Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SSX1 (SSX family member 1)

Identity

Alias_namessynovial sarcoma, X breakpoint 1
Alias_symbol (synonym)CT5.1
Other aliasSSRC
HGNC (Hugo) SSX1
LocusID (NCBI) 6756
Atlas_Id 87
Location Xp11.23  [Link to chromosome band Xp11]
Location_base_pair Starts at 48255317 and ends at 48267444 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
SS18 (18q11.2) / SSX1 (Xp11.23)SS18L1 (20q13.33) / SSX1 (Xp11.23)SSX1 (Xp11.23) / SS18 (18q11.2)
SSX1 (Xp11.23) / SS18L1 (20q13.33)SSX1 (Xp11.23) / SSX1 (Xp11.23)SSX1 (Xp11.23) / SYT1 (12q21.2)
SSX1 (Xp11.23) / SYT4 (18q12.3)SYT1 (12q21.2) / SSX1 (Xp11.23)SS18L1 20q13.33 / SSX1 Xp11.23
SS18 18q11.2 / SSX1 Xp11.23SSX1 Xp11.23 / SS18 18q11.2

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Breakpoints

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 5 ]

Solid Tumors ProstateOverviewID5041 softissuTumID5042 SynovialSarcomtX20ID5464 SynovSarcID5044 TT_t0X18p11q11ID6592

External links

Nomenclature
HGNC (Hugo)SSX1   11335
Cards
Entrez_Gene (NCBI)SSX1  6756  SSX family member 1
AliasesCT5.1; SSRC
GeneCards (Weizmann)SSX1
Ensembl hg19 (Hinxton)ENSG00000126752 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000126752 [Gene_View]  ENSG00000126752 [Sequence]  chrX:48255317-48267444 [Contig_View]  SSX1 [Vega]
ICGC DataPortalENSG00000126752
TCGA cBioPortalSSX1
AceView (NCBI)SSX1
Genatlas (Paris)SSX1
WikiGenes6756
SOURCE (Princeton)SSX1
Genetics Home Reference (NIH)SSX1
Genomic and cartography
GoldenPath hg38 (UCSC)SSX1  -     chrX:48255317-48267444 +  Xp11.23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SSX1  -     Xp11.23   [Description]    (hg19-Feb_2009)
GoldenPathSSX1 - Xp11.23 [CytoView hg19]  SSX1 - Xp11.23 [CytoView hg38]
ImmunoBaseENSG00000126752
Mapping of homologs : NCBISSX1 [Mapview hg19]  SSX1 [Mapview hg38]
OMIM300813   312820   
Gene and transcription
Genbank (Entrez)BC001003 BC125151 BC128611 BC133693 BC150487
RefSeq transcript (Entrez)NM_001278691 NM_005635
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SSX1
Cluster EST : UnigeneHs.434142 [ NCBI ]
CGAP (NCI)Hs.434142
Alternative Splicing GalleryENSG00000126752
Gene ExpressionSSX1 [ NCBI-GEO ]   SSX1 [ EBI - ARRAY_EXPRESS ]   SSX1 [ SEEK ]   SSX1 [ MEM ]
Gene Expression Viewer (FireBrowse)SSX1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6756
GTEX Portal (Tissue expression)SSX1
Human Protein AtlasENSG00000126752-SSX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ16384   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ16384  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ16384
Splice isoforms : SwissVarQ16384
PhosPhoSitePlusQ16384
Domaine pattern : Prosite (Expaxy)KRAB_RELATED (PS50806)   
Domains : Interpro (EBI)KRAB    KRAB_dom_sf    Krueppel-associated_box-rel    SSX    SSXRD_motif   
Domain families : Pfam (Sanger)KRAB (PF01352)    SSXRD (PF09514)   
Domain families : Pfam (NCBI)pfam01352    pfam09514   
Domain families : Smart (EMBL)KRAB (SM00349)  
Conserved Domain (NCBI)SSX1
DMDM Disease mutations6756
Blocks (Seattle)SSX1
SuperfamilyQ16384
Human Protein Atlas [tissue]ENSG00000126752-SSX1 [tissue]
Peptide AtlasQ16384
HPRD02428
IPIIPI00001519   
Protein Interaction databases
DIP (DOE-UCLA)Q16384
IntAct (EBI)Q16384
FunCoupENSG00000126752
BioGRIDSSX1
STRING (EMBL)SSX1
ZODIACSSX1
Ontologies - Pathways
QuickGOQ16384
Ontology : AmiGOnucleic acid binding  transcription corepressor activity  protein binding  nucleus  regulation of transcription, DNA-templated  negative regulation of nucleic acid-templated transcription  
Ontology : EGO-EBInucleic acid binding  transcription corepressor activity  protein binding  nucleus  regulation of transcription, DNA-templated  negative regulation of nucleic acid-templated transcription  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkSSX1
Atlas of Cancer Signalling NetworkSSX1
Wikipedia pathwaysSSX1
Orthology - Evolution
OrthoDB6756
GeneTree (enSembl)ENSG00000126752
Phylogenetic Trees/Animal Genes : TreeFamSSX1
HOGENOMQ16384
Homologs : HomoloGeneSSX1
Homology/Alignments : Family Browser (UCSC)SSX1
Gene fusions - Rearrangements
Fusion : MitelmanSS18L1/SSX1 [20q13.33/Xp11.23]  [t(X;20)(p11;q13)]  
Fusion : MitelmanSS18/SSX1 [18q11.2/Xp11.23]  [ins(X;18)(p11;q11q21)]  [t(X;18)(p11;q11)]  
Fusion : QuiverSSX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSSX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SSX1
dbVarSSX1
ClinVarSSX1
1000_GenomesSSX1 
Exome Variant ServerSSX1
ExAC (Exome Aggregation Consortium)ENSG00000126752
GNOMAD BrowserENSG00000126752
Varsome BrowserSSX1
Genetic variants : HAPMAP6756
Genomic Variants (DGV)SSX1 [DGVbeta]
DECIPHERSSX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSSX1 
Mutations
ICGC Data PortalSSX1 
TCGA Data PortalSSX1 
Broad Tumor PortalSSX1
OASIS PortalSSX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSSX1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSSX1
Mutations and Diseases : HGMDSSX1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)X-chromosome gene database
BioMutasearch SSX1
DgiDB (Drug Gene Interaction Database)SSX1
DoCM (Curated mutations)SSX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SSX1 (select a term)
intoGenSSX1
Cancer3DSSX1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300813    312820   
Orphanet3738   
DisGeNETSSX1
MedgenSSX1
Genetic Testing Registry SSX1
NextProtQ16384 [Medical]
TSGene6756
GENETestsSSX1
Target ValidationSSX1
Huge Navigator SSX1 [HugePedia]
snp3D : Map Gene to Disease6756
BioCentury BCIQSSX1
ClinGenSSX1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6756
Chemical/Pharm GKB GenePA36159
Clinical trialSSX1
Miscellaneous
canSAR (ICR)SSX1 (select the gene name)
DataMed IndexSSX1
Probes
Litterature
PubMed47 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSSX1
EVEXSSX1
GoPubMedSSX1
iHOPSSX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Aug 26 18:30:39 CEST 2019
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