TNFSF4 TNF superfamily member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TNFSF4provided by HGNC
Official Full Name: TNF superfamily member 4provided by HGNC
Primary source: HGNC:HGNC:11934
See related: Ensembl:ENSG00000117586 MIM:603594; AllianceGenome:HGNC:11934
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GP34; CD252; OX4OL; TXGP1; CD134L; OX-40L; TNLG2B
Summary: This gene encodes a cytokine of the tumor necrosis factor (TNF) ligand family. The encoded protein functions in T cell antigen-presenting cell (APC) interactions and mediates adhesion of activated T cells to endothelial cells. Polymorphisms in this gene have been associated with Sjogren's syndrome and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (173172870..173450733, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (172541831..172768144, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (173152870..173176470, 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
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?

Differential expression of immune checkpoints (OX40/OX40L and PD-1/PD-L1) in decidua of unexplained recurrent spontaneous abortion women.
Title: Differential expression of immune checkpoints (OX40/OX40L and PD-1/PD-L1) in decidua of unexplained recurrent spontaneous abortion women.
PCSK9 Suppresses M2-Like Tumor-Associated Macrophage Polarization by Regulating the Secretion of OX40L from Hepatocellular Carcinoma Cells.
Title: PCSK9 Suppresses M2-Like Tumor-Associated Macrophage Polarization by Regulating the Secretion of OX40L from Hepatocellular Carcinoma Cells.
TNFSF4 is a risk factor for rheumatoid arthritis but not for primary Sjogren's syndrome in the Mexican population.
Title: TNFSF4 is a risk factor for rheumatoid arthritis but not for primary Sjögren's syndrome in the Mexican population.
Clinical Significance of OX40 and OX40 Ligand in the Peripheral Blood of Patients with Myasthenia Gravis.
Title: Clinical Significance of OX40 and OX40 Ligand in the Peripheral Blood of Patients with Myasthenia Gravis.
Expansion of cytotoxic natural killer cells in multiple myeloma patients using K562 cells expressing OX40 ligand and membrane-bound IL-18 and IL-21.
Title: Expansion of cytotoxic natural killer cells in multiple myeloma patients using K562 cells expressing OX40 ligand and membrane-bound IL-18 and IL-21.
Association of TNFSF4 polymorphisms with systemic lupus erythematosus: a meta-analysis.
Title: Association of TNFSF4 polymorphisms with systemic lupus erythematosus: a meta-analysis.
Association of TNFSF4 Gene Polymorphisms and Plasma TNFSF4 Level with Risk of Systemic Lupus Erythematosus in a Chinese Population.
Title: Association of TNFSF4 Gene Polymorphisms and Plasma TNFSF4 Level with Risk of Systemic Lupus Erythematosus in a Chinese Population.
Roles of OX40 and OX40 Ligand in Mycosis Fungoides and Sezary Syndrome.
Title: Roles of OX40 and OX40 Ligand in Mycosis Fungoides and Sézary Syndrome.
The haplotypes of various TNF related genes associated with scleritis in Chinese Han.
Title: The haplotypes of various TNF related genes associated with scleritis in Chinese Han.
CD40 Activity on Mesenchymal Cells Negatively Regulates OX40L to Maintain Bone Marrow Immune Homeostasis Under Stress Conditions.
Title: CD40 Activity on Mesenchymal Cells Negatively Regulates OX40L to Maintain Bone Marrow Immune Homeostasis Under Stress Conditions.

Submit: New GeneRIF Correction See all GeneRIFs (121)

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

Associated conditions

Description	Tests
Myocardial infarction, susceptibility to MedGen: C1832662 OMIM: 608446 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of celiac disease in North America confirms FRMD4B as new celiac locus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis for severe diabetic retinopathy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiple common variants for celiac disease influencing immune gene expression. 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

G42294 (e-PCR)
- UniSTS:93967

RH17450 (e-PCR)
- UniSTS:72553

SHGC-12820 (e-PCR)
- UniSTS:62162

G15923 (e-PCR)
- UniSTS:18393

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytokine activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	TAS Traceable Author Statement more info	PubMed
enables tumor necrosis factor receptor binding	IEA Inferred from Electronic Annotation more info
enables tumor necrosis factor receptor superfamily binding	IBA Inferred from Biological aspect of Ancestor more info
enables tumor necrosis factor receptor superfamily binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in T-helper 2 cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in acute inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to lipopolysaccharide	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to prostaglandin E stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to nematode	ISS Inferred from Sequence or Structural Similarity more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in memory T cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of T-helper 1 cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interleukin-17 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of regulatory T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of type II interferon production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of B cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of CD4-positive, alpha-beta T cell costimulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of CD4-positive, alpha-beta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T cell cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T cell proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T-helper 2 cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of alpha-beta T cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of chemokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytokine production	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of immunoglobulin mediated immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of immunoglobulin production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interleukin-10 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-12 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-13 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-4 production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interleukin-4-dependent isotype switching to IgE isotypes	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-6 production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of memory T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of type 2 immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of type II interferon production	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of adaptive immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to nitrogen dioxide	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to virus	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tumor necrosis factor ligand superfamily member 4

Names: CD134 ligand; OX40 antigen ligand; glycoprotein Gp34; tax-transcriptionally activated glycoprotein 1 (34kD); tumor necrosis factor (ligand) superfamily member 4; tumor necrosis factor ligand 2B; tumor necrosis factor superfamily member 4

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.

Genomic

NG_011477.2 RefSeqGene

Range

248402..272002

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001297562.2 → NP_001284491.1 tumor necrosis factor ligand superfamily member 4 isoform 2

See identical proteins and their annotated locations for NP_001284491.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

BC041663, R45433

Consensus CDS

CCDS72985.1

UniProtKB/Swiss-Prot

P23510

Related

ENSP00000356691.1, ENST00000367718.5

Conserved Domains (1) summary

smart00207
Location:24 → 133

TNF; Tumour necrosis factor family
NM_003326.5 → NP_003317.1 tumor necrosis factor ligand superfamily member 4 isoform 1

See identical proteins and their annotated locations for NP_003317.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL022310, BC041663, R45433, X79929

Consensus CDS

CCDS1306.1

UniProtKB/Swiss-Prot

P23510, Q5JZA5, Q8IV74, Q9HCN9

UniProtKB/TrEMBL

A0A024R937, A0A0U5CJ97, Q6FGS4

Related

ENSP00000281834.3, ENST00000281834.4

Conserved Domains (1) summary

smart00207
Location:74 → 183

TNF; Tumour necrosis factor family

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

173172870..173450733 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429908.1 → XP_047285864.1 tumor necrosis factor ligand superfamily member 4 isoform X5
XM_047429896.1 → XP_047285852.1 tumor necrosis factor ligand superfamily member 4 isoform X2
XM_047429902.1 → XP_047285858.1 tumor necrosis factor ligand superfamily member 4 isoform X4
XM_011509964.3 → XP_011508266.2 tumor necrosis factor ligand superfamily member 4 isoform X1
XM_017002228.2 → XP_016857717.1 tumor necrosis factor ligand superfamily member 4 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

172541831..172768144 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338602.1 → XP_054194577.1 tumor necrosis factor ligand superfamily member 4 isoform X4
XM_054338600.1 → XP_054194575.1 tumor necrosis factor ligand superfamily member 4 isoform X1
XM_054338601.1 → XP_054194576.1 tumor necrosis factor ligand superfamily member 4 isoform X3