TNFRSF4
protein-codingTNF receptor superfamily member 4, the group of CD molecules|Tumor necrosis factor receptor superfamily
Gene summary
The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor has been shown to activate NF-kappaB through its interaction with adaptor proteins TRAF2 and TRAF5. Knockout studies in mice suggested that this receptor promotes the expression of apoptosis inhibitors BCL2 and BCL2lL1/BCL2-XL, and thus suppresses apoptosis. The knockout studies also suggested the roles of this receptor in CD4+ T cell response, as well as in T cell-dependent B cell proliferation and differentiation. [provided by RefSeq, Jul 2008]
- TXGP1L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0014268
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014268
Submitter: ClinGen
*TNFRSF4* has been reported in relation to combined immunodeficiency due to OX40 deficiency in one proband with a homozygous missense variant in 2013 (Byun et al., PMID:23897980). The one described patient from Byun et al. presented with Kaposi sarcoma along with a low proportion of peripheral effector memory CD4+ T cells and decreased cytokine response including no IFN-γ production by the patient’s PBMCs in response to recall antigens, suggestive of a deficiency in antigen-specific memory CD4+ T cells. The heterozygous parents and siblings were reportedly unaffected. The mechanism of pathogenicity appears to be loss of function. This gene-disease association is also supported by the biochemical function of OX40, where OX40 and the OX40 ligand are both expressed on T cells 24 to 48 hours following antigen presentation to a T cell. During activation, OX40 via OX40 ligand signaling influences several T cell effector mechanisms. These mechanisms include cytokine production, continued CD4+ activation, increased T cell survival, increased effector phenotypes and reduced regulatory phenotypes (PMID:26215166). Additionally, the disease relationship is supported by expression, where OX40 mRNA in lymphoid tissue greatly increases following T cell activation (PMID:8228223). The gene disease relationship is also supported by rescue, where transfection of WT-OX40 rescued OX40 ligand binding on PHA activated T cells, unlike patient variant R65C (PMID:23897980). Finally, OX40 deficient mice recapitulate several features of the disease phenotype including marked impairment of memory CD4+ T cells in response to recall antigens and decreased cytokine response to vaccinations (PMID:10975814). In summary, there is limited evidence to support this gene-disease relationship. Although more genetic evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This gene-disease pair was originally evaluated by the SCID-CID GCEP on June, 15 2023 (SOP Version 9). It was reevaluated on September 17, 2026 (SOP Version 12). As a result of this reevaluation, the classification did not change.
Inheritance Pattern: AR
Disease ID:MONDO:0014268
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014268
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014268
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious
Intervention: Allergy/Immunology/Infectious
Rationale: Individuals may be susceptible to severe infections, as well as related oncologic sequelae (eg, Kaposi sarcoma), and early and aggressive treatment of infections and related sequelae may be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TNFRSF4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003327.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 89 | 2 | 95 | ||
| missense | 150 | 12 | 162 | |||
| nonsense | 1 | 1 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 10 | 10 | ||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 173 | 101 | 2 | 276 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003318.1 | 7 | MANE Select | |
| Ensembl | ENSP00000368538.3 | 7 | MANE Select | |
| RefSeq | NP_001397638.1 | 6 | Standard | |
| Ensembl | ENSP00000514726.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cytokine-cytokine receptor interaction - Homo sapiens (human)
- TNFR2 non-canonical NF-kB pathway
- Cytokine Signaling in Immune system
- Immune System
- TNFs bind their physiological receptors
Biological Process
- inflammatory response
- immune response
- cellular defense response
- positive regulation of B cell proliferation
- tumor necrosis factor-mediated signaling pathway
Molecular Function
- virus receptor activity
- tumor necrosis factor-activated receptor activity
- protein binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- cell surface
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379236
- Coding exons
- 7
- Length
- 2813
- Individuals with no LoFs
- 124534
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 19
- Defined
- 124553
- p
- 0.0000763
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.623 | 142 | 164 | 0.863 | 0.0000110 | 1712 |
| Missense (PolyPhen) | 26 | 38.092 | 0.68256 | 467 | ||
| Synonymous | 0.163 | 73 | 74.8 | 0.976 | 0.00000549 | 583 |
| Loss of Function | 0.860 | 7 | 9.92 | 0.705 | 4.22e-7 | 130 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00010 | 0.000093 | rare |
| European (Non-Finnish) | 0.00013 | 0.00012 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for TNFSF4/OX40L/GP34. Is a costimulatory molecule implicated in long-term T-cell immunity. {ECO:0000269|PubMed:7704935}.;
- Disease
- DISEASE: Immunodeficiency 16 (IMD16) [MIM:615593]: An autosomal recessive primary immunodeficiency associated with classic Kaposi sarcoma of childhood and poor T-cell recall immune responses due to complete functional OX40 deficiency. {ECO:0000269|PubMed:23897980}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.604
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |