Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SS18 (synovial sarcoma translocation, chromosome 18)

Written2006-05Mamoru Ouchida
Department of Molecular Genetics, Graduate School of Medicine, Dentistry, Pharmaceutical Sciences, Okayama University. Shikata-cho 2-5-1, Okayama 700-8558, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias_namesSSXT
synovial sarcoma translocation, chromosome 18
SS18, nBAF chromatin remodeling complex subunit
Alias_symbol (synonym)SYT
Other aliasMGC116875
HGNC (Hugo) SS18
LocusID (NCBI) 6760
Atlas_Id 84
Location 18q11.2  [Link to chromosome band 18q11]
Location_base_pair Starts at 26016253 and ends at 26090647 bp from pter ( according to hg19-Feb_2009)  [Mapping SS18.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)
MEF2D (1q22) / SS18 (18q11.2)SS18 (18q11.2) / DOCK2 (5q35.1)SS18 (18q11.2) / MEF2D (1q22)
SS18 (18q11.2) / NRAS (1p13.2)SS18 (18q11.2) / RINT1 (7q22.3)SS18 (18q11.2) / SLC5A11 (16p12.1)
SS18 (18q11.2) / SS18 (18q11.2)SS18 (18q11.2) / SSX1 (Xp11.23)SS18 (18q11.2) / SSX2 (Xp11.22)
SS18 (18q11.2) / SSX2B (Xp11.22)SS18 (18q11.2) / SSX4 (Xp11.23)SS18 (18q11.2) / SSX4B (Xp11.23)
SS18 (18q11.2) / SSX7 (Xp11.22)SS18 (18q11.2) / TESMIN (11q13.3)SS18 (18q11.2) / USP6 (17p13.2)
SSX1 (Xp11.23) / SS18 (18q11.2)SSX2 (Xp11.22) / SS18 (18q11.2)SSX4 (Xp11.23) / SS18 (18q11.2)
TRAPPC8 (18q12.1) / SS18 (18q11.2)

DNA/RNA

Note Member of the SS18 family. SYT, one of the alternative gene names, has continued to be used in the literature for this gene.
Description 11 exons, spaning approximately 75 kb of genomic DNA in the telomere-to-centromere orientation on chromosome 18q11.2 The promoter region lacks CAAT and TATA boxes but contains CpG islands, suggesting that SS18 is a housekeeping gene.
Transcription Exon 8 is spliced out with different ratio in the various tissues by alternative splicing.
Pseudogene SS18L2 (3p21)

Protein

Description 418 amino acids. 2 domains; the SHN domain (the SYT N-terminal homology domain) that is found in proteins from a wide variety of species ranging from plants to human, and the QPGY domain at the C-terminal part, rich in glutamine, proline, glycine and tyrosine. Four putative src-homology binding domains and two annexin-like direct repeats were exhibited in the SS18 protein. SS18 protein binds to p300, hBRM, AF10 and SIN3A proteins. The QPGY domain activates transcription when coupled to a DNA-binding domain.
Expression Ubiquitous
Localisation Nuclear
Function Transcriptional coactivator
Homology SS18L1, SS18L2

Implicated in

Note
  
Entity Synovial sarcoma
Prognosis A high grade sarcoma that leads to death in at least 25% of patients within five years of diagnosis. Prognosis may be different between the synovial sarcoma patients with SYT-SSX1 and SYT-SSX2.
Cytogenetics t(X;18)(p11.2;q11.2)
Hybrid/Mutated Gene SYT-SSX1, SYT-SSX2, SYT-SSX4; the exon 10 of the SS18 (SYT) gene is fused to exon 6 of the SSX genes.
Abnormal Protein The last 8 amino acid residues of the SS18 (SYT) protein are replaced by 78 amino acids from the C-terminal part of SSX proteins.
  

Breakpoints

 

Bibliography

Identification of novel genes, SYT and SSX, involved in the t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma.
Clark J, Rocques PJ, Crew AJ, Gill S, Shipley J, Chan AM, Gusterson BA, Cooper CS
Nature genetics. 1994 ; 7 (4) : 502-508.
PMID 7951320
 
p300 interacts with the nuclear proto-oncoprotein SYT as part of the active control of cell adhesion.
Eid JE, Kung AL, Scully R, Livingston DM
Cell. 2000 ; 102 (6) : 839-848.
PMID 11030627
 
SYT, a partner of SYT-SSX oncoprotein in synovial sarcomas, interacts with mSin3A, a component of histone deacetylase complex.
Ito T, Ouchida M, Ito S, Jitsumori Y, Morimoto Y, Ozaki T, Kawai A, Inoue H, Shimizu K
Laboratory investigation; a journal of technical methods and pathology. 2004 ; 84 (11) : 1484-1490.
PMID 15467731
 
SYT-SSX gene fusion as a determinant of morphology and prognosis in synovial sarcoma.
Kawai A, Woodruff J, Healey JH, Brennan MF, Antonescu CR, Ladanyi M
The New England journal of medicine. 1998 ; 338 (3) : 153-160.
PMID 9428816
 
Splicing isoform of SYT-SSX fusion protein accelerates transcriptional activity and cell proliferation.
Morimoto Y, Ouchida M, Ozaki T, Kawai A, Ito T, Yoshida A, Inoue H, Shimizu K
Cancer letters. 2003 ; 199 (1) : 35-43.
PMID 12963121
 
A reverse transcriptase-polymerase chain reaction assay in the diagnosis of soft tissue sarcomas.
Naito N, Kawai A, Ouchida M, Dan'ura T, Morimoto Y, Ozaki T, Shimizu K, Inoue H
Cancer. 2000 ; 89 (9) : 1992-1998.
PMID 11064357
 
A novel fusion gene, SYT-SSX4, in synovial sarcoma.
Skytting B, Nilsson G, Brodin B, Xie Y, Lundeberg J, Uhlén M, Larsson O
Journal of the National Cancer Institute. 1999 ; 91 (11) : 974-975.
PMID 10359553
 
Functional domains of the SYT and SYT-SSX synovial sarcoma translocation proteins and co-localization with the SNF protein BRM in the nucleus.
Thaete C, Brett D, Monaghan P, Whitehouse S, Rennie G, Rayner E, Cooper CS, Goodwin G
Human molecular genetics. 1999 ; 8 (4) : 585-591.
PMID 10072425
 
Mapping and characterization of the mouse and human SS18 genes, two human SS18-like genes and a mouse Ss18 pseudogene.
de Bruijn DR, Kater-Baats E, Eleveld M, Merkx G, Geurts Van Kessel A
Cytogenetics and cell genetics. 2001 ; 92 (3-4) : 310-319.
PMID 11435705
 

Citation

This paper should be referenced as such :
Ouchida, M
SS18 (synovial sarcoma translocation, chromosome 18)
Atlas Genet Cytogenet Oncol Haematol. 2006;10(4):228-229.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SS18ID84ch18q11.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(1;18)(q22;q11) MEF2D/SS18
t(1;18)(q22;q11) SS18/MEF2D


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 10 ]
  Prostate tumors: an overview
Soft tissue tumors: an overview
Soft Tissues: Synovial sarcoma with t(X;18)(p11;q11) SS18/
t(5;18)(q35;q11) SS18/DOCK2
t(X;18)(p11;q11) SS18/SSX4
t(X;18)(p11;q11) SS18/SSX
t(X;18)(p11;q11) SS18/SSX1
t(X;18)(p11;q11) SS18/SSX2
t(16;18)(p12;q11) SS18/SLC5A11
t(18;18)(q11;q12) TRAPPC8/SS18


External links

Nomenclature
HGNC (Hugo)SS18   11340
Cards
AtlasSS18ID84ch18q11
Entrez_Gene (NCBI)SS18  6760  SS18 subunit of BAF chromatin remodeling complex
AliasesSSXT; SYT
GeneCards (Weizmann)SS18
Ensembl hg19 (Hinxton)ENSG00000141380 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000141380 [Gene_View]  ENSG00000141380 [Sequence]  chr18:26016253-26090647 [Contig_View]  SS18 [Vega]
ICGC DataPortalENSG00000141380
TCGA cBioPortalSS18
AceView (NCBI)SS18
Genatlas (Paris)SS18
WikiGenes6760
SOURCE (Princeton)SS18
Genetics Home Reference (NIH)SS18
Genomic and cartography
GoldenPath hg38 (UCSC)SS18  -     chr18:26016253-26090647 -  18q11.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SS18  -     18q11.2   [Description]    (hg19-Feb_2009)
GoldenPathSS18 - 18q11.2 [CytoView hg19]  SS18 - 18q11.2 [CytoView hg38]
ImmunoBaseENSG00000141380
Mapping of homologs : NCBISS18 [Mapview hg19]  SS18 [Mapview hg38]
OMIM600192   
Gene and transcription
Genbank (Entrez)AF161377 AF244972 AF343880 AK289510 AK296949
RefSeq transcript (Entrez)NM_001007559 NM_001308201 NM_005637
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SS18
Cluster EST : UnigeneHs.129261 [ NCBI ]
CGAP (NCI)Hs.129261
Alternative Splicing GalleryENSG00000141380
Gene ExpressionSS18 [ NCBI-GEO ]   SS18 [ EBI - ARRAY_EXPRESS ]   SS18 [ SEEK ]   SS18 [ MEM ]
Gene Expression Viewer (FireBrowse)SS18 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6760
GTEX Portal (Tissue expression)SS18
Human Protein AtlasENSG00000141380-SS18 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15532   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ15532  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ15532
Splice isoforms : SwissVarQ15532
PhosPhoSitePlusQ15532
Domains : Interpro (EBI)SS18_fam   
Domain families : Pfam (Sanger)SSXT (PF05030)   
Domain families : Pfam (NCBI)pfam05030   
Conserved Domain (NCBI)SS18
DMDM Disease mutations6760
Blocks (Seattle)SS18
SuperfamilyQ15532
Human Protein Atlas [tissue]ENSG00000141380-SS18 [tissue]
Peptide AtlasQ15532
HPRD02559
IPIIPI00940186   IPI01011245   IPI01015658   IPI01013913   IPI01012306   IPI00452919   IPI00902472   IPI00018069   
Protein Interaction databases
DIP (DOE-UCLA)Q15532
IntAct (EBI)Q15532
FunCoupENSG00000141380
BioGRIDSS18
STRING (EMBL)SS18
ZODIACSS18
Ontologies - Pathways
QuickGOQ15532
Ontology : AmiGOmicrotubule cytoskeleton organization  cell morphogenesis  protein binding  nucleus  cytoplasmic microtubule  SWI/SNF complex  nuclear receptor transcription coactivator activity  intracellular signal transduction  response to drug  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  ephrin receptor signaling pathway  npBAF complex  neuronal stem cell population maintenance  
Ontology : EGO-EBImicrotubule cytoskeleton organization  cell morphogenesis  protein binding  nucleus  cytoplasmic microtubule  SWI/SNF complex  nuclear receptor transcription coactivator activity  intracellular signal transduction  response to drug  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  ephrin receptor signaling pathway  npBAF complex  neuronal stem cell population maintenance  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkSS18
Atlas of Cancer Signalling NetworkSS18
Wikipedia pathwaysSS18
Orthology - Evolution
OrthoDB6760
GeneTree (enSembl)ENSG00000141380
Phylogenetic Trees/Animal Genes : TreeFamSS18
HOGENOMQ15532
Homologs : HomoloGeneSS18
Homology/Alignments : Family Browser (UCSC)SS18
Gene fusions - Rearrangements
Fusion : MitelmanSS18/DOCK2 [18q11.2/5q35.1]  
Fusion : MitelmanSS18/SSX1 [18q11.2/Xp11.23]  [ins(X;18)(p11;q11q21)]  [t(X;18)(p11;q11)]  
Fusion : MitelmanSS18/SSX2 [18q11.2/Xp11.22]  [t(X;16;18)(p11;q22;q11)]  [t(X;18)(p11;q11)]  
Fusion : MitelmanSS18/SSX2B [18q11.2/Xp11.22]  [t(X;18)(p11;q11)]  
Fusion : MitelmanSS18/SSX4 [18q11.2/Xp11.23]  [t(X;18)(p11;q11)]  
Fusion : MitelmanTRAPPC8/SS18 [18q12.1/18q11.2]  [t(18;18)(q11;q12)]  
Fusion : COSMICSSX2 [Xp11.22]  -  SS18 [18q11.2]  [fusion_524]  [fusion_576]  [fusion_580]  [fusion_585]  [fusion_586]  
Fusion PortalSS18 18q11.2 DOCK2 5q35.1 PRAD
Fusion PortalTRAPPC8 18q12.1 SS18 18q11.2 BRCA
Fusion : TICdbSS18 [18q11.2]  -  SSX1 [Xp11.23]
Fusion : TICdbSS18 [18q11.2]  -  SSX2 [Xp11.22]
Fusion : TICdbSS18 [18q11.2]  -  SSX4 [Xp11.23]
Fusion : FusionGDB25531    36105    36106    36107    36108    36109    36110    36111    36112    36113    36114    36115    36116    36117    36212   
39407    42280   
Fusion : Fusion_HubAC010168.2--SS18    ADNP2--SS18    CDH2--SS18    CRTC1--SS18    DTNA--SS18    KIAA1328--SS18    LRG1--SS18    MBP--SS18    MEF2D--SS18    METTL15--SS18    MIB2--SS18    MPP7--SS18    NUP54--SS18    OGT--SS18    OSBPL1A--SS18   
PPP6R3--SS18    PSIP1--SS18    SAMSN1--SS18    SS18--B4GALT6    SS18--CHST9    SS18--CSNK1E    SS18--DCUN1D4    SS18--DOCK2    SS18--H3F3B    SS18--KCTD1    SS18--LRG1    SS18--MTL5    SS18--NRAS    SS18--RINT1    SS18--SLC5A11   
SS18--SS18    SS18--SSX    SS18--SSX1    SS18--SSX2    SS18--SSX2B    SS18--SSX4    SS18--SSX4B    SS18--SSX7    SS18--SSX8    SS18--TAF4B    SS18--ZNF521    SSX--SS18    SSX1--SS18    SSX2--SS18    SSX4--SS18   
TRAPPC8--SS18    USP14--SS18    USP6--SS18    YAP1--SS18   
Fusion : QuiverSS18
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSS18 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SS18
dbVarSS18
ClinVarSS18
1000_GenomesSS18 
Exome Variant ServerSS18
ExAC (Exome Aggregation Consortium)ENSG00000141380
GNOMAD BrowserENSG00000141380
Varsome BrowserSS18
Genetic variants : HAPMAP6760
Genomic Variants (DGV)SS18 [DGVbeta]
DECIPHERSS18 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSS18 
Mutations
ICGC Data PortalSS18 
TCGA Data PortalSS18 
Broad Tumor PortalSS18
OASIS PortalSS18 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSS18  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSS18
Mutations and Diseases : HGMDSS18
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SS18
DgiDB (Drug Gene Interaction Database)SS18
DoCM (Curated mutations)SS18 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SS18 (select a term)
intoGenSS18
NCG5 (London)SS18
Cancer3DSS18(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600192   
Orphanet3738   
DisGeNETSS18
MedgenSS18
Genetic Testing Registry SS18
NextProtQ15532 [Medical]
TSGene6760
GENETestsSS18
Target ValidationSS18
Huge Navigator SS18 [HugePedia]
snp3D : Map Gene to Disease6760
BioCentury BCIQSS18
ClinGenSS18
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6760
Chemical/Pharm GKB GenePA36164
Clinical trialSS18
Miscellaneous
canSAR (ICR)SS18 (select the gene name)
DataMed IndexSS18
Probes
Litterature
PubMed77 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSS18
EVEXSS18
GoPubMedSS18
iHOPSS18
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Nov 13 22:02:34 CET 2019

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.