Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SSX4 (SSX family member 4)

Identity

Alias (NCBI)CT5.4
HGNC (Hugo) SSX4
HGNC Alias symbCT5.4
HGNC Previous namesynovial sarcoma, X breakpoint 4
LocusID (NCBI) 6759
Atlas_Id 42409
Location Xp11.23  [Link to chromosome band Xp11]
Location_base_pair Starts at 48383527 and ends at 48393343 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) / SSX4 (Xp11.23)SS18L1 (20q13.33) / SSX4 (Xp11.23)SSX4 (Xp11.23) / SS18 (18q11.2)
SSX4 (Xp11.23) / SS18L1 (20q13.33)SYT1 (12q21.2) / SSX4 (Xp11.23)

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  Soft tissue tumors: an overview
Testis: Spermatocytic seminoma
t(X;18)(p11;q11) SS18/SSX4

External links

Nomenclature
HGNC (Hugo)SSX4   11338
Cards
Entrez_Gene (NCBI)SSX4  6759  SSX family member 4
AliasesCT5.4
GeneCards (Weizmann)SSX4
Ensembl hg19 (Hinxton)ENSG00000268009 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000268009 [Gene_View]  ENSG00000268009 [Sequence]  chrX:48383527-48393343 [Contig_View]  SSX4 [Vega]
ICGC DataPortalENSG00000268009
TCGA cBioPortalSSX4
AceView (NCBI)SSX4
Genatlas (Paris)SSX4
WikiGenes6759
SOURCE (Princeton)SSX4
Genetics Home Reference (NIH)SSX4
Genomic and cartography
GoldenPath hg38 (UCSC)SSX4  -     chrX:48383527-48393343 +  Xp11.23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SSX4  -     Xp11.23   [Description]    (hg19-Feb_2009)
GoldenPathSSX4 - Xp11.23 [CytoView hg19]  SSX4 - Xp11.23 [CytoView hg38]
ImmunoBaseENSG00000268009
genome Data Viewer NCBISSX4 [Mapview hg19]  
OMIM300326   
Gene and transcription
Genbank (Entrez)AX740218 BC005325 BC103864 BC137394 BC137395
RefSeq transcript (Entrez)NM_005636 NM_175729
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SSX4
Alternative Splicing GalleryENSG00000268009
Gene ExpressionSSX4 [ NCBI-GEO ]   SSX4 [ EBI - ARRAY_EXPRESS ]   SSX4 [ SEEK ]   SSX4 [ MEM ]
Gene Expression Viewer (FireBrowse)SSX4 [ Firebrowse - Broad ]
GenevisibleExpression of SSX4 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6759
GTEX Portal (Tissue expression)SSX4
Human Protein AtlasENSG00000268009-SSX4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO60224   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO60224  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO60224
Splice isoforms : SwissVarO60224
PhosPhoSitePlusO60224
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)SSX4
DMDM Disease mutations6759
Blocks (Seattle)SSX4
SuperfamilyO60224
Human Protein Atlas [tissue]ENSG00000268009-SSX4 [tissue]
Peptide AtlasO60224
HPRD02266
Protein Interaction databases
DIP (DOE-UCLA)O60224
IntAct (EBI)O60224
FunCoupENSG00000268009
BioGRIDSSX4
STRING (EMBL)SSX4
ZODIACSSX4
Ontologies - Pathways
QuickGOO60224
Ontology : AmiGOnucleic acid binding  nucleus  regulation of transcription, DNA-templated  
Ontology : EGO-EBInucleic acid binding  nucleus  regulation of transcription, DNA-templated  
NDEx NetworkSSX4
Atlas of Cancer Signalling NetworkSSX4
Wikipedia pathwaysSSX4
Orthology - Evolution
OrthoDB6759
GeneTree (enSembl)ENSG00000268009
Phylogenetic Trees/Animal Genes : TreeFamSSX4
HOGENOMO60224
Homologs : HomoloGeneSSX4
Homology/Alignments : Family Browser (UCSC)SSX4
Gene fusions - Rearrangements
Fusion : MitelmanSS18/SSX4 [18q11.2/Xp11.23]  
Fusion : QuiverSSX4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSSX4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SSX4
dbVarSSX4
ClinVarSSX4
MonarchSSX4
1000_GenomesSSX4 
Exome Variant ServerSSX4
GNOMAD BrowserENSG00000268009
Varsome BrowserSSX4
Genetic variants : HAPMAP6759
Genomic Variants (DGV)SSX4 [DGVbeta]
DECIPHERSSX4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSSX4 
Mutations
ICGC Data PortalSSX4 
TCGA Data PortalSSX4 
Broad Tumor PortalSSX4
OASIS PortalSSX4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSSX4  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSSX4
Mutations and Diseases : HGMDSSX4
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SSX4
DgiDB (Drug Gene Interaction Database)SSX4
DoCM (Curated mutations)SSX4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SSX4 (select a term)
intoGenSSX4
Cancer3DSSX4(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300326   
Orphanet
DisGeNETSSX4
MedgenSSX4
Genetic Testing Registry SSX4
NextProtO60224 [Medical]
TSGene6759
GENETestsSSX4
Target ValidationSSX4
Huge Navigator SSX4 [HugePedia]
snp3D : Map Gene to Disease6759
BioCentury BCIQSSX4
ClinGenSSX4
Clinical trials, drugs, therapy
Protein Interactions : CTD6759
Pharm GKB GenePA36162
Clinical trialSSX4
Miscellaneous
canSAR (ICR)SSX4 (select the gene name)
HarmonizomeSSX4
DataMed IndexSSX4
Probes
Litterature
PubMed23 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSSX4
EVEXSSX4
GoPubMedSSX4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 14 14:34:28 CEST 2020
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