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SARNP (cytokine induced protein 29 kDa)

Written2005-08Jean-Loup Huret, Sylvie Senon
Genetics, Dept Medical Information, University of Poitiers; CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)THO1
Hcc-1
CIP29
Other aliasHCC-1
HGNC (Hugo) SARNP
LocusID (NCBI) 84324
Atlas_Id 42967
Location 12q13.2  [Link to chromosome band 12q13]
Location_base_pair Starts at 55757270 and ends at 55817756 bp from pter ( according to hg19-Feb_2009)  [Mapping SARNP.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)
KMT2A (11q23.3) / SARNP (12q13.2)RBMS2 (12q13.3) / SARNP (12q13.2)RILPL1 (12q24.31) / SARNP (12q13.2)
SARNP (12q13.2) / HDLBP (2q37.3)SARNP (12q13.2) / KMT2A (11q23.3)SARNP (12q13.2) / STMP1 (7q33)
TOMM20 (1q42.3) / SARNP (12q13.2)
Note HCC-1 is an alias for CIP29 (12q13), but also for CCL14 (17q11.2)

Protein

Description 210 amino acids, 29 kDa;contains from N term to C term a SAP domain and 2 nuclear localization domains, and also 3 possible N-glycosylation sites and 9 potential phosphorylation sites. A SAP domain is a putative DNA binding motif involved in chromosomal organization and may regulate transcription, DNA repair, RNA processing.
Expression Widely expressed in fetal and adult tissues, as well as cancer cell lines; upregulated by EPO (erythropoietin), TPO (thrombopoietin), FL (FLT3 Ligand), and SCF (stem cell factor). Associated with cell cycle progression
Localisation Nucleus but some staining was also found in the cytoplasm.

Implicated in

Note
  
Entity M4 acute myeloid leukemia (AML) with t(11;12)(q23;q13) --> KMT2A/SARNP
Note only one case to date
Prognosis unknown
Hybrid/Mutated Gene 5' MLL - 3' CIP29 including the 9 first exons of MLL, and nearly the entire CIP29
Abnormal Protein The fusion protein includes from N term to C term the AT hooks and the methyltransferase domain of MLL and the SAP domain and the C term nuclear localization domains of CIP29.
  

Bibliography

Growth inhibitory effect of Hcc-1/CIP29 is associated with induction of apoptosis, not just with G2/M arrest.
Fukuda S, Pelus LM
Cellular and molecular life sciences : CMLS. 2005 ; 62 (13) : 1526-1527.
PMID 15924260
 
Cloning and characterization of a proliferation-associated cytokine-inducible protein, CIP29.
Fukuda S, Wu DW, Stark K, Pelus LM
Biochemical and biophysical research communications. 2002 ; 292 (3) : 593-600.
PMID 11922608
 
A novel partner gene CIP29 containing a SAP domain with MLL identified in infantile myelomonocytic leukemia.
Hashii Y, Kim JY, Sawada A, Tokimasa S, Hiroyuki F, Ohta H, Makiko K, Takihara Y, Ozono K, Hara J
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2004 ; 18 (9) : 1546-1548.
PMID 15284855
 

Citation

This paper should be referenced as such :
Huret, JL ; Senon, S
CIP29 (cytokine induced protein 29 kDa)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(4):305-305.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CIP29ID42967ch12q13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(11;12)(q23;q13) KMT2A/SARNP


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(12;12)(q13;q24) RILPL1/SARNP


External links

Nomenclature
HGNC (Hugo)SARNP   24432
Cards
AtlasCIP29ID42967ch12q13
Entrez_Gene (NCBI)SARNP  84324  SAP domain containing ribonucleoprotein
AliasesCIP29; HCC1; HSPC316; THO1
GeneCards (Weizmann)SARNP
Ensembl hg19 (Hinxton)ENSG00000205323 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000205323 [Gene_View]  ENSG00000205323 [Sequence]  chr12:55757270-55817756 [Contig_View]  SARNP [Vega]
ICGC DataPortalENSG00000205323
TCGA cBioPortalSARNP
AceView (NCBI)SARNP
Genatlas (Paris)SARNP
WikiGenes84324
SOURCE (Princeton)SARNP
Genetics Home Reference (NIH)SARNP
Genomic and cartography
GoldenPath hg38 (UCSC)SARNP  -     chr12:55757270-55817756 -  12q13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SARNP  -     12q13.2   [Description]    (hg19-Feb_2009)
GoldenPathSARNP - 12q13.2 [CytoView hg19]  SARNP - 12q13.2 [CytoView hg38]
ImmunoBaseENSG00000205323
Mapping of homologs : NCBISARNP [Mapview hg19]  SARNP [Mapview hg38]
OMIM610049   
Gene and transcription
Genbank (Entrez)AF161434 AF486281 AK222719 AK290508 BC007099
RefSeq transcript (Entrez)NM_033082
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SARNP
Cluster EST : UnigeneHs.505676 [ NCBI ]
CGAP (NCI)Hs.505676
Alternative Splicing GalleryENSG00000205323
Gene ExpressionSARNP [ NCBI-GEO ]   SARNP [ EBI - ARRAY_EXPRESS ]   SARNP [ SEEK ]   SARNP [ MEM ]
Gene Expression Viewer (FireBrowse)SARNP [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)84324
GTEX Portal (Tissue expression)SARNP
Human Protein AtlasENSG00000205323-SARNP [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP82979   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP82979  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP82979
Splice isoforms : SwissVarP82979
PhosPhoSitePlusP82979
Domaine pattern : Prosite (Expaxy)SAP (PS50800)   
Domains : Interpro (EBI)SAP_dom    SAP_dom_sf   
Domain families : Pfam (Sanger)SAP (PF02037)   
Domain families : Pfam (NCBI)pfam02037   
Domain families : Smart (EMBL)SAP (SM00513)  
Conserved Domain (NCBI)SARNP
DMDM Disease mutations84324
Blocks (Seattle)SARNP
PDB (RSDB)2DO1   
PDB Europe2DO1   
PDB (PDBSum)2DO1   
PDB (IMB)2DO1   
Structural Biology KnowledgeBase2DO1   
SCOP (Structural Classification of Proteins)2DO1   
CATH (Classification of proteins structures)2DO1   
SuperfamilyP82979
Human Protein Atlas [tissue]ENSG00000205323-SARNP [tissue]
Peptide AtlasP82979
HPRD16716
IPIIPI00014938   IPI01015600   IPI01022436   IPI01021985   
Protein Interaction databases
DIP (DOE-UCLA)P82979
IntAct (EBI)P82979
FunCoupENSG00000205323
BioGRIDSARNP
STRING (EMBL)SARNP
ZODIACSARNP
Ontologies - Pathways
QuickGOP82979
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  transcription export complex  RNA polymerase II proximal promoter sequence-specific DNA binding  DNA-binding transcription repressor activity, RNA polymerase II-specific  RNA binding  protein binding  nucleus  nucleoplasm  RNA export from nucleus  mRNA export from nucleus  mRNA export from nucleus  regulation of translation  protein C-terminus binding  nuclear speck  mRNA 3'-end processing  cytoplasmic ribonucleoprotein granule  RS domain binding  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  transcription export complex  RNA polymerase II proximal promoter sequence-specific DNA binding  DNA-binding transcription repressor activity, RNA polymerase II-specific  RNA binding  protein binding  nucleus  nucleoplasm  RNA export from nucleus  mRNA export from nucleus  mRNA export from nucleus  regulation of translation  protein C-terminus binding  nuclear speck  mRNA 3'-end processing  cytoplasmic ribonucleoprotein granule  RS domain binding  
REACTOMEP82979 [protein]
REACTOME PathwaysR-HSA-73856 [pathway]   
NDEx NetworkSARNP
Atlas of Cancer Signalling NetworkSARNP
Wikipedia pathwaysSARNP
Orthology - Evolution
OrthoDB84324
GeneTree (enSembl)ENSG00000205323
Phylogenetic Trees/Animal Genes : TreeFamSARNP
HOGENOMP82979
Homologs : HomoloGeneSARNP
Homology/Alignments : Family Browser (UCSC)SARNP
Gene fusions - Rearrangements
Fusion : MitelmanRILPL1/SARNP [12q24.31/12q13.2]  [t(12;12)(q13;q24)]  
Fusion : COSMICKMT2A [11q23.3]  -  SARNP [12q13.2]  [fusion_1848]  
Fusion PortalRILPL1 12q24.31 SARNP 12q13.2 BRCA
Fusion : FusionGDB14236    16454    24809    25491    27413    31250    31590    32637    32638    32639    32640    32641    32642    32643    32644   
32645    32646    34090    39063    43439    43679   
Fusion : Fusion_HubAC073063.1--SARNP    AC073063.10--SARNP    ARSE--SARNP    CBX5--SARNP    CHD8--SARNP    CPSF4--SARNP    CUX1--SARNP    DNM1L--SARNP    DRAM1--SARNP    GABRA3--SARNP    HMGA2--SARNP    KMT2A--SARNP    MLL--SARNP    MON2--SARNP    MYO10--SARNP   
N4BP2L2--SARNP    ORMDL2--SARNP    R3HDM2--SARNP    RBMS2--SARNP    RILPL1--SARNP    RNF41--SARNP    SARNP--ATP5J2-PTCD1    SARNP--C7ORF73    SARNP--ENY2    SARNP--HDLBP    SARNP--LEMD3    SARNP--MLL    SARNP--MMP19    SARNP--PAN2    SARNP--SENP1   
SPRED1--SARNP    SUOX--SARNP    TOMM20--SARNP    TXLNG--SARNP    UACA--SARNP    UTP18--SARNP    WBP11--SARNP    ZNF562--SARNP   
Fusion : QuiverSARNP
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSARNP [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SARNP
dbVarSARNP
ClinVarSARNP
1000_GenomesSARNP 
Exome Variant ServerSARNP
ExAC (Exome Aggregation Consortium)ENSG00000205323
GNOMAD BrowserENSG00000205323
Varsome BrowserSARNP
Genetic variants : HAPMAP84324
Genomic Variants (DGV)SARNP [DGVbeta]
DECIPHERSARNP [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSARNP 
Mutations
ICGC Data PortalSARNP 
TCGA Data PortalSARNP 
Broad Tumor PortalSARNP
OASIS PortalSARNP [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSARNP  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSARNP
Mutations and Diseases : HGMDSARNP
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SARNP
DgiDB (Drug Gene Interaction Database)SARNP
DoCM (Curated mutations)SARNP (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SARNP (select a term)
intoGenSARNP
NCG5 (London)SARNP
Cancer3DSARNP(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610049   
Orphanet
DisGeNETSARNP
MedgenSARNP
Genetic Testing Registry SARNP
NextProtP82979 [Medical]
TSGene84324
GENETestsSARNP
Target ValidationSARNP
Huge Navigator SARNP [HugePedia]
snp3D : Map Gene to Disease84324
BioCentury BCIQSARNP
ClinGenSARNP
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD84324
Chemical/Pharm GKB GenePA165513309
Clinical trialSARNP
Miscellaneous
canSAR (ICR)SARNP (select the gene name)
DataMed IndexSARNP
Probes
Litterature
PubMed46 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSARNP
EVEXSARNP
GoPubMedSARNP
iHOPSARNP
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Nov 13 21:10:25 CET 2019

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jlhuret@AtlasGeneticsOncology.org.