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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

<D>BRWD3
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]
GenevisibleExpression 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 (PS5024)   
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
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerBRWD3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)BRWD3
dbVar
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
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$Entrgz,/b>
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 : Thu Oct 12 16:17:38 CEST 2017

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