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

    Gene ID: 6760, updated on 28-Oct-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, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 26.0), adrenal (RPKM 22.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SS18 in Genome Data Viewer
    Location:
    18q11.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26016253..26091219, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (26210888..26285993, complement)
    RS_2024_09 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 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. Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma. Tamborini E, et al. Br J Cancer, 2001 Apr 20. PMID 11308259, Free PMC Article
    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. A novel variant of SYT-SSX1 fusion gene in a case of spindle cell synovial sarcoma. Krsková L, et al. Diagn Mol Pathol, 2007 Sep. PMID 17721327
    4. Cryptic chromosome rearrangement resulting in SYT-SSX2 fusion gene in a monophasic synovial sarcoma. Torres L, et al. Cancer Genet Cytogenet, 2008 Nov. PMID 18992642
    5. 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

    See all (105) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Undifferentiated Round Cell Sarcoma With CRTC1::SS18 Fusion: Expanding Clinicopathologic Features of a Rare Translocation Sarcoma With Prominent Desmoplastic Stroma.
      Title: Undifferentiated Round Cell Sarcoma With CRTC1::SS18 Fusion: Expanding Clinicopathologic Features of a Rare Translocation Sarcoma With Prominent Desmoplastic Stroma.
    2. 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.
    3. 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.
    4. 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.
    5. SS18 regulates pluripotent-somatic transition through phase separation.
      Title: SS18 regulates pluripotent-somatic transition through phase separation.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (51)

    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 
    located_in 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
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    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_2024_08

    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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