TNFSF4
TNF superfamily member 4, the group of CD molecules|Tumor necrosis factor superfamily
Basic information
Region (hg38): 1:173183730-173207331
Previous symbols: [ "TXGP1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (4 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF4 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 3 | 2 | 1 |
Variants in TNFSF4
This is a list of pathogenic ClinVar variants found in the TNFSF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-173186569-C-T | not specified | Uncertain significance (Nov 07, 2023) | ||
| 1-173186590-G-A | Likely benign (Apr 03, 2018) | |||
| 1-173186683-G-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 1-173186721-C-T | not specified | Uncertain significance (Dec 12, 2023) | ||
| 1-173186806-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 1-173188537-G-A | Benign (Jun 18, 2018) | |||
| 1-173188559-C-T | not specified | Likely benign (Aug 10, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TNFSF4 | protein_coding | protein_coding | ENST00000281834 | 3 | 23580 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0494 | 0.702 | 125344 | 0 | 2 | 125346 | 0.00000798 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.925 | 68 | 93.1 | 0.730 | 0.00000437 | 1202 |
| Missense in Polyphen | 10 | 25.127 | 0.39798 | 331 | ||
| Synonymous | 0.580 | 34 | 38.6 | 0.881 | 0.00000180 | 355 |
| Loss of Function | 0.651 | 2 | 3.27 | 0.611 | 1.39e-7 | 39 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000291 | 0.0000291 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000102 | 0.00000882 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that binds to TNFRSF4. Co-stimulates T-cell proliferation and cytokine production.;
- Disease
- DISEASE: Systemic lupus erythematosus (SLE) [MIM:152700]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269|PubMed:18059267}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. The upstream region of TNFSF4 contains a single risk haplotype for SLE, which is correlated with increased expression of both cell-surface TNFSF4 and TNFSF4 transcripts. Increased levels of TNFSF4 are thought to augment T-cell-APC interaction and the functional consequences of T-cell activation, thereby destabilizing peripheral tolerance.;
- Pathway
- Cytokine-cytokine receptor interaction - Homo sapiens (human);Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;Vitamin D Receptor Pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors
(Consensus)
Recessive Scores
- pRec
- 0.308
Intolerance Scores
- loftool
- 0.273
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.258
- hipred
- N
- hipred_score
- 0.215
- ghis
- 0.608
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0681
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tnfsf4
- Phenotype
- immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- defense response to nematode;acute inflammatory response;positive regulation of T cell cytokine production;regulation of adaptive immune response;positive regulation of type 2 immune response;positive regulation of immunoglobulin mediated immune response;inflammatory response;immune response;signal transduction;positive regulation of cell population proliferation;response to virus;regulation of signaling receptor activity;negative regulation of interferon-gamma production;negative regulation of interleukin-17 production;positive regulation of interferon-gamma production;positive regulation of interleukin-10 production;positive regulation of interleukin-12 production;positive regulation of interleukin-13 production;positive regulation of interleukin-4 production;positive regulation of interleukin-6 production;tumor necrosis factor-mediated signaling pathway;memory T cell activation;T-helper 2 cell activation;response to nitrogen dioxide;positive regulation of CD4-positive, alpha-beta T cell differentiation;positive regulation of memory T cell differentiation;negative regulation of DNA-binding transcription factor activity;negative regulation of regulatory T cell differentiation;negative regulation of T-helper 1 cell differentiation;positive regulation of T-helper 2 cell differentiation;negative regulation of transcription, DNA-templated;positive regulation of alpha-beta T cell proliferation;regulation of inflammatory response;positive regulation of inflammatory response;positive regulation of B cell activation;positive regulation of immunoglobulin secretion;cellular response to lipopolysaccharide;cellular response to prostaglandin E stimulus;chemokine (C-C motif) ligand 11 production;positive regulation of CD4-positive, alpha-beta T cell costimulation;positive regulation of interleukin-4-dependent isotype switching to IgE isotypes
- Cellular component
- extracellular space;plasma membrane;integral component of plasma membrane;cell surface
- Molecular function
- signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;protein binding;tumor necrosis factor receptor superfamily binding