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Aliases for SSX1 Gene

Aliases for SSX1 Gene

  • SSX Family Member 1 2 3 5
  • Synovial Sarcoma, X Breakpoint 1 2 3 4
  • Cancer/Testis Antigen Family 5, Member 1 2 3
  • Cancer/Testis Antigen 5.1 3 4
  • CT5.1 3 4
  • Sarcoma, Synovial, X-Chromosome-Related 1 3
  • Protein SSX1 3
  • SSRC 3

External Ids for SSX1 Gene

Previous GeneCards Identifiers for SSX1 Gene

  • GC0XP046917
  • GC0XP046332
  • GC0XP046794
  • GC0XP047160
  • GC0XP047871
  • GC0XP047999
  • GC0XP047958
  • GC0XP048114
  • GC0XP045828

Summaries for SSX1 Gene

Entrez Gene Summary for SSX1 Gene

  • The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneous humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. This gene, and also the SSX2 and SSX4 family members, have been involved in t(X;18)(p11.2;q11.2) translocations that are characteristically found in all synovial sarcomas. This translocation results in the fusion of the synovial sarcoma translocation gene on chromosome 18 to one of the SSX genes on chromosome X. The encoded hybrid proteins are likely responsible for transforming activity. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Jul 2013]

CIViC summary for SSX1 Gene

GeneCards Summary for SSX1 Gene

SSX1 (SSX Family Member 1) is a Protein Coding gene. Diseases associated with SSX1 include Sarcoma, Synovial and Sarcoma. Among its related pathways are Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and transcription corepressor activity. An important paralog of this gene is SSX4.

UniProtKB/Swiss-Prot for SSX1 Gene

  • Could act as a modulator of transcription.

Gene Wiki entry for SSX1 Gene

Additional gene information for SSX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SSX1 Gene

Genomics for SSX1 Gene

GeneHancer (GH) Regulatory Elements for SSX1 Gene

Promoters and enhancers for SSX1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XI048255 Promoter 1.1 EPDnew 550.8 +0.0 35 0.1 HDAC1 PKNOX1 ATF1 TAF9B RB1 NFRKB POLR2B E2F8 FOS ATF7 SSX1 ENSG00000232813
GH0XI048256 Promoter 0.5 EPDnew 550.8 +1.1 1115 0.1 SSX1 ENSG00000232813
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SSX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SSX1 gene promoter:

Genomic Locations for SSX1 Gene

Genomic Locations for SSX1 Gene
12,128 bases
Plus strand

Genomic View for SSX1 Gene

Genes around SSX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SSX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SSX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SSX1 Gene

Proteins for SSX1 Gene

  • Protein details for SSX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein SSX1
    Protein Accession:
    Secondary Accessions:
    • A3KN76
    • Q08AJ2
    • Q5JQ64

    Protein attributes for SSX1 Gene

    188 amino acids
    Molecular mass:
    21931 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SSX1 Gene

Post-translational modifications for SSX1 Gene

No Post-translational modifications

Other Protein References for SSX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SSX1 Gene

Domains & Families for SSX1 Gene

Gene Families for SSX1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SSX1 Gene

Suggested Antigen Peptide Sequences for SSX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SSX family.
  • Belongs to the SSX family.
genes like me logo Genes that share domains with SSX1: view

Function for SSX1 Gene

Molecular function for SSX1 Gene

GENATLAS Biochemistry:
protein SSX1 with homology to Kruppel associated box,KRAB,transcriptional corepressor,complexing with polycomb group (PcG) proteins RING1 or BMI1 and associating with chromatin,fused with SYT (SSXT) in synovial sarcoma with translocation t(X;18)(p11.2;q11.2) (see BSSX)
UniProtKB/Swiss-Prot Function:
Could act as a modulator of transcription.

Gene Ontology (GO) - Molecular Function for SSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003714 transcription corepressor activity TAS 10072425
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SSX1: view
genes like me logo Genes that share phenotypes with SSX1: view

Human Phenotype Ontology for SSX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for SSX1 Gene

miRTarBase miRNAs that target SSX1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for SSX1 Gene

Localization for SSX1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SSX1 gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus TAS,IEA --
genes like me logo Genes that share ontologies with SSX1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SSX1 Gene

Pathways & Interactions for SSX1 Gene

genes like me logo Genes that share pathways with SSX1: view

Pathways by source for SSX1 Gene

1 KEGG pathway for SSX1 Gene

Gene Ontology (GO) - Biological Process for SSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:1903507 negative regulation of nucleic acid-templated transcription IEA --
genes like me logo Genes that share ontologies with SSX1: view

No data available for SIGNOR curated interactions for SSX1 Gene

Drugs & Compounds for SSX1 Gene

No Compound Related Data Available

Transcripts for SSX1 Gene

mRNA/cDNA for SSX1 Gene

Unigene Clusters for SSX1 Gene

Synovial sarcoma, X breakpoint 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SSX1 Gene

No ASD Table

Relevant External Links for SSX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SSX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SSX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SSX1 Gene

This gene is overexpressed in Testis (x46.4).

NURSA nuclear receptor signaling pathways regulating expression of SSX1 Gene:


SOURCE GeneReport for Unigene cluster for SSX1 Gene:


mRNA Expression by UniProt/SwissProt for SSX1 Gene:

Tissue specificity: Expressed at high level in the testis. Expressed at low level in thyroid. Not detected in tonsil, colon, lung, spleen, prostate, kidney, striated and smooth muscles. Detected in rhabdomyosarcoma and fibrosarcoma cell lines. Not detected in mesenchymal and epithelial cell lines.

Evidence on tissue expression from TISSUES for SSX1 Gene

  • Skin(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SSX1 Gene

Germ Layers:
  • mesoderm
  • skeleton
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
genes like me logo Genes that share expression patterns with SSX1: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for SSX1 Gene

Orthologs for SSX1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SSX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SSX1 34
  • 96 (a)
LOC465644 33
  • 95.92 (n)
(Canis familiaris)
Mammalia -- 34
  • 50 (a)
(Mus musculus)
Mammalia Ssxa1 34
  • 44 (a)
Gm21876 34
  • 43 (a)
Gm5751 34
  • 37 (a)
Ssxb5 34
  • 36 (a)
Ssxb8 34
  • 35 (a)
Ssxb9 34
  • 34 (a)
Ssxb3 34
  • 34 (a)
Ssxb10 34
  • 34 (a)
Ssxb1 34
  • 34 (a)
Gm14459 34
  • 33 (a)
Gm6592 34
  • 33 (a)
Ssxb2 34
  • 32 (a)
Ssx9 34
  • 32 (a)
Ssxb6 34
  • 30 (a)
(Bos Taurus)
Mammalia SSX5 34
  • 32 (a)
Species where no ortholog for SSX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SSX1 Gene

Gene Tree for SSX1 (if available)
Gene Tree for SSX1 (if available)

Paralogs for SSX1 Gene

Paralogs for SSX1 Gene

(14) SIMAP similar genes for SSX1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SSX1: view

Variants for SSX1 Gene

Sequence variations from dbSNP and Humsavar for SSX1 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs111617084 -- 48,258,191(+) T/C intron_variant
rs111623639 -- 48,266,818(+) G/A intron_variant
rs111664227 -- 48,261,906(+) C/T intron_variant
rs111695052 -- 48,265,354(+) A/T intron_variant
rs111727958 -- 48,257,934(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SSX1 Gene

Variant ID Type Subtype PubMed ID
dgv2288e212 CNV loss 25503493
esv25781 CNV gain 19812545
esv2671998 CNV deletion 23128226
esv2740145 CNV deletion 23290073
esv2740147 CNV deletion 23290073
esv2752324 CNV gain 17911159
esv2758866 CNV gain+loss 17122850
esv32909 CNV gain+loss 17666407
nsv519165 CNV loss 19592680
nsv519305 CNV gain 19592680
nsv523595 CNV gain 19592680

Variation tolerance for SSX1 Gene

Residual Variation Intolerance Score: 96.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.99; 36.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SSX1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SSX1 Gene

Disorders for SSX1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for SSX1 Gene - From: HGMD, OMIM, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
sarcoma, synovial
  • synovial sarcoma
  • connective and soft tissue neoplasm
synovium cancer
  • malignant tumor of synovium
spindle cell synovial sarcoma
  • synovial sarcoma with spindle cell components
epithelioid cell synovial sarcoma
  • epithelioid synovial sarcoma
- elite association - COSMIC cancer census association via MalaCards
Search SSX1 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving SSX1 may be a cause of synovial sarcoma. Translocation t(X;18)(p11.2;q11.2). The translocation is specifically found in more than 80% of synovial sarcoma. The fusion products SSXT-SSX1 or SSXT-SSX2 are probably responsible for transforming activity. Heterogeneity in the position of the breakpoint can occur (low frequency). {ECO:0000269 PubMed:7539744}.

Additional Disease Information for SSX1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SSX1: view

No data available for Genatlas for SSX1 Gene

Publications for SSX1 Gene

  1. Identification of two alternative fusion genes, SYT-SSX1 and SYT-SSX2, in t(X;18)(p11.2;q11.2)-positive synovial sarcomas. (PMID: 7655467) de Leeuw B … Geurts van Kessel A (Human molecular genetics 1995) 2 3 4 58
  2. Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial sarcoma. (PMID: 7539744) Crew AJ … Cooper CS (The EMBO journal 1995) 3 4 22 58
  3. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. (PMID: 19204726) Chapuis J … Lambert JC (Molecular psychiatry 2009) 3 44 58
  4. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SSX1 Gene

Sources for SSX1 Gene

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