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SS18 SS18 subunit of BAF chromatin remodeling complex [ Homo sapiens (human) ]

Gene ID: 6760, updated on 3-Apr-2024

Summary

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Official Symbol
SS18provided by HGNC
Official Full Name
SS18 subunit of BAF chromatin remodeling complexprovided by HGNC
Primary source
HGNC:HGNC:11340
See related
Ensembl:ENSG00000141380 MIM:600192; AllianceGenome:HGNC:11340
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SYT; SSXT; SMARCL1
Summary
Enables nuclear receptor coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Part of SWI/SNF complex. Implicated in synovial sarcoma. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 26.0), adrenal (RPKM 22.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
18q11.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26016253..26091219, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (26210888..26285993, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (23596217..23671183, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:23407561-23408062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:23408063-23408562 Neighboring gene RNA, 7SL, cytoplasmic 97, pseudogene Neighboring gene VISTA enhancer hs1566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13176 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23531372-23531568 Neighboring gene uncharacterized LOC124904271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13178 Neighboring gene ribosomal protein S24 pseudogene 18 Neighboring gene proteasome 20S subunit alpha 8 Neighboring gene dihydrofolate reductase pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Correlating SS18-SSX immunohistochemistry (IHC) with SS18 fluorescent in situ hybridization (FISH) in synovial sarcomas: a study of 36 cases. Tay TKY, et al. Virchows Arch, 2021 Oct. PMID 34091760
  2. The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma. McBride MJ, et al. Nat Struct Mol Biol, 2020 Sep. PMID 32747783, Free PMC Article
  3. SS18-SSX-Dependent YAP/TAZ Signaling in Synovial Sarcoma. Isfort I, et al. Clin Cancer Res, 2019 Jun 15. PMID 30814111
  4. A clinicopathologic study on SS18 fusion positive head and neck synovial sarcomas. Owosho AA, et al. Oral Oncol, 2017 Mar. PMID 28249647, Free PMC Article
  5. Synovial sarcoma in knee joint, mimicking low-grade sarcoma confirmed by molecular detection of SYT gene split. Kimura H, et al. Anticancer Res, 2014 Jun. PMID 24922679

See all (100) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SS18-SSX Expression in a Contemporary Cohort of Primary Renal Synovial Sarcoma: A Multi-Institutional Experience of Fourteen Patients.
    Title: SS18-SSX Expression in a Contemporary Cohort of Primary Renal Synovial Sarcoma: A Multi-Institutional Experience of Fourteen Patients.
  2. Microcribriform Adenocarcinoma of Salivary Glands: A Unique Tumor Entity Characterized by an SS18::ZBTB7A Fusion.
    Title: Microcribriform Adenocarcinoma of Salivary Glands: A Unique Tumor Entity Characterized by an SS18::ZBTB7A Fusion.
  3. Correlating SS18-SSX immunohistochemistry (IHC) with SS18 fluorescent in situ hybridization (FISH) in synovial sarcomas: a study of 36 cases.
    Title: Correlating SS18-SSX immunohistochemistry (IHC) with SS18 fluorescent in situ hybridization (FISH) in synovial sarcomas: a study of 36 cases.
  4. SS18 regulates pluripotent-somatic transition through phase separation.
    Title: SS18 regulates pluripotent-somatic transition through phase separation.
  5. The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.
    Title: The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.
  6. Synovial sarcoma is a soft tissue malignancy characterized by a reciprocal t(X;18) translocation. This results into SS18-SSX fusion protein which activates YAP/TAZ signaling in synovial sarcoma.
    Title: SS18-SSX-Dependent YAP/TAZ Signaling in Synovial Sarcoma.
  7. A novel MEF2C-SS18 gene fusion and unique histologic and immunophenotypic features characterize a heretofore undefined low-grade salivary adenocarcinoma for described as a microsecretory adenocarcinoma.
    Title: Microsecretory Adenocarcinoma: A Novel Salivary Gland Tumor Characterized by a Recurrent MEF2C-SS18 Fusion.
  8. Case Reports: identify a novel recurrent gene fusion, CRTC1-SS18, in undifferentiated small round cell sarcoma.
    Title: Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1-SS18 gene fusion.
  9. SS18-SSX1 deregulates developmental programs to drive transformation by hijacking a transcriptional repressive complex to aberrantly activate gene expression
    Title: The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma.
  10. Synovial sarcoma (SS) is considered as high-grade tumors with a poor prognosis. Novel therapies targeted at fusion oncogene, SS18-SSX-derived peptide vaccine, epidermal growth factor receptor, and vascular endothelial growth factor are the future hope in SS.
    Title: Primary pulmonary synovial sarcoma: A reappraisal.
Submit: New GeneRIF Correction See all GeneRIFs (50)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
EBI GWAS Catalog
Genome-wide association study of chronic periodontitis in a general German population.
EBI GWAS Catalog
Genome-wide association study of selenium concentrations.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC116875

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nuclear receptor coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cell morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in ephrin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in microtubule cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in neuronal stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell population proliferation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of stem cell population maintenance NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of GBAF complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of SWI/SNF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin NAS
Non-traceable Author Statement
more info
 PubMed 
located_in microtubule cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
part_of npBAF complex IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein SSXT
Names
SS18, nBAF chromatin remodeling complex subunit
synovial sarcoma translocated to X chromosome protein
synovial sarcoma translocation, chromosome 18
synovial sarcoma, translocated to X chromosome

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001007559.3 → NP_001007560.1  protein SSXT isoform 1

    See identical proteins and their annotated locations for NP_001007560.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC091021, AF343880, AU279615, AW081610, X79201
    Consensus CDS
    CCDS32807.1
    UniProtKB/Swiss-Prot
    B0YJ95, Q15532, Q16404, Q4VAX1, Q9BXC6
    UniProtKB/TrEMBL
    A8K0E5
    Related
    ENSP00000414516.2, ENST00000415083.7
    Conserved Domains (1) summary
    pfam05030
    Location:14 → 73
    SSXT; SSXT protein (N-terminal region)

  2. NM_001308201.2 → NP_001295130.1  protein SSXT isoform 3

    See identical proteins and their annotated locations for NP_001295130.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC091021, AK296949, AW081610, DC378335, X79201
    Consensus CDS
    CCDS77168.1
    UniProtKB/TrEMBL
    A8K0E5, B4DLD3
    Related
    ENSP00000438066.2, ENST00000542420.6
    Conserved Domains (1) summary
    pfam05030
    Location:1 → 50
    SSXT; SSXT protein (N-terminal region)

  3. NM_005637.4 → NP_005628.2  protein SSXT isoform 2

    See identical proteins and their annotated locations for NP_005628.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC091021, AU279615, AW081610, X79201
    Consensus CDS
    CCDS54183.1
    UniProtKB/TrEMBL
    Q4VAX0, Q6FGL9
    Related
    ENSP00000269137.7, ENST00000269137.11
    Conserved Domains (1) summary
    pfam05030
    Location:14 → 73
    SSXT; SSXT protein (N-terminal region)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    26016253..26091219 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437767.1 → XP_047293723.1  protein SSXT isoform X3

  2. XM_047437763.1 → XP_047293719.1  protein SSXT isoform X2

  3. XM_047437766.1 → XP_047293722.1  protein SSXT isoform X2

  4. XM_047437762.1 → XP_047293718.1  protein SSXT isoform X2

  5. XM_047437765.1 → XP_047293721.1  protein SSXT isoform X2

  6. XM_047437764.1 → XP_047293720.1  protein SSXT isoform X2

  7. XM_047437760.1 → XP_047293716.1  protein SSXT isoform X2

  8. XM_047437768.1 → XP_047293724.1  protein SSXT isoform X3

  9. XM_011526145.2 → XP_011524447.1  protein SSXT isoform X1

    See identical proteins and their annotated locations for XP_011524447.1

    UniProtKB/TrEMBL
    A8K0E5, B4DLD3
    Conserved Domains (1) summary
    pfam05030
    Location:1 → 50
    SSXT; SSXT protein (N-terminal region)

  10. XM_047437761.1 → XP_047293717.1  protein SSXT isoform X2

  11. XM_047437769.1 → XP_047293725.1  protein SSXT isoform X4

    UniProtKB/TrEMBL
    B4DR34

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    26210888..26285993 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319035.1 → XP_054175010.1  protein SSXT isoform X3

  2. XM_054319026.1 → XP_054175001.1  protein SSXT isoform X1

    UniProtKB/TrEMBL
    B4DLD3

  3. XM_054319034.1 → XP_054175009.1  protein SSXT isoform X3

  4. XM_054319030.1 → XP_054175005.1  protein SSXT isoform X2

  5. XM_054319033.1 → XP_054175008.1  protein SSXT isoform X2

  6. XM_054319029.1 → XP_054175004.1  protein SSXT isoform X2

  7. XM_054319032.1 → XP_054175007.1  protein SSXT isoform X2

  8. XM_054319031.1 → XP_054175006.1  protein SSXT isoform X2

  9. XM_054319027.1 → XP_054175002.1  protein SSXT isoform X2

  10. XM_054319028.1 → XP_054175003.1  protein SSXT isoform X2

  11. XM_054319036.1 → XP_054175011.1  protein SSXT isoform X4

    UniProtKB/TrEMBL
    B4DR34
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15532.3 GenPept UniProtKB/Swiss-Prot:Q15532

Gene LinkOut

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