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SSX2B SSX family member 2B [ Homo sapiens (human) ]

Gene ID: 727837, updated on 31-Jan-2024

Summary

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Official Symbol
SSX2Bprovided by HGNC
Official Full Name
SSX family member 2Bprovided by HGNC
Primary source
HGNC:HGNC:22263
See related
Ensembl:ENSG00000268447 AllianceGenome:HGNC:22263
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
SSX; CT5.2; CT5.2b; HOM-MEL-40
Summary
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 SSX1 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. This gene also has an identical duplicate, GeneID: 6757, located about 45 kb upstream in the opposite orientation on chromosome X. [provided by RefSeq, Jul 2013]
Expression
Restricted expression toward testis (RPKM 18.4) See more
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Genomic context

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Location:
Xp11.22
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (52751252..52761536)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (52036196..52046488)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (52780329..52790617)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ornithine aminotransferase pseudogene Neighboring gene ornithine aminotransferase pseudogene Neighboring gene S100A11 pseudogene 8 Neighboring gene SSX family member 21, pseudogene

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. Identification of two alternative fusion genes, SYT-SSX1 and SYT-SSX2, in t(X;18)(p11.2;q11.2)-positive synovial sarcomas. de Leeuw B, et al. Hum Mol Genet, 1995 Jun. PMID 7655467
  2. Fusion of SYT to two genes, SSX1 and SSX2, encoding proteins with homology to the Kruppel-associated box in human synovial sarcoma. Crew AJ, et al. EMBO J, 1995 May 15. PMID 7539744, Free PMC Article
  3. Molecular diagnosis of synovial sarcoma and characterization of a variant SYT-SSX2 fusion transcript. Fligman I, et al. Am J Pathol, 1995 Dec. PMID 7495284, Free PMC Article
  4. Heterogeneous expression of the SSX cancer/testis antigens in human melanoma lesions and cell lines. dos Santos NR, et al. Cancer Res, 2000 Mar 15. PMID 10749136
  5. Identification of novel genes, SYT and SSX, involved in the t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma. Clark J, et al. Nat Genet, 1994 Aug. PMID 7951320

See all (19) 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.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

  • MGC21532, MGC88485

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
protein SSX2
Names
cancer/testis antigen 5.2
cancer/testis antigen family 5, member 2b
synovial sarcoma, X breakpoint 2B
tumor antigen HOM-MEL-40

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_001164417.3 → NP_001157889.1  protein SSX2 isoform b

    See identical proteins and their annotated locations for NP_001157889.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) contains a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC244505, BC016957, BC071827
    Consensus CDS
    CCDS48129.1
    UniProtKB/Swiss-Prot
    Q16385, Q5JS26, Q96IP7, Q9BU88
    Related
    ENSP00000470740.2, ENST00000596480.6
    Conserved Domains (3) summary
    cd07765
    Location:24 → 61
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00349
    Location:23 → 82
    KRAB; krueppel associated box
    pfam09514
    Location:156 → 187
    SSXRD; SSXRD motif

  2. NM_001278701.2 → NP_001265630.1  protein SSX2 isoform a

    See identical proteins and their annotated locations for NP_001265630.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC244505, BC071827
    Consensus CDS
    CCDS65267.1
    UniProtKB/Swiss-Prot
    Q16385
    Related
    ENSP00000477922.1, ENST00000612490.1
    Conserved Domains (1) summary
    smart00349
    Location:23 → 82
    KRAB; krueppel associated box

  3. NM_001278702.2 → NP_001265631.1  protein SSX2 isoform c

    See identical proteins and their annotated locations for NP_001265631.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (c) contains a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC244505, BC016957, BC071827, BE391023
    UniProtKB/TrEMBL
    R9QTR3
    Conserved Domains (3) summary
    cd07765
    Location:24 → 61
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00349
    Location:23 → 82
    KRAB; krueppel associated box
    pfam09514
    Location:182 → 213
    SSXRD; SSXRD motif

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    52751252..52761536
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    52036196..52046488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16385.2 GenPept UniProtKB/Swiss-Prot:Q16385

Gene LinkOut

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