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

Summary

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: mouse all
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Genomic context

Location:: 1p13.1-p12

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (117143587..117210927, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (117154077..117221391, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (117686209..117753549, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Aberrant expression of B7-H4 and B7-H5 contributes to the development of cutaneous squamous cell carcinoma.
Title: Aberrant expression of B7-H4 and B7-H5 contributes to the development of cutaneous squamous cell carcinoma.
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.
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.
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.
B7x in cancer immunity and immunotherapy.
Title: B7x in cancer immunity and immunotherapy.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (160)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL009459 (e-PCR)
- UniSTS:53302

SHGC-1545 (e-PCR)
- UniSTS:65339

SHGC-75394 (e-PCR)
- UniSTS:7059

NoName (e-PCR)
- UniSTS:481957

AL033564 (e-PCR)
- UniSTS:94175

DXS7636 (e-PCR)
- UniSTS:37619

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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)

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
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
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

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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

117143587..117210927 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_060925.1 Alternate T2T-CHM13v2.0

Range

117154077..117221391 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338745.1 → XP_054194720.1 V-set domain-containing T-cell activation inhibitor 1 isoform X2
XM_054338744.1 → XP_054194719.1 V-set domain-containing T-cell activation inhibitor 1 isoform X1