TNFRSF4

protein-coding

TNF 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]

Previous symbols:
  • TXGP1L

MANE transcript

NM_003327.4

Inheritance

AR

ClinVar variants

U:173B:103

Top phenotype

Immunodeficiency 16

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr1:1,211,326-1,214,153

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~2.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

combined immunodeficiency due to OX40 deficiencyLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0014268

Submitter: Labcorp Genetics (formerly Invitae)

combined immunodeficiency due to OX40 deficiencyLIMITED

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.

combined immunodeficiency due to OX40 deficiencyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014268

Submitter: PanelApp Australia

combined immunodeficiency due to OX40 deficiencyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014268

Submitter: Ambry Genetics

combined immunodeficiency due to OX40 deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014268

Submitter: Orphanet

Clinical Genomic Database (CGD)

Immunodeficiency 16AR

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

Refs: 20156905; 23897980Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNFRSF4 variants in ClinVar

4 Conditions Cataloged
Combined immunodeficiency due to OX40 deficiencyTotal: 344
not specifiedTotal: 84
not providedTotal: 25
TNFRSF4-related disorderTotal: 6

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
89
clinvar
2
clinvar
95
missense
150
clinvar
12
clinvar
162
nonsense
1
clinvar
1
start loss
1
clinvar
1
frameshift
10
clinvar
10
splice donor/acceptor (+/-2bp)
7
clinvar
7
Total001731012276
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003327.4RefSeqNP_003318.17MANE Select
ENST00000379236.4EnsemblENSP00000368538.37MANE Select
NM_001410709.1RefSeqNP_001397638.16Standard
ENST00000699969.1EnsemblENSP00000514726.16Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6231421640.8630.00001101712
Missense (PolyPhen)2638.0920.68256467
Synonymous0.1637374.80.9760.00000549583
Loss of Function0.86079.920.7054.22e-7130

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00013rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.000100.000093rare
European (Non-Finnish)0.000130.00012rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.