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VTCN1 V-set domain containing T cell activation inhibitor 1 [ Homo sapiens (human) ]

Gene ID: 79679, updated on 3-Apr-2024

Summary

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Official Symbol
VTCN1provided by HGNC
Official Full Name
V-set domain containing T cell activation inhibitor 1provided by HGNC
Primary source
HGNC:HGNC:28873
See related
Ensembl:ENSG00000134258 MIM:608162; AllianceGenome:HGNC:28873
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
B7X; B7H4; B7S1; B7-H4; B7h.5; VCTN1; PRO1291
Summary
This gene encodes a protein belonging to the B7 costimulatory protein family. Proteins in this family are present on the surface of antigen-presenting cells and interact with ligand bound to receptors on the surface of T cells. Studies have shown that high levels of the encoded protein has been correlated with tumor progression. A pseudogene of this gene is located on chromosome 20. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in kidney (RPKM 5.0), pancreas (RPKM 2.8) and 9 other tissues See more
Orthologs
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Genomic context

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See VTCN1 in Genome Data Viewer
Location:
1p13.1-p12
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (117143587..117210927, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (117154077..117221391, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117686209..117753549, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1580 Neighboring gene uncharacterized LOC124904387 Neighboring gene MPRA-validated peak386 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:117689065-117690264 Neighboring gene tripartite motif containing 45 Neighboring gene ribosomal protein S15a pseudogene 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117714175-117714737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117714738-117715299 Neighboring gene Sharpr-MPRA regulatory region 504 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:117811525-117812043 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:117842461-117842998 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117842999-117843536 Neighboring gene long intergenic non-protein coding RNA 1525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117900419-117901060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117918162-117918686 Neighboring gene mannosidase alpha class 1A member 2 Neighboring gene MPRA-validated peak388 silencer

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. B7x in cancer immunity and immunotherapy. Mortezaee K. Int Immunopharmacol, 2023 May. PMID 37028278
  2. The stromal tumor-infiltrating lymphocytes, cancer stemness, epithelial-mesenchymal transition, and B7-H4 expression in ovarian serous carcinoma. Hwang C, et al. J Ovarian Res, 2023 Jan 6. PMID 36609273, Free PMC Article
  3. The immunological role of B7-H4 in pregnant women with Sars-Cov2 infection. Duan L, et al. Am J Reprod Immunol, 2022 Dec. PMID 36121927, Free PMC Article
  4. B7-H4 correlates with clinical outcome and immunotherapeutic benefit in muscle-invasive bladder cancer. Liu Z, et al. Eur J Cancer, 2022 Aug. PMID 35717821
  5. Silencing of B7H4 Represses the Development of Oral Squamous Cell Carcinoma Through Promotion of M1 Macrophage Polarization. Chi J, et al. J Oral Maxillofac Surg, 2022 Aug. PMID 35568099

See all (169) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Diagnostic, clinicopathological features and prognostic value of B7x expression in Chinese women with breast cancer: A meta-analysis.
    Title: Diagnostic, clinicopathological features and prognostic value of B7x expression in Chinese women with breast cancer: A meta-analysis.
  2. An Investigation of the Effects of B7-H4 Gene rs10754339 and miR-125a Gene rs12976445 on Cancer Susceptibility.
    Title: An Investigation of the Effects of B7-H4 Gene rs10754339 and miR-125a Gene rs12976445 on Cancer Susceptibility.
  3. Association of B7H3 and B7H4 gene polymorphisms and protein expression with the development and prognosis of autoimmune thyroid diseases.
    Title: Association of B7H3 and B7H4 gene polymorphisms and protein expression with the development and prognosis of autoimmune thyroid diseases.
  4. B7x in cancer immunity and immunotherapy.
    Title: B7x in cancer immunity and immunotherapy.
  5. The stromal tumor-infiltrating lymphocytes, cancer stemness, epithelial-mesenchymal transition, and B7-H4 expression in ovarian serous carcinoma.
    Title: The stromal tumor-infiltrating lymphocytes, cancer stemness, epithelial-mesenchymal transition, and B7-H4 expression in ovarian serous carcinoma.
  6. Effect of B7-H4 downregulation induced by Toxoplasma gondii infection on dysfunction of decidual macrophages contributes to adverse pregnancy outcomes.
    Title: Effect of B7-H4 downregulation induced by Toxoplasma gondii infection on dysfunction of decidual macrophages contributes to adverse pregnancy outcomes.
  7. The immunological role of B7-H4 in pregnant women with Sars-Cov2 infection.
    Title: The immunological role of B7-H4 in pregnant women with Sars-Cov2 infection.
  8. Altered Levels of Negative Costimulatory Molecule V-Set Domain-Containing T-Cell Activation Inhibitor-1 (VTCN1) and Metalloprotease Nardilysin (NRD1) are Associated with Generalized Active Vitiligo.
    Title: Altered Levels of Negative Costimulatory Molecule V-Set Domain-Containing T-Cell Activation Inhibitor-1 (VTCN1) and Metalloprotease Nardilysin (NRD1) are Associated with Generalized Active Vitiligo.
  9. Silencing of B7-H4 induces intracellular oxidative stress and inhibits cell viability of breast cancer cells via downregulating PRDX3.
    Title: Silencing of B7-H4 induces intracellular oxidative stress and inhibits cell viability of breast cancer cells via downregulating PRDX3.
  10. Silencing of B7H4 Represses the Development of Oral Squamous Cell Carcinoma Through Promotion of M1 Macrophage Polarization.
    Title: Silencing of B7H4 Represses the Development of Oral Squamous Cell Carcinoma Through Promotion of M1 Macrophage Polarization.
Submit: New GeneRIF Correction See all GeneRIFs (159)

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
Identification of a novel susceptibility locus for juvenile idiopathic arthritis by genome-wide association analysis.
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

  • FLJ22418

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
enables signaling receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in T cell receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in adaptive immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of T cell activation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of T cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of T cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of interleukin-2 production IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cytokine production IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to protozoan IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
V-set domain-containing T-cell activation inhibitor 1
Names
B7 family member, H4
B7 homolog 4
B7 superfamily member 1
T cell costimulatory molecule B7x
immune costimulatory protein B7-H4

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_001253849.2 → NP_001240778.1  V-set domain-containing T-cell activation inhibitor 1 isoform 2

    See identical proteins and their annotated locations for NP_001240778.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region and uses a downstream start codon compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AI686571, AK303466, AL391476
    Consensus CDS
    CCDS58019.1
    UniProtKB/Swiss-Prot
    Q7Z7D3
    Related
    ENSP00000444724.1, ENST00000539893.5
    Conserved Domains (1) summary
    cl11960
    Location:2 → 44
    Ig; Immunoglobulin domain

  2. NM_001253850.2 → NP_001240779.1  V-set domain-containing T-cell activation inhibitor 1 isoform 3

    See identical proteins and their annotated locations for NP_001240779.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
    Source sequence(s)
    AI686571, AL391476, DQ103757
    Consensus CDS
    CCDS58020.1
    UniProtKB/Swiss-Prot
    Q7Z7D3
    Related
    ENSP00000328168.3, ENST00000328189.7

  3. NM_024626.4 → NP_078902.2  V-set domain-containing T-cell activation inhibitor 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_078902.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
    Source sequence(s)
    AI686571, AL391476, AY280972, CN259811, DB198367
    Consensus CDS
    CCDS894.1
    UniProtKB/Swiss-Prot
    Q0GN76, Q45VN0, Q5WPZ3, Q6P097, Q7Z7D3, Q9H6B2
    UniProtKB/TrEMBL
    Q5T2L0
    Related
    ENSP00000358470.3, ENST00000369458.8
    Conserved Domains (2) summary
    smart00410
    Location:46 → 144
    IG_like; Immunoglobulin like
    cl11960
    Location:49 → 146
    Ig; Immunoglobulin domain

RNA

  1. NR_045603.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI686571, AL391476, BC065717

  2. NR_045604.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI686571, AK310812, AL391476

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    117143587..117210927 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002335.3 → XP_016857824.1  V-set domain-containing T-cell activation inhibitor 1 isoform X2

    UniProtKB/TrEMBL
    Q5T2L0
    Conserved Domains (2) summary
    smart00410
    Location:51 → 149
    IG_like; Immunoglobulin like
    cl11960
    Location:54 → 151
    Ig; Immunoglobulin domain

  2. XM_011542143.2 → XP_011540445.2  V-set domain-containing T-cell activation inhibitor 1 isoform X1

    UniProtKB/TrEMBL
    Q5T2L0

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    117154077..117221391 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338745.1 → XP_054194720.1  V-set domain-containing T-cell activation inhibitor 1 isoform X2

  2. XM_054338744.1 → XP_054194719.1  V-set domain-containing T-cell activation inhibitor 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z7D3.1 GenPept UniProtKB/Swiss-Prot:Q7Z7D3

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