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BRWD3 (bromodomain and WD repeat domain containing 3)

Written2006-09Claudia Kalla
DKFZ, Div. Molecular Genetics (B060), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)FLJ38568
MRX93
Other aliasBRODL
HGNC (Hugo) BRWD3
LocusID (NCBI) 254065
Atlas_Id 42978
Location Xq21.1  [Link to chromosome band Xq21]
Location_base_pair Starts at 80669488 and ends at 80809734 bp from pter ( according to hg19-Feb_2009)  [Mapping BRWD3.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ARHGAP20 (11q23.1) / BRWD3 (Xq21.1)BRWD3 (Xq21.1) / ARHGAP20 (11q23.1)BRWD3 (Xq21.1) / HMGN5 (Xq21.1)

DNA/RNA

 
  Genomic organization (A) and transcript variants (B) of BRWD3. (A) Gene structure (drawn to scale): black boxes represent exons. (B) Transcripts (drawn to scale): boxes, exons; UTR, untranslated region; light shaded box, coding region; shaded and dark shaded boxes, nucleotide sequences coding for protein domains (WD40: WD40 tandem repeats; BROMO: bromodomain). For transcript variants BRWD3-C to BRWD3-P only the largest possible coding regions are indicated, though translation of different short proteins by using the start sites of BRWD3-A and BRWD3-B might also be possible.
Description 44 exons spanning 132.7 kb genomic DNA
Transcription 5.6-6.2 kb mRNA, coding sequence: 4.2-5.4 kb
Alternative splicing results in the expression of at least 15 transcript variants (BRWD3-A to BRWD3-P): The two most abundant transcript variants A and B are the result of alternative splicing of the first four exons (BRWD3-A contains exons 1 to 4, whereas BRWD3-B starts with an extended version of exon 4). BRWD3-C to BRWD3-P represent alternatively spliced variants of A and B, which contain additional exons 6a, 6b, and/or 12a and lack exons 3, 5, 6, 7, 8, and/or 9.
Pseudogene None.

Protein

 
  Schematic representation of protein variants BRWD3-A and BRWD3-B as deduced from the transcripts. WD40: WD40 tandem repeats; BROMO: bromodomain. Translation initiation in exons 11 and 13 of transcripts BRWD3-C to BRWD3-P produces proteins, which retain four and three of the eight WD40 repeats, respectively.
Description The amino-terminal region consists of eight tandem WD40 repeats, which had been identified as the structural determinant of the beta -subunit of the G-proteins that mediateting transmembrane signal transduction. The carboxy terminus is predicted to contain two bromodomains with the potential to mediate protein-protein interactions in DNA-binding proteins. BRWD3-C to BRWD3-P are amino-terminally truncated versions of BRWD3-A and BRWD3-B, which retain three or four of the eight WD40 repeats and both bromodomains.
Expression Expressed in a variety of adult tissues (lymphocytes, brain, heart, kidney, placenta) and in fetal liver.
Function By performing a systematic genomewide survey for genes required for JAK/STAT pathway activity (involved in cell proliferation and haematopoiesis), the Drosophila homologon of BRWD3 was isolated as a member of the JAK/STAT signalling cascade acting downstream of JAK. In vivo analysis demonstrated that disrupted Drosophila BRWD3 functions as a suppressor of leukemia-like blood cell tumors.
Homology Drosophila melanogaster: BRWD3
Mouse: Brwd3
Pan troglodytes: BRWD3

Implicated in

Note
  
Entity t(X;11)(q21;q23)
Note In the tumour cells of one case of B-cell chronic lymphocytic leukemia (B-CLL), BRWD3 was affected by a translocation that rearranged the gene with ARHGAP20 (11q23). No fusion transcripts were generated. BRWD3 transcript expression is downregulated in B-CLL lymphocytes vs. CD19+ control B cells.
Disease B-cell chronic lymphocytic leukemia
Cytogenetics t(X;11)(q21;q23)
Hybrid/Mutated Gene ARHGAP20 - BRWD3
Abnormal Protein None detected.
  

Bibliography

Translocation t(X;11)(q13;q23) in B-cell chronic lymphocytic leukemia disrupts two novel genes.
Kalla C, Nentwich H, Schlotter M, Mertens D, Wildenberger K, Döhner H, Stilgenbauer S, Lichter P
Genes, chromosomes & cancer. 2005 ; 42 (2) : 128-143.
PMID 15543602
 
Identification of JAK/STAT signalling components by genome-wide RNA interference.
Müller P, Kuttenkeuler D, Gesellchen V, Zeidler MP, Boutros M
Nature. 2005 ; 436 (7052) : 871-875.
PMID 16094372
 

Citation

This paper should be referenced as such :
Kalla, C
BRWD3 (bromodomain, WD repeat domain containing 3)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(1):10-11.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/BRWD3ID42978chXq21.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(X;11)(q13;q23) KMT2A/FOXO4
t(X;11)(q21;q23) BRWD3/ARHGAP20


External links

Nomenclature
HGNC (Hugo)BRWD3   17342
Cards
AtlasBRWD3ID42978chXq21
Entrez_Gene (NCBI)BRWD3  254065  bromodomain and WD repeat domain containing 3
AliasesBRODL; MRX93
GeneCards (Weizmann)BRWD3
Ensembl hg19 (Hinxton)ENSG00000165288 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000165288 [Gene_View]  chrX:80669488-80809734 [Contig_View]  BRWD3 [Vega]
ICGC DataPortalENSG00000165288
TCGA cBioPortalBRWD3
AceView (NCBI)BRWD3
Genatlas (Paris)BRWD3
WikiGenes254065
SOURCE (Princeton)BRWD3
Genetics Home Reference (NIH)BRWD3
Genomic and cartography
GoldenPath hg38 (UCSC)BRWD3  -     chrX:80669488-80809734 -  Xq21.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)BRWD3  -     Xq21.1   [Description]    (hg19-Feb_2009)
EnsemblBRWD3 - Xq21.1 [CytoView hg19]  BRWD3 - Xq21.1 [CytoView hg38]
Mapping of homologs : NCBIBRWD3 [Mapview hg19]  BRWD3 [Mapview hg38]
OMIM300553   300659   
Gene and transcription
Genbank (Entrez)AA716141 AK090573 AK095887 AY497046 AY497047
RefSeq transcript (Entrez)NM_153252
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)BRWD3
Cluster EST : UnigeneHs.613180 [ NCBI ]
CGAP (NCI)Hs.613180
Alternative Splicing GalleryENSG00000165288
Gene ExpressionBRWD3 [ NCBI-GEO ]   BRWD3 [ EBI - ARRAY_EXPRESS ]   BRWD3 [ SEEK ]   BRWD3 [ MEM ]
Gene Expression Viewer (FireBrowse)BRWD3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)254065
GTEX Portal (Tissue expression)BRWD3
Human Protein AtlasENSG00000165288-BRWD3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ6RI45   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ6RI45  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ6RI45
Splice isoforms : SwissVarQ6RI45
PhosPhoSitePlusQ6RI45
Domaine pattern : Prosite (Expaxy)BROMODOMAIN_2 (PS50014)    WD_REPEATS_1 (PS00678)    WD_REPEATS_2 (PS50082)    WD_REPEATS_REGION (PS50294)   
Domains : Interpro (EBI)Bromodomain    WD40/YVTN_repeat-like_dom    WD40_repeat    WD40_repeat_CS    WD40_repeat_dom   
Domain families : Pfam (Sanger)Bromodomain (PF00439)    WD40 (PF00400)   
Domain families : Pfam (NCBI)pfam00439    pfam00400   
Domain families : Smart (EMBL)BROMO (SM00297)  WD40 (SM00320)  
Conserved Domain (NCBI)BRWD3
DMDM Disease mutations254065
Blocks (Seattle)BRWD3
SuperfamilyQ6RI45
Human Protein Atlas [tissue]ENSG00000165288-BRWD3 [tissue]
Peptide AtlasQ6RI45
HPRD06564
IPIIPI00167547   IPI00844349   IPI00843754   IPI00844236   IPI00844073   
Protein Interaction databases
DIP (DOE-UCLA)Q6RI45
IntAct (EBI)Q6RI45
FunCoupENSG00000165288
BioGRIDBRWD3
STRING (EMBL)BRWD3
ZODIACBRWD3
Ontologies - Pathways
QuickGOQ6RI45
Ontology : AmiGOnucleus  regulation of transcription from RNA polymerase II promoter  cytoskeleton organization  regulation of cell shape  
Ontology : EGO-EBInucleus  regulation of transcription from RNA polymerase II promoter  cytoskeleton organization  regulation of cell shape  
NDEx NetworkBRWD3
Atlas of Cancer Signalling NetworkBRWD3
Wikipedia pathwaysBRWD3
Orthology - Evolution
OrthoDB254065
GeneTree (enSembl)ENSG00000165288
Phylogenetic Trees/Animal Genes : TreeFamBRWD3
HOVERGENQ6RI45
HOGENOMQ6RI45
Homologs : HomoloGeneBRWD3
Homology/Alignments : Family Browser (UCSC)BRWD3
Gene fusions - Rearrangements
Tumor Fusion PortalBRWD3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerBRWD3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)BRWD3
dbVarBRWD3
ClinVarBRWD3
1000_GenomesBRWD3 
Exome Variant ServerBRWD3
ExAC (Exome Aggregation Consortium)ENSG00000165288
GNOMAD BrowserENSG00000165288
Genetic variants : HAPMAP254065
Genomic Variants (DGV)BRWD3 [DGVbeta]
DECIPHERBRWD3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisBRWD3 
Mutations
ICGC Data PortalBRWD3 
TCGA Data PortalBRWD3 
Broad Tumor PortalBRWD3
OASIS PortalBRWD3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICBRWD3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDBRWD3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)X-chromosome gene database
BioMutasearch BRWD3
DgiDB (Drug Gene Interaction Database)BRWD3
DoCM (Curated mutations)BRWD3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)BRWD3 (select a term)
intoGenBRWD3
NCG5 (London)BRWD3
Cancer3DBRWD3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300553    300659   
Orphanet
DisGeNETBRWD3
MedgenBRWD3
Genetic Testing Registry BRWD3
NextProtQ6RI45 [Medical]
TSGene254065
GENETestsBRWD3
Target ValidationBRWD3
Huge Navigator BRWD3 [HugePedia]
snp3D : Map Gene to Disease254065
BioCentury BCIQBRWD3
ClinGenBRWD3 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD254065
Chemical/Pharm GKB GenePA134900775
Clinical trialBRWD3
Miscellaneous
canSAR (ICR)BRWD3 (select the gene name)
Probes
Litterature
PubMed16 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineBRWD3
EVEXBRWD3
GoPubMedBRWD3
iHOPBRWD3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:45:35 CET 2017

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