VTCN1 Gene (Protein Coding)

V-Set Domain Containing T Cell Activation Inhibitor 1

GC01M117143
GIFtS:
41
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 chromosom... See more...

Aliases for VTCN1 Gene

Aliases for VTCN1 Gene

  • V-Set Domain Containing T Cell Activation Inhibitor 1 2 3 5
  • B7-H4 2 3 4
  • B7H4 2 3 4
  • V-Set Domain-Containing T-Cell Activation Inhibitor 1 3 4
  • Immune Costimulatory Protein B7-H4 3 4
  • B7 Superfamily Member 1 2 3
  • B7 Family Member, H4 2 3
  • B7 Homolog 4 3 4
  • B7h.5 3 4
  • B7S1 2 3
  • T Cell Costimulatory Molecule B7x 3
  • T-Cell Costimulatory Molecule B7x 4
  • Protein B7S1 4
  • FLJ22418 2
  • PRO1291 3
  • VCTN1 3
  • VTCN1 5
  • B7X 3
  • B7x 2

External Ids for VTCN1 Gene

Previous GeneCards Identifiers for VTCN1 Gene

  • GC01M117399
  • GC01M117686
  • GC01M115544

Summaries for VTCN1 Gene

Entrez Gene Summary for VTCN1 Gene

  • 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]

GeneCards Summary for VTCN1 Gene

VTCN1 (V-Set Domain Containing T Cell Activation Inhibitor 1) is a Protein Coding gene. Diseases associated with VTCN1 include Ovarian Cancer. Among its related pathways are Cell adhesion molecules and NF-kappaB Signaling. Gene Ontology (GO) annotations related to this gene include signaling receptor binding. An important paralog of this gene is BTN3A3.

UniProtKB/Swiss-Prot Summary for VTCN1 Gene

  • Negatively regulates T-cell-mediated immune response by inhibiting T-cell activation, proliferation, cytokine production and development of cytotoxicity. When expressed on the cell surface of tumor macrophages, plays an important role, together with regulatory T-cells (Treg), in the suppression of tumor-associated antigen-specific T-cell immunity. Involved in promoting epithelial cell transformation.

Gene Wiki entry for VTCN1 Gene

Additional gene information for VTCN1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VTCN1 Gene

Genomics for VTCN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for VTCN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J117210 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 250.7 +0.5 453 3.1 ZNF217 ELF1 CTBP1 TBP SMARCE1 DPF2 CREB1 FOSL2 ZNF687 MNT 5MWI_A-008 VTCN1 ENSG00000212266 TRIM45
GH01J117120 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 16.4 +88.9 88894 3 CHD2 TBP ZBTB10 SP1 SMAD5 MBD2 ZNF217 CTCF SIX4 NONO TRIM45 WDR3 ATP1A1-AS1 VTCN1 ENSG00000212266 TTF2 piR-42686 lnc-TTF2-2
GH01J117266 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas 11 -58.6 -58604 6 ZNF217 ZBTB7B ELF1 CEBPB MBD2 CUX1 CTBP1 SIN3A YY1 ZBTB40 VTCN1 TRIM45 MAN1A2 LINC01525 lnc-VTCN1-2 ENSG00000277141
GH01J117181 Enhancer 1 Ensembl ENCODE 11.2 +29.0 29044 1.2 ZNF217 BHLHE40 ARNT REST MBD2 VEZF1 NONO ZEB2 CTBP1 FOSL1 VTCN1 piR-32325-008 5MWI_A-008 TRIM45
GH01J117146 Enhancer 1 Ensembl ENCODE 10.5 +63.4 63384 3.2 ZSCAN16 FEZF1 DEK ZIC2 ZNF610 CEBPB ZNF513 ELK1 CUX1 EP300 VTCN1 ATP1A1-AS1 ENSG00000271427 TTF2 RPS15AP9 piR-32325-008 TRIM45
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VTCN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VTCN1

Top Transcription factor binding sites by QIAGEN in the VTCN1 gene promoter:
  • AP-1
  • AREB6
  • E47
  • Ik-1
  • Lhx3a
  • LHX3b
  • POU2F1
  • POU2F1a
  • Tal-1

Genomic Locations for VTCN1 Gene

Latest Assembly
chr1:117,143,587-117,210,985
(GRCh38/hg38)
Size:
67,399 bases
Orientation:
Minus strand

Previous Assembly
chr1:117,686,209-117,753,549
(GRCh37/hg19 by Entrez Gene)
Size:
67,341 bases
Orientation:
Minus strand

chr1:117,686,209-117,753,556
(GRCh37/hg19 by Ensembl)
Size:
67,348 bases
Orientation:
Minus strand

Genomic View for VTCN1 Gene

Genes around VTCN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VTCN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VTCN1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VTCN1 Gene

Proteins for VTCN1 Gene

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  • Protein details for VTCN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z7D3-VTCN1_HUMAN
    Recommended name:
    V-set domain-containing T-cell activation inhibitor 1
    Protein Accession:
    Q7Z7D3
    Secondary Accessions:
    • Q0GN76
    • Q45VN0
    • Q5WPZ3
    • Q6P097
    • Q9H6B2

    Protein attributes for VTCN1 Gene

    Size:
    282 amino acids
    Molecular mass:
    30878 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • May serve as a predictive marker for renal cell carcinoma.

    Three dimensional structures from OCA and Proteopedia for VTCN1 Gene

    Alternative splice isoforms for VTCN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VTCN1 Gene

Protein Expression for VTCN1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for VTCN1 Gene

  • N-glycosylated.
  • Glycosylation at Asn112 and Asn216
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • VTCN1_HUMAN (1897)

Other Protein References for VTCN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for VTCN1
  • Boster Bio Antibodies for VTCN1

No data available for DME Specific Peptides for VTCN1 Gene

Domains & Families for VTCN1 Gene

Gene Families for VTCN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for VTCN1 Gene

InterPro:
Blocks:
  • Immunoglobulin V-set
ProtoNet:

Suggested Antigen Peptide Sequences for VTCN1 Gene

GenScript: Design optimal peptide antigens:
  • V-set domain containing T cell activation inhibitor 1 (Q5T2L0_HUMAN)
  • cDNA FLJ51592, highly similar to Homo sapiens V-set domain containing T cell activation inhibitor 1 (VTCN1), mRNA (Q6P097_HUMAN)
  • T-cell costimulatory molecule B7x (VTCN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7Z7D3

UniProtKB/Swiss-Prot:

VTCN1_HUMAN :
  • Belongs to the immunoglobulin superfamily. BTN/MOG family.
Family:
  • Belongs to the immunoglobulin superfamily. BTN/MOG family.
genes like me logo Genes that share domains with VTCN1: view

Function for VTCN1 Gene

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  6. Cell Lines for research

Molecular function for VTCN1 Gene

UniProtKB/Swiss-Prot Function:
Negatively regulates T-cell-mediated immune response by inhibiting T-cell activation, proliferation, cytokine production and development of cytotoxicity. When expressed on the cell surface of tumor macrophages, plays an important role, together with regulatory T-cells (Treg), in the suppression of tumor-associated antigen-specific T-cell immunity. Involved in promoting epithelial cell transformation.
UniProtKB/Swiss-Prot Induction:
Up-regulated by IL6/interleukin-6 and IL10/interleukin-10 and inhibited by CSF2/GM-CSF and IL4/interleukin-4 on antigen-presenting cells (APCs).

Phenotypes From GWAS Catalog for VTCN1 Gene

Gene Ontology (GO) - Molecular Function for VTCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005102 signaling receptor binding IBA 21873635
genes like me logo Genes that share ontologies with VTCN1: view
genes like me logo Genes that share phenotypes with VTCN1: view

Animal Models for VTCN1 Gene

MGI Knock Outs for VTCN1:

Animal Models for research

  • Taconic Biosciences Mouse Models for VTCN1

miRNA for VTCN1 Gene

miRTarBase miRNAs that target VTCN1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VTCN1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VTCN1 Gene

Localization for VTCN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VTCN1 Gene

Cell membrane. Single-pass type I membrane protein. Note=Expressed at the cell surface. A soluble form has also been detected. {ECO:0000255, ECO:0000269 PubMed:12818165, ECO:0000269 PubMed:15878339, ECO:0000269 PubMed:16782226}.

Subcellular locations from

COMPARTMENTS
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 VTCN1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Cell Junctions (2)
  • Focal adhesion sites (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VTCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0009897 external side of plasma membrane IDA 16606666
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VTCN1: view

Pathways & Interactions for VTCN1 Gene

PathCards logo

SuperPathways for VTCN1 Gene

genes like me logo Genes that share pathways with VTCN1: view

Pathways by source for VTCN1 Gene

1 KEGG pathway for VTCN1 Gene
1 Cell Signaling Technology pathway for VTCN1 Gene

Interacting Proteins for VTCN1 Gene

STRING Interaction Network Preview (showing top 2 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000358470 Q7Z7D3-VTCN1_HUMAN for VTCN1 Gene via STRING IID

GPS-Prot Interaction Network for VTCN1

Gene Ontology (GO) - Biological Process for VTCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001562 response to protozoan IEA --
GO:0001817 regulation of cytokine production IBA 21873635
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0032743 positive regulation of interleukin-2 production IEA --
genes like me logo Genes that share ontologies with VTCN1: view

No data available for SIGNOR curated interactions for VTCN1 Gene

Drugs & Compounds for VTCN1 Gene

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No Compound Related Data Available

Transcripts for VTCN1 Gene

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mRNA/cDNA for VTCN1 Gene

3 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VTCN1

Alternative Splicing Database (ASD) splice patterns (SP) for VTCN1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c
SP1: -
SP2: - -
SP3: -
SP4: - - -

Relevant External Links for VTCN1 Gene

GeneLoc Exon Structure for
VTCN1

Expression for VTCN1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VTCN1 Gene

mRNA expression in normal human tissues for VTCN1 Gene
mRNA expression by BioGPS for VTCN1 GenemRNA expression by GTEx for VTCN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VTCN1 Gene

This gene is overexpressed in Minor Salivary Gland (x14.9), Breast - Mammary Tissue (x12.4), Pancreas (x9.3), and Kidney - Cortex (x5.1).

Protein differential expression in normal tissues from HIPED for VTCN1 Gene

This gene is overexpressed in Urine (55.1) and Milk (11.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VTCN1 Gene



Protein tissue co-expression partners for VTCN1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VTCN1

SOURCE GeneReport for Unigene cluster for VTCN1 Gene:

Hs.546434

mRNA Expression by UniProt/SwissProt for VTCN1 Gene:

Q7Z7D3-VTCN1_HUMAN
Tissue specificity: Overexpressed in breast, ovarian, endometrial, renal cell (RCC) and non-small-cell lung cancers (NSCLC). Expressed on activated T- and B-cells, monocytes and dendritic cells, but not expressed in most normal tissues (at protein level). Widely expressed, including in kidney, liver, lung, ovary, placenta, spleen and testis.

Evidence on tissue expression from TISSUES for VTCN1 Gene

  • Blood(4.5)
  • Pancreas(2.3)
  • Lymph node(2.2)
  • Kidney(2.2)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with VTCN1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for VTCN1 Gene

Orthologs for VTCN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VTCN1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia VTCN1 30 31
  • 99.53 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia VTCN1 30 31
  • 91.25 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia VTCN1 30 31
  • 90.07 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia VTCN1 31
  • 87 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Vtcn1 30 17 31
  • 84.52 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Vtcn1 30
  • 84.4 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 21 (a)
 ManyToMany
Chicken
(Gallus gallus)
 Aves VTCN1 30 31
  • 63.37 (n)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia vtcn1 30
  • 53.79 (n)
Zebrafish
(Danio rerio)
 Actinopterygii si:dkey-174k18.6 30
  • 50.07 (n)
VTCN1 31
  • 34 (a)
 OneToOne
Species where no ortholog for VTCN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for VTCN1 Gene

ENSEMBL:
Gene Tree for VTCN1 (if available)
TreeFam:
Gene Tree for VTCN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VTCN1: view image

Paralogs for VTCN1 Gene

Paralogs for VTCN1 Gene

Pseudogenes.org Pseudogenes for VTCN1 Gene

genes like me logo Genes that share paralogs with VTCN1: view

Variants for VTCN1 Gene

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dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VTCN1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for VTCN1 Gene

Variant ID Type Subtype PubMed ID
esv2716640 CNV deletion 23290073
nsv1007386 CNV loss 25217958
nsv1009706 CNV gain 25217958
nsv1145363 CNV deletion 24896259

Variation tolerance for VTCN1 Gene

Residual Variation Intolerance Score: 66.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.35; 41.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VTCN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VTCN1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VTCN1 Gene

Disorders for VTCN1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VTCN1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
ovarian cancer
  • ovarian cancer, somatic
- elite association - COSMIC cancer census association via MalaCards
Search VTCN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VTCN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with VTCN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VTCN1 Gene

Publications for VTCN1 Gene

  1. B7-H4, a molecule of the B7 family, negatively regulates T cell immunity. (PMID: 12818165) Sica GL … Chen L (Immunity 2003) 2 3 4
  2. Identification of a novel susceptibility locus for juvenile idiopathic arthritis by genome-wide association analysis. (PMID: 19116933) Hinks A … British Society of Paediatric and Adolescent Rheumatology Study Group (Arthritis and rheumatism 2009) 3 41
  3. B7-H4 gene polymorphisms are associated with sporadic breast cancer in a Chinese Han population. (PMID: 19903360) Zhang J … Li D (BMC cancer 2009) 3 41
  4. B7-H4 (DD-O110) is overexpressed in high risk uterine endometrioid adenocarcinomas and inversely correlated with tumor T-cell infiltration. (PMID: 17509674) Miyatake T … Shroyer KR (Gynecologic oncology 2007) 3 4
  5. B7-H4 expression identifies a novel suppressive macrophage population in human ovarian carcinoma. (PMID: 16606666) Kryczek I … Zou W (The Journal of experimental medicine 2006) 3 4

ExternalLinks

View latest publications for VTCN1 gene in Mastermind

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