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SMAP1 (stromal membrane-associated protein 1)

Written2008-03Kenji Tanabe, Shunsuke Kon, Masanobu Satake
Department of Molecular Immunology, Institute of Development, Aging,, Cancer, Tohoku University, Sendai, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias_namesstromal membrane-associated protein 1
stromal membrane-associated GTPase-activating protein 1
Alias_symbol (synonym)FLJ13159
SMAP-1
Other aliasFLJ42245
HGNC (Hugo) SMAP1
LocusID (NCBI) 60682
Atlas_Id 42974
Location 6q13  [Link to chromosome band 6q13]
Location_base_pair Starts at 70667771 and ends at 70862013 bp from pter ( according to hg19-Feb_2009)  [Mapping SMAP1.png]
Local_order Between D6S455 and D6S1673
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
B3GAT2 (6q13) / SMAP1 (6q13)KMT2A (11q23.3) / SMAP1 (6q13)MYNN (3q26.2) / SMAP1 (6q13)
RARS2 (6q15) / SMAP1 (6q13)SMAP1 (6q13) / C14orf132 (14q32.2)SMAP1 (6q13) / CGA (6q14.3)
SMAP1 (6q13) / FAR2 (12p11.22)SMAP1 (6q13) / NBEA (13q13.3)SMAP1 (6q13) / POLR2G (11q12.3)

DNA/RNA

Description The gene spans an approximately 190 kb region, and is composed of 11 exons.
Transcription There is only one transcription initiation site. However, due to alternative splicing, generated are two types of transcripts, isoforms A and B. The length of each transcript is either 3344 (isoform A) or 3263 nt (isoform B). The isoform A retains, and the isoform B lacks in-flame exon 5, respectively.

Protein

Note SMAP1 is a member in the ArfGAP protein family.
 
  GAP, an ArfGAP domain; K-rich, a lysine-rich region; CHC, a clathrin heavy chain-binding motif; CALM, a clathrin assembly protein (CALM)-binding domain.
Description There are two isoform proteins. One translated from an isoform A transcript is constituted by 467, and the other from an isoform B is by 440 aa residues. A protein diagram shown above represents an isoform B type.
Expression Both isoform transcripts are detected in various human tissues. Expression appears to be almost ubiquitous.
Localisation SMAP1 protein is detected in the cytoplasm of cells, and appears to be highly concentrated near the plasma membrane.
Function SMAP1 functions as a GTPase-activating protein for an Arf6 GTPase. Arf6 is a Ras-related, small GTPase, and regulates clathrin-dependent and -independent endocytosis as well as actin dynamics. SMAP1 is specifically involved in the Arf6-regulated, clathrin-dependent endocytosis. This is achieved by direct interaction of SMAP1 with clathrin heavy chain.
Homology As a highly homologous gene to SMAP1, SMAP2 is identified on 1p34.1-35.3. SMAP1 and SMAP2 constitute a small subfamily in the ArfGAP family. SMAP2 protein is specifically involved in the early endosomes to trans-Golgi network transport.

Implicated in

Note
  
Entity t(6;11)(q13;q23) in acute leukemia.
Note Two cases have been reported so far.
Disease One case is from an M4 subtype of acute myeloid leukemia. A type of leukemia is not described for the other case.
Hybrid/Mutated Gene One leukemia patient possessed the 46, XX, t(6;11)(q13;q23) karyotype. In this patient, reciprocal translocation occured between intron 11 of MLL gene and intron 6 of SMAP1 gene. The chimeric 5'-MLL-SMAP1-3' transcript encodes a chimeric MLL-SMAP1 protein.
Abnormal Protein MLL-SMAP1
 
Schematic illustration of chimeric MLL-SMAP1 protein. The authentic MLL and SMAP1 proteins are also shown.
AT hook, an AT-hook domain; NLS, a nuclear localization signal; MT, a methyltransferase domain; PHD, a plant homeodomain zinc finger; BROMO, a bromo domain; SET, a su(var)3-9, enhancer-of-zeste, trithorax domain. GAP, an ArfGAP domain; K-rich, a lysine-rich region; CHC, a clathrin heavy chain-binding motif; CALM, a clathrin assembly protein (CALM)-binding domain.
  

Bibliography

Ten novel 11q23 chromosomal partner sites. European 11q23 Workshop participants.
Harrison CJ, Cuneo A, Clark R, Johansson B, Lafage-Pochitaloff M, Mugneret F, Moorman AV, Secker-Walker LM
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 1998 ; 12 (5) : 811-822.
PMID 9593286
 
Cloning, characterization and chromosome mapping of the human SMAP1 gene.
Marcos I, Borrego S, Rodríguez de Córdoba S, Gal´n JJ, Antiñolo G
Gene. 2002 ; 292 (1-2) : 167-171.
PMID 12119110
 
Diagnostic tool for the identification of MLL rearrangements including unknown partner genes.
Meyer C, Schneider B, Reichel M, Angermueller S, Strehl S, Schnittger S, Schoch C, Jansen MW, van Dongen JJ, Pieters R, Haas OA, Dingermann T, Klingebiel T, Marschalek R
Proceedings of the National Academy of Sciences of the United States of America. 2005 ; 102 (2) : 449-454.
PMID 15626757
 
SMAP2, a novel ARF GTPase-activating protein, interacts with clathrin and clathrin assembly protein and functions on the AP-1-positive early endosome/trans-Golgi network.
Natsume W, Tanabe K, Kon S, Yoshida N, Watanabe T, Torii T, Satake M
Molecular biology of the cell. 2006 ; 17 (6) : 2592-2603.
PMID 16571680
 
Involvement of a novel ADP-ribosylation factor GTPase-activating protein, SMAP, in membrane trafficking: implications in cancer cell biology.
Tanabe K, Kon S, Natsume W, Torii T, Watanabe T, Satake M
Cancer science. 2006 ; 97 (9) : 801-806.
PMID 16805823
 
A novel GTPase-activating protein for ARF6 directly interacts with clathrin and regulates clathrin-dependent endocytosis.
Tanabe K, Torii T, Natsume W, Braesch-Andersen S, Watanabe T, Satake M
Molecular biology of the cell. 2005 ; 16 (4) : 1617-1628.
PMID 15659652
 

Citation

This paper should be referenced as such :
Tanabe, K ; Kon, S ; Satake, M
SMAP1 (stromal membrane-associated protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(1):68-69.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SMAP1ID42974ch6q13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(6;11)(q13;q23) KMT2A/SMAP1


External links

Nomenclature
HGNC (Hugo)SMAP1   19651
Cards
AtlasSMAP1ID42974ch6q13
Entrez_Gene (NCBI)SMAP1  60682  small ArfGAP 1
AliasesSMAP-1
GeneCards (Weizmann)SMAP1
Ensembl hg19 (Hinxton)ENSG00000112305 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000112305 [Gene_View]  chr6:70667771-70862013 [Contig_View]  SMAP1 [Vega]
ICGC DataPortalENSG00000112305
TCGA cBioPortalSMAP1
AceView (NCBI)SMAP1
Genatlas (Paris)SMAP1
WikiGenes60682
SOURCE (Princeton)SMAP1
Genetics Home Reference (NIH)SMAP1
Genomic and cartography
GoldenPath hg38 (UCSC)SMAP1  -     chr6:70667771-70862013 +  6q13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMAP1  -     6q13   [Description]    (hg19-Feb_2009)
EnsemblSMAP1 - 6q13 [CytoView hg19]  SMAP1 - 6q13 [CytoView hg38]
Mapping of homologs : NCBISMAP1 [Mapview hg19]  SMAP1 [Mapview hg38]
OMIM611372   
Gene and transcription
Genbank (Entrez)AF442495 AK023221 AK074340 AK124239 AK222711
RefSeq transcript (Entrez)NM_001044305 NM_001281439 NM_001281440 NM_021940
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMAP1
Cluster EST : UnigeneHs.485717 [ NCBI ]
CGAP (NCI)Hs.485717
Alternative Splicing GalleryENSG00000112305
Gene ExpressionSMAP1 [ NCBI-GEO ]   SMAP1 [ EBI - ARRAY_EXPRESS ]   SMAP1 [ SEEK ]   SMAP1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMAP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)60682
GTEX Portal (Tissue expression)SMAP1
Human Protein AtlasENSG00000112305-SMAP1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8IYB5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8IYB5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8IYB5
Splice isoforms : SwissVarQ8IYB5
PhosPhoSitePlusQ8IYB5
Domaine pattern : Prosite (Expaxy)ARFGAP (PS50115)   
Domains : Interpro (EBI)ArfGAP   
Domain families : Pfam (Sanger)ArfGap (PF01412)   
Domain families : Pfam (NCBI)pfam01412   
Domain families : Smart (EMBL)ArfGap (SM00105)  
Conserved Domain (NCBI)SMAP1
DMDM Disease mutations60682
Blocks (Seattle)SMAP1
PDB (SRS)2CRR   
PDB (PDBSum)2CRR   
PDB (IMB)2CRR   
PDB (RSDB)2CRR   
Structural Biology KnowledgeBase2CRR   
SCOP (Structural Classification of Proteins)2CRR   
CATH (Classification of proteins structures)2CRR   
SuperfamilyQ8IYB5
Human Protein Atlas [tissue]ENSG00000112305-SMAP1 [tissue]
Peptide AtlasQ8IYB5
HPRD18072
IPIIPI00102096   IPI00604487   IPI00185325   IPI00908797   IPI00514489   IPI00640608   
Protein Interaction databases
DIP (DOE-UCLA)Q8IYB5
IntAct (EBI)Q8IYB5
FunCoupENSG00000112305
BioGRIDSMAP1
STRING (EMBL)SMAP1
ZODIACSMAP1
Ontologies - Pathways
QuickGOQ8IYB5
Ontology : AmiGOGTPase activator activity  cytoplasm  plasma membrane  clathrin binding  positive regulation of GTPase activity  positive regulation of erythrocyte differentiation  metal ion binding  regulation of clathrin-dependent endocytosis  
Ontology : EGO-EBIGTPase activator activity  cytoplasm  plasma membrane  clathrin binding  positive regulation of GTPase activity  positive regulation of erythrocyte differentiation  metal ion binding  regulation of clathrin-dependent endocytosis  
Pathways : KEGGEndocytosis   
NDEx NetworkSMAP1
Atlas of Cancer Signalling NetworkSMAP1
Wikipedia pathwaysSMAP1
Orthology - Evolution
OrthoDB60682
GeneTree (enSembl)ENSG00000112305
Phylogenetic Trees/Animal Genes : TreeFamSMAP1
HOVERGENQ8IYB5
HOGENOMQ8IYB5
Homologs : HomoloGeneSMAP1
Homology/Alignments : Family Browser (UCSC)SMAP1
Gene fusions - Rearrangements
Fusion : MitelmanSMAP1/C14orf132 [6q13/14q32.2]  
Fusion : MitelmanSMAP1/CGA [6q13/6q14.3]  [t(6;6)(q13;q14)]  
Fusion : MitelmanSMAP1/FAR2 [6q13/12p11.22]  [t(6;12)(q13;p11)]  
Fusion: TCGA_MDACCRARS2 6q15 SMAP1 6q13 BRCA
Fusion: TCGA_MDACCSMAP1 6q13 C14orf132 14q32.2 BRCA
Fusion: TCGA_MDACCSMAP1 6q13 CGA 6q14.3 PRAD
Fusion: TCGA_MDACCSMAP1 6q13 FAR2 12p11.22 SKCM
Tumor Fusion PortalSMAP1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMAP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMAP1
dbVarSMAP1
ClinVarSMAP1
1000_GenomesSMAP1 
Exome Variant ServerSMAP1
ExAC (Exome Aggregation Consortium)ENSG00000112305
GNOMAD BrowserENSG00000112305
Genetic variants : HAPMAP60682
Genomic Variants (DGV)SMAP1 [DGVbeta]
DECIPHERSMAP1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMAP1 
Mutations
ICGC Data PortalSMAP1 
TCGA Data PortalSMAP1 
Broad Tumor PortalSMAP1
OASIS PortalSMAP1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMAP1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMAP1
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 SMAP1
DgiDB (Drug Gene Interaction Database)SMAP1
DoCM (Curated mutations)SMAP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMAP1 (select a term)
intoGenSMAP1
NCG5 (London)SMAP1
Cancer3DSMAP1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM611372   
Orphanet
DisGeNETSMAP1
MedgenSMAP1
Genetic Testing Registry SMAP1
NextProtQ8IYB5 [Medical]
TSGene60682
GENETestsSMAP1
Target ValidationSMAP1
Huge Navigator SMAP1 [HugePedia]
snp3D : Map Gene to Disease60682
BioCentury BCIQSMAP1
ClinGenSMAP1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD60682
Chemical/Pharm GKB GenePA134893764
Clinical trialSMAP1
Miscellaneous
canSAR (ICR)SMAP1 (select the gene name)
Probes
Litterature
PubMed18 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMAP1
EVEXSMAP1
GoPubMedSMAP1
iHOPSMAP1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 15:03:13 CET 2017

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