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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
Alias_symbol (synonym)SYT
HGNC (Hugo) SS18
LocusID (NCBI) 6760
Atlas_Id 84
Location 18q11.2  [Link to chromosome band 18q11]
Location_base_pair Starts at 23596217 and ends at 23670611 bp from pter ( according to hg19-Feb_2009)  [Mapping SS18.png]
Fusion genes
(updated 2016)
SS18 (18q11.2) / DOCK2 (5q35.1)SS18 (18q11.2) / MTL5 (11q13.3)SS18 (18q11.2) / NRAS (1p13.2)
SS18 (18q11.2) / RINT1 (7q22.3)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) / 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 Solid tumors implicated (Data extracted from papers in the Atlas) [ 4 ]
  Prostate tumors: an overview
Soft tissue tumors: an overview
Soft Tissues: Biphasic svial sarcoma with t(X;20)(p11;q13) SS18L1/SSX1
Soft Tissues: Synovial sarcoma with t(X;18)(p11;q11) SS18/


External links

Nomenclature
HGNC (Hugo)SS18   11340
Cards
AtlasSS18ID84ch18q11
Entrez_Gene (NCBI)SS18  6760  synovial sarcoma translocation, chromosome 18
AliasesSSXT; SYT
GeneCards (Weizmann)SS18
Ensembl hg19 (Hinxton)ENSG00000141380 [Gene_View]  chr18:23596217-23670611 [Contig_View]  SS18 [Vega]
Ensembl hg38 (Hinxton)ENSG00000141380 [Gene_View]  chr18:23596217-23670611 [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 hg19 (UCSC)SS18  -     chr18:23596217-23670611 -  18q11.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SS18  -     18q11.2   [Description]    (hg38-Dec_2013)
EnsemblSS18 - 18q11.2 [CytoView hg19]  SS18 - 18q11.2 [CytoView hg38]
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)NC_000018 NC_018929 NT_010966 NW_004929410
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]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6760
GTEX Portal (Tissue expression)SS18
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 AtlasENSG00000141380
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  transcription, DNA-templated  ligand-dependent nuclear receptor transcription coactivator activity  intracellular signal transduction  response to drug  positive regulation of transcription from RNA polymerase II promoter  ephrin receptor signaling pathway  npBAF complex  neuronal stem cell population maintenance  
Ontology : EGO-EBImicrotubule cytoskeleton organization  cell morphogenesis  protein binding  nucleus  cytoplasmic microtubule  transcription, DNA-templated  ligand-dependent nuclear receptor transcription coactivator activity  intracellular signal transduction  response to drug  positive regulation of transcription from RNA polymerase II promoter  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
HOVERGENQ15532
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 : COSMICSS18 [18q11.2]  -  SSX1 [Xp11.23]  [fusion_499]  [fusion_504]  [fusion_505]  [fusion_506]  [fusion_513]  [fusion_514]  [fusion_515]  
[fusion_519]  [fusion_520]  [fusion_521]  [fusion_527]  [fusion_528]  [fusion_577]  [fusion_581]  
Fusion : COSMICSS18 [18q11.2]  -  SSX2 [Xp11.22]  [fusion_500]  [fusion_501]  [fusion_516]  [fusion_517]  [fusion_523]  [fusion_530]  [fusion_567]  
[fusion_573]  [fusion_574]  [fusion_579]  [fusion_583]  [fusion_584]  [fusion_587]  
Fusion : COSMICSS18 [18q11.2]  -  SSX4 [Xp11.23]  [fusion_502]  [fusion_503]  [fusion_507]  [fusion_508]  [fusion_525]  [fusion_526]  
Fusion : COSMICSSX1 [Xp11.23]  -  SS18 [18q11.2]  [fusion_575]  [fusion_578]  
Fusion : COSMICSSX2 [Xp11.22]  -  SS18 [18q11.2]  [fusion_524]  [fusion_576]  [fusion_580]  [fusion_585]  [fusion_586]  
Fusion: TCGASS18 18q11.2 DOCK2 5q35.1 PRAD
Fusion: TCGATRAPPC8 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]
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)SS18 (select the gene name)
Genetic variants : HAPMAP6760
Genomic Variants (DGV)SS18 [DGVbeta]
DECIPHER (Syndromes)18:23596217-23670611  ENSG00000141380
CONAN: Copy Number AnalysisSS18 
Mutations
ICGC Data PortalSS18 
TCGA Data PortalSS18 
Broad Tumor PortalSS18
OASIS PortalSS18 [ Somatic mutations - Copy number]
Cancer Gene: CensusSS18 
Somatic Mutations in Cancer : COSMICSS18  [overview]  [genome browser]  [tissue]  [distribution]  
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] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600192   
Orphanet3738   
MedgenSS18
Genetic Testing Registry SS18
NextProtQ15532 [Medical]
TSGene6760
GENETestsSS18
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)
Probes
Litterature
PubMed66 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

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indexed on : Fri Nov 18 19:58:59 CET 2016

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