Yudt LM, Stark M, Robbins CM, Moses TY, Hostetter G, Wagner U, Kakareka J, Salem G, Pohida T, Heenan P, Duray P, Kallioniemi O, Hayward NK, Trent JM, Meltzer PS
Nature genetics. 2003 ; 33 (1) : 19-20.
PMID 12447372
 
BRAF as a potential therapeutic target in melanoma and other malignancies.
Tuveson DA, Weber BL, Herlyn M
Cancer cell. 2003 ; 4 (2) : 95-98.
PMID 12957284
 
Activated BRAF targets proximal colon tumors with mismatch repair deficiency and MLH1 inactivation.
Domingo E, Espˆ‚n E, Armengol M, Oliveira C, Pinto M, Duval A, Brennetot C, Seruca R, Hamelin R, Yamamoto H, Schwartz S Jr
Genes, chromosomes & cancer. 2004 ; 39 (2) : 138-142.
PMID 14695993
 
BRAF screening as a low-cost effective strategy for simplifying HNPCC genetic testing.
Domingo E, Laiho P, Ollikainen M, Pinto M, Wang L, French AJ, Westra J, Frebourg T, Espˆ‚n E, Armengol M, Hamelin R, Yamamoto H, Hofstra RM, Seruca R, Lindblom A, Peltomˆ§ki P, Thibodeau SN, Aaltonen LA, Schwartz S Jr
Journal of medical genetics. 2004 ; 41 (9) : 664-668.
PMID 15342696
 
Ovarian tumorigenesis: a proposed model based on morphological and molecular genetic analysis.
Shih IeM, Kurman RJ
The American journal of pathology. 2004 ; 164 (5) : 1511-1518.
PMID 15111296
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written09-2004Enric Domingo, Simo Schwartz Jr
Oncologia Molecular i Envelliment, Centre d'Investigacions en Bioquímica i Biologia Molecular (CIBBIM) Hospital Universitari Vall d'Hebron Passeig Vall d'Hebron 119-129 Barcelona 08035, Catalonia, Spain

Citation

This paper should be referenced as such :
Domingo, E ; Schwartz, S Jr
BRAF (v-raf murine sarcoma viral oncogene homolog B1
Atlas Genet Cytogenet Oncol Haematol. 2004;8(4):294-298.
Free online version   Free pdf version   [Bibliographic record ]
URL : http://AtlasGeneticsOncology.org/Genes/BRAFID828.html

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indexed on : Sat Oct 4 12:50:23 CEST 2014

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