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RANBP9 (RAN binding protein 9)

Written2012-03Kwang-Hyun Baek, Bharathi Suresh
CHA Stem Cell Institute, CHA University, 606-16 Yeoksam 1-Dong, Gangnam-Gu, Seoul 135-081, Korea (KHB); Department of Biomedical Science, CHA University, CHA General Hospital, Seoul 135-081, Republic of Korea (BS)

(Note : for Links provided by Atlas : click)


HGNC Alias symbRanBPM
HGNC Alias nameRan Binding Protein in the Microtubule organizing center
LocusID (NCBI) 10048
Atlas_Id 42040
Location 6p23  [Link to chromosome band 6p23]
Location_base_pair Starts at 13621498 and ends at 13711835 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping RANBP9.png]
Local_order It is located on Chromosome 6.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
RANBP9 (6p23) / ATXN1 (6p22.3)RANBP9 (6p23) / BLOC1S5 (6p24.3)RANBP9 (6p23) / CDKAL1 (6p22.3)
RANBP9 (6p23) / RANBP9 (6p23)RANBP9 (6p23) / TPMT (6p22.3)RANBP9 (6p23) / TXNDC5 (6p24.3)
SERHL (22q13.2) / RANBP9 (6p23)


Description Constists of 14 exons.
Transcription The coding region of the gene starts from exon 1 to exon 14 (60th bps to 2249th bps). The length of the transcript is 2190 bps.
Pseudogene No known pseudogenes.


Description RanBPM was originally identified as a centrosomal 55 kDa protein and is involved in microtubule nucleation at the centrosome (Nakamura et al., 1998). A later work by the same group revealed that the full-length RanBPM encodes for 729 amino acids and its molecular weight is 90 kDa (Nishitani et al., 2001).
RanBPM protein contains multiple conserved domains which provide potential protein-protein interaction sites such as an N-terminus proline rich domain (PRD), a splA and Ryr (SPRY) domain (212-333 aa), a lissencephaly type-I-like homology (LisH) motif (365-397 aa), a carboxy terminal to LisH (CTLH) motif (403-460 aa), and a CT11-RanBPM (CRA) motif (615-717 aa) at the C terminus of RanBPM (Murrin and Talbot, 2007). These domains play a significant role in interaction of RanBPM with a wide range of transmembrane and intracellular proteins.
Expression RanBPM is ubiquitously expressed in human and murine cell lines and tissues of kidney, uterus, ovary, bladder, spleen, thymus, brain, skeletal muscle, lung, prostate, testes, small intestine, colon and peripheral blood lymphocytes (Rao et al., 2002; Wang et al., 2002). In contrast, reduced expression was observed in cancer cells and in several human tumor tissues.
Localisation RanBPM is localized in the nucleus, cytoplasm, plasma membrane and cell juctions (Nishitani et al., 2001; Umeda et al., 2003; Denti et al., 2004; Chang et al., 2010).
Function The direct binding of RanBPM with p73α, results in the nuclear translocation of cytoplasmic RanBPM. RanBPM is involved in the stabilization of p73 protein by preventing its degradation through the ubiquitin-proteasomal pathway and increases its proapoptotic function (Kramer et al., 2005). Expression of RanBPM augments T-type Ca2+ currents in HEK293/Cav3.1 cells (Kim et al., 2009). RanBPM was found to abolish the inhibitory effect of PKC on Cav3.1 currents, suggesting a key role of RanBPM in Cav3.1 channel-mediated signaling pathways. RanBPM interacts with brain-specific protein p42IP4, and modulates the p42IP4 function to regulate synaptic plasticity, actin cytoskeleton remodeling and mitogen-activated protein kinase cascade (Haase et al., 2008).
RanBPM also exhibits negative regulation. It binds with Mu opioid receptor (MOP), and inhibits the agonist-induced receptor internalization without altering MOP signaling through adenylyl cyclase, suggesting the regulatory effect of RanBPM on MOP activity in mammalian cells (Talbot et al., 2009). CD39, a prototypic member of the NTPDase family, forms a complex with RanBPM (Wu et al., 2006). This association substantially down-regulates the NTPDase activity of CD39.
RanBPM also acts as a ligand for the Rho-GEF domain (Bowman et al., 2008). RanBPM along with Rho-GEF domain of obscurin regulates the assembly of titin during the formation of the Z-disk and A/I junction, showing a vital role of RanBPM in myofibrillogenesis.
RanBPM stimulates the transcriptional activity of different proteins. RanBPM interacts with androgen receptor (AR) (Rao et al., 2002). AR belongs to a large steroid receptor family which also includes glucocorticoid (GR), progesterone, and mineralocorticoid receptors. RanBPM was found to enhance AR transactivation in a ligand-dependent fashion. Similar results were observed with GR activity, whereas the estrogen receptor activity remains unaffected. Furthermore, RanBPM was found to enhance the activity of thyroid hormone receptors (TRs), a member of nuclear receptor superfamily in a ligand-independent manner (Poirier et al., 2006), which confirms the selective action of RanBPM on receptors activity.
Expression of RanBPM influences the activity of Rta, which activates the transcription of Epstein-Barr virus (EBV) lytic genes and the lytic cycle, indicating a new role of RanBPM as a viral protein regulator. Sumoylation of Rta enhances its activity to complete the EBV lytic development in an efficient way (Chang et al., 2008). RanBPM promotes Rta sumoylation by interacting with Ubc9, which states the participation of RanBPM in EBV lytic activation.
RanBPM interacts with several proteins which are involved in neurological function. By interacting with PlexinA receptor, RanBPM mediates Semaphorin 3A signaling which is involved in axonal growth (Togashi et al., 2006). It also interacts with calbindin D28K (Lutz et al., 2003) and TAF4 to regulate neuritogenesis in neural stem cells (Brunkhorst et al., 2005). Expression of RanBPM in primary neurons decreased L1-dependent neurite outgrowth and extension (Cheng et al., 2005). RanBPM showed high expression in the Kenyon cells of the larval mushroom body (MB), and its expression is sufficient to rescue all behavioral phenotypes (Scantlebury et al., 2010). By performing genetic epistasis experiments, authors observed the participation of RanBPM with the FMRP (Fragile X Mental Retardation Protein) in the development of neuromuscular junction. Citron kinase (CITK) plays an important role in neurogenic mitoses. RanBPM potentially interacts with CITK and plays a novel role in the progression of neocortical precursors through M-phase at the ventricular surface (Chang et al., 2010).
Homology Human RanBPM shows 90% nucleotide homology with mouse RanBPM.

Implicated in

Entity Various cancers
Note RanBPM binds to and modulates the function of a wide range of proteins. RanBPM interacts with oncoprotein Mgl-1 (Suresh et al., 2010) in mammalian cultured cells and modulates stability of Mgl-1 and functionally extends the half-life of Mgl-1 by preventing its protein turnover through the ubiquitin-proteasomal pathway. Furthermore, the overexpression of RanBPM inhibits the activity of Mgl-1 both in cell migration and colony formation assays, which reveal the novel role of RanBPM as an activator of tumor suppressor.


The rho-guanine nucleotide exchange factor domain of obscurin regulates assembly of titin at the Z-disk through interactions with Ran binding protein 9.
Bowman AL, Catino DH, Strong JC, Randall WR, Kontrogianni-Konstantopoulos A, Bloch RJ.
Mol Biol Cell. 2008 Sep;19(9):3782-92. Epub 2008 Jun 25.
PMID 18579686
Enhancement of transactivation activity of Rta of Epstein-Barr virus by RanBPM.
Chang LK, Liu ST, Kuo CW, Wang WH, Chuang JY, Bianchi E, Hong YR.
J Mol Biol. 2008 May 30;379(2):231-42. Epub 2008 Apr 10.
PMID 18455188
RanBPM regulates the progression of neuronal precursors through M-phase at the surface of the neocortical ventricular zone.
Chang Y, Paramasivam M, Girgenti MJ, Walikonis RS, Bianchi E, LoTurco JJ.
Dev Neurobiol. 2010 Jan;70(1):1-15.
PMID 19790105
RanBPM is an L1-interacting protein that regulates L1-mediated mitogen-activated protein kinase activation.
Cheng L, Lemmon S, Lemmon V.
J Neurochem. 2005 Aug;94(4):1102-10. Epub 2005 Jul 5.
PMID 16000162
RanBPM is a phosphoprotein that associates with the plasma membrane and interacts with the integrin LFA-1.
Denti S, Sirri A, Cheli A, Rogge L, Innamorati G, Putignano S, Fabbri M, Pardi R, Bianchi E.
J Biol Chem. 2004 Mar 26;279(13):13027-34. Epub 2004 Jan 13.
PMID 14722085
RanBPM, a novel interaction partner of the brain-specific protein p42IP4/centaurin alpha-1.
Haase A, Nordmann C, Sedehizade F, Borrmann C, Reiser G.
J Neurochem. 2008 Jun 1;105(6):2237-48.
PMID 18298663
Modulation of Ca(v)3.1 T-type Ca2+ channels by the ran binding protein RanBPM.
Kim T, Kim S, Yun HM, Chung KC, Han YS, Shin HS, Rhim H.
Biochem Biophys Res Commun. 2009 Jan 2;378(1):15-20. Epub 2008 Sep 16.
PMID 18801335
Protein stability and function of p73 are modulated by a physical interaction with RanBPM in mammalian cultured cells.
Kramer S, Ozaki T, Miyazaki K, Kato C, Hanamoto T, Nakagawara A.
Oncogene. 2005 Jan 27;24(5):938-44.
PMID 15558019
Calbindin D28K interacts with Ran-binding protein M: identification of interacting domains by NMR spectroscopy.
Lutz W, Frank EM, Craig TA, Thompson R, Venters RA, Kojetin D, Cavanagh J, Kumar R.
Biochem Biophys Res Commun. 2003 Apr 18;303(4):1186-92.
PMID 12684061
RanBPM, a scaffolding protein in the immune and nervous systems.
Murrin LC, Talbot JN.
J Neuroimmune Pharmacol. 2007 Sep;2(3):290-5. Epub 2007 Jun 28. (REVIEW)
PMID 18040864
When overexpressed, a novel centrosomal protein, RanBPM, causes ectopic microtubule nucleation similar to gamma-tubulin.
Nakamura M, Masuda H, Horii J, Kuma K, Yokoyama N, Ohba T, Nishitani H, Miyata T, Tanaka M, Nishimoto T.
J Cell Biol. 1998 Nov 16;143(4):1041-52.
PMID 9817760
Full-sized RanBPM cDNA encodes a protein possessing a long stretch of proline and glutamine within the N-terminal region, comprising a large protein complex.
Nishitani H, Hirose E, Uchimura Y, Nakamura M, Umeda M, Nishii K, Mori N, Nishimoto T.
Gene. 2001 Jul 11;272(1-2):25-33.
PMID 11470507
Identification and characterization of RanBPM, a novel coactivator of thyroid hormone receptors.
Poirier MB, Laflamme L, Langlois MF.
J Mol Endocrinol. 2006 Apr;36(2):313-25.
PMID 16595702
RanBPM, a nuclear protein that interacts with and regulates transcriptional activity of androgen receptor and glucocorticoid receptor.
Rao MA, Cheng H, Quayle AN, Nishitani H, Nelson CC, Rennie PS.
J Biol Chem. 2002 Dec 13;277(50):48020-7. Epub 2002 Oct 1.
PMID 12361945
The Drosophila gene RanBPM functions in the mushroom body to regulate larval behavior.
Scantlebury N, Zhao XL, Rodriguez Moncalvo VG, Camiletti A, Zahanova S, Dineen A, Xin JH, Campos AR.
PLoS One. 2010 May 14;5(5):e10652.
PMID 20498842
Stability and function of mammalian lethal giant larvae-1 oncoprotein are regulated by the scaffolding protein RanBPM.
Suresh B, Ramakrishna S, Kim YS, Kim SM, Kim MS, Baek KH.
J Biol Chem. 2010 Nov 12;285(46):35340-9. Epub 2010 Sep 9.
PMID 20829363
Regulation of mu opioid receptor internalization by the scaffold protein RanBPM.
Talbot JN, Skifter DA, Bianchi E, Monaghan DT, Toews ML, Murrin LC.
Neurosci Lett. 2009 Dec 11;466(3):154-8. Epub 2009 Sep 27.
PMID 19788913
RanBPM contributes to Semaphorin3A signaling through plexin-A receptors.
Togashi H, Schmidt EF, Strittmatter SM.
J Neurosci. 2006 May 3;26(18):4961-9.
PMID 16672672
A novel nuclear protein, Twa1, and Muskelin comprise a complex with RanBPM.
Umeda M, Nishitani H, Nishimoto T.
Gene. 2003 Jan 16;303:47-54.
PMID 12559565
Activation of Ras/Erk pathway by a novel MET-interacting protein RanBPM.
Wang D, Li Z, Messing EM, Wu G.
J Biol Chem. 2002 Sep 27;277(39):36216-22. Epub 2002 Jul 29.
PMID 12147692
RanBPM associates with CD39 and modulates ecto-nucleotidase activity.
Wu Y, Sun X, Kaczmarek E, Dwyer KM, Bianchi E, Usheva A, Robson SC.
Biochem J. 2006 May 15;396(1):23-30.
PMID 16478441


This paper should be referenced as such :
Baek, KH ; Suresh, B
RANBP9 (RAN binding protein 9)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(8):549-551.
Free journal version : [ pdf ]   [ DOI ]

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 5 ]
  t(6;6)(p22;p23) RANBP9/ATXN1
t(6;6)(p22;p23) RANBP9/CDKAL1
t(6;6)(p22;p23) RANBP9/TPMT
t(6;6)(p23;p24) RANBP9/BLOC1S5
t(6;6)(p23;p24) RANBP9/TXNDC5

External links

HGNC (Hugo)RANBP9   13727
Entrez_Gene (NCBI)RANBP9    RAN binding protein 9
AliasesBPM-L; BPM90; RANBPM; RanBP7
GeneCards (Weizmann)RANBP9
Ensembl hg19 (Hinxton)ENSG00000010017 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000010017 [Gene_View]  ENSG00000010017 [Sequence]  chr6:13621498-13711835 [Contig_View]  RANBP9 [Vega]
ICGC DataPortalENSG00000010017
Genatlas (Paris)RANBP9
SOURCE (Princeton)RANBP9
Genetics Home Reference (NIH)RANBP9
Genomic and cartography
GoldenPath hg38 (UCSC)RANBP9  -     chr6:13621498-13711835 -  6p23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RANBP9  -     6p23   [Description]    (hg19-Feb_2009)
GoldenPathRANBP9 - 6p23 [CytoView hg19]  RANBP9 - 6p23 [CytoView hg38]
genome Data Viewer NCBIRANBP9 [Mapview hg19]  
Gene and transcription
Genbank (Entrez)AB008515 AB055311 AF064606 AF306510 AK313334
RefSeq transcript (Entrez)NM_005493
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RANBP9
Alternative Splicing GalleryENSG00000010017
Gene ExpressionRANBP9 [ NCBI-GEO ]   RANBP9 [ EBI - ARRAY_EXPRESS ]   RANBP9 [ SEEK ]   RANBP9 [ MEM ]
Gene Expression Viewer (FireBrowse)RANBP9 [ Firebrowse - Broad ]
GenevisibleExpression of RANBP9 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10048
GTEX Portal (Tissue expression)RANBP9
Human Protein AtlasENSG00000010017-RANBP9 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96S59   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96S59  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96S59
Splice isoforms : SwissVarQ96S59
Domaine pattern : Prosite (Expaxy)B302_SPRY (PS50188)    CTLH (PS50897)    LISH (PS50896)   
Domains : Interpro (EBI)B30.2/SPRY    ConA-like_dom_sf    CRA_dom    CTLH/CRA    CTLH_C    LisH    SPRY_dom    SPRY_RanBP9/10   
Domain families : Pfam (Sanger)CLTH (PF10607)    LisH (PF08513)    SPRY (PF00622)   
Domain families : Pfam (NCBI)pfam10607    pfam08513    pfam00622   
Domain families : Smart (EMBL)CRA (SM00757)  CTLH (SM00668)  LisH (SM00667)  SPRY (SM00449)  
Conserved Domain (NCBI)RANBP9
Blocks (Seattle)RANBP9
PDB (RSDB)5JI7    5JI9    5JIU   
PDB Europe5JI7    5JI9    5JIU   
PDB (PDBSum)5JI7    5JI9    5JIU   
PDB (IMB)5JI7    5JI9    5JIU   
Structural Biology KnowledgeBase5JI7    5JI9    5JIU   
SCOP (Structural Classification of Proteins)5JI7    5JI9    5JIU   
CATH (Classification of proteins structures)5JI7    5JI9    5JIU   
Human Protein Atlas [tissue]ENSG00000010017-RANBP9 [tissue]
Peptide AtlasQ96S59
IPIIPI00465275   IPI00554545   IPI00513912   
Protein Interaction databases
IntAct (EBI)Q96S59
Ontologies - Pathways
Ontology : AmiGOubiquitin ligase complex  MAPK cascade  protein binding  nucleus  cytoplasm  cytoplasm  cytosol  microtubule associated complex  plasma membrane  cytoskeleton organization  microtubule nucleation  cell surface receptor signaling pathway  axon guidance  Ran GTPase binding  Ran GTPase binding  enzyme binding  protein-containing complex assembly  negative regulation of ERK1 and ERK2 cascade  
Ontology : EGO-EBIubiquitin ligase complex  MAPK cascade  protein binding  nucleus  cytoplasm  cytoplasm  cytosol  microtubule associated complex  plasma membrane  cytoskeleton organization  microtubule nucleation  cell surface receptor signaling pathway  axon guidance  Ran GTPase binding  Ran GTPase binding  enzyme binding  protein-containing complex assembly  negative regulation of ERK1 and ERK2 cascade  
REACTOMEQ96S59 [protein]
REACTOME PathwaysR-HSA-8851805 [pathway]   
NDEx NetworkRANBP9
Atlas of Cancer Signalling NetworkRANBP9
Wikipedia pathwaysRANBP9
Orthology - Evolution
GeneTree (enSembl)ENSG00000010017
Phylogenetic Trees/Animal Genes : TreeFamRANBP9
Homologs : HomoloGeneRANBP9
Homology/Alignments : Family Browser (UCSC)RANBP9
Gene fusions - Rearrangements
Fusion : MitelmanRANBP9/ATXN1 [6p23/6p22.3]  
Fusion : MitelmanRANBP9/BLOC1S5 [6p23/6p24.3]  
Fusion : MitelmanRANBP9/CDKAL1 [6p23/6p22.3]  
Fusion : MitelmanRANBP9/TPMT [6p23/6p22.3]  
Fusion : MitelmanRANBP9/TXNDC5 [6p23/6p24.3]  
Fusion PortalRANBP9 6p23 ATXN1 6p22.3 LGG
Fusion PortalRANBP9 6p23 MUTED LGG
Fusion PortalRANBP9 6p23 TPMT 6p22.3 BRCA
Fusion PortalRANBP9 6p23 TXNDC5 6p24.3 LGG
Fusion : QuiverRANBP9
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRANBP9 [hg38]
Exome Variant ServerRANBP9
GNOMAD BrowserENSG00000010017
Varsome BrowserRANBP9
Genomic Variants (DGV)RANBP9 [DGVbeta]
DECIPHERRANBP9 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRANBP9 
ICGC Data PortalRANBP9 
TCGA Data PortalRANBP9 
Broad Tumor PortalRANBP9
OASIS PortalRANBP9 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRANBP9  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DRANBP9
Mutations and Diseases : HGMDRANBP9
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
BioMutasearch RANBP9
DgiDB (Drug Gene Interaction Database)RANBP9
DoCM (Curated mutations)RANBP9 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RANBP9 (select a term)
NCG6 (London) select RANBP9
Cancer3DRANBP9(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry RANBP9
NextProtQ96S59 [Medical]
Target ValidationRANBP9
Huge Navigator RANBP9 [HugePedia]
Clinical trials, drugs, therapy
Protein Interactions : CTD
Pharm GKB GenePA34215
Clinical trialRANBP9
canSAR (ICR)RANBP9 (select the gene name)
DataMed IndexRANBP9
PubMed137 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 1 19:00:01 CET 2021

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