Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SSX1 (SSX family member 1)

Identity

Alias (NCBI)CT5.1
SSRC
HGNC (Hugo) SSX1
HGNC Alias symbCT5.1
HGNC Alias namecancer/testis antigen family 5, member 1
HGNC Previous namesynovial sarcoma, X breakpoint 1
LocusID (NCBI) 6756
Atlas_Id 87
Location Xp11.23  [Link to chromosome band Xp11]
Location_base_pair Starts at 48255392 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)SSX1 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) [ 6 ]
  Prostate tumors: an overview
Soft tissue tumors: an overview
Testis: Spermatocytic seminoma
Soft Tissues: Synovial sarcoma with t(X;20)(p11;q13) SS18L1/SSX1
Soft Tissues: Synovial sarcoma with t(X;18)(p11.2;q11.2) SS18-SSX1/SSX2
t(X;18)(p11;q11) SS18/SSX1

External links

Nomenclature
HGNC (Hugo)SSX1   11335
Cards
Entrez_Gene (NCBI)SSX1    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:48255392-48267444 [Contig_View]  SSX1 [Vega]
ICGC DataPortalENSG00000126752
TCGA cBioPortalSSX1
AceView (NCBI)SSX1
Genatlas (Paris)SSX1
SOURCE (Princeton)SSX1
Genetics Home Reference (NIH)SSX1
Genomic and cartography
GoldenPath hg38 (UCSC)SSX1  -     chrX:48255392-48267444 +  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
genome Data Viewer NCBISSX1 [Mapview hg19]  
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
Alternative Splicing GalleryENSG00000126752
Gene ExpressionSSX1 [ NCBI-GEO ]   SSX1 [ EBI - ARRAY_EXPRESS ]   SSX1 [ SEEK ]   SSX1 [ MEM ]
Gene Expression Viewer (FireBrowse)SSX1 [ Firebrowse - Broad ]
GenevisibleExpression of SSX1 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
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
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]  
Fusion : MitelmanSS18/SSX1 [18q11.2/Xp11.23]  
Fusion : QuiverSSX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSSX1 [hg38]
dbVarSSX1
ClinVarSSX1
MonarchSSX1
1000_GenomesSSX1 
Exome Variant ServerSSX1
GNOMAD BrowserENSG00000126752
Varsome BrowserSSX1
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]
Cancer Gene: CensusSSX1 
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]
GENETestsSSX1
Target ValidationSSX1
Huge Navigator SSX1 [HugePedia]
ClinGenSSX1
Clinical trials, drugs, therapy
MyCancerGenomeSSX1
Protein Interactions : CTD
Pharm GKB GenePA36159
PharosQ16384
Clinical trialSSX1
Miscellaneous
canSAR (ICR)SSX1 (select the gene name)
HarmonizomeSSX1
DataMed IndexSSX1
Probes
Litterature
PubMed48 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSSX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 1 18:39:24 CET 2021
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