TNFSF10
TNF superfamily member 10, the group of CD molecules|Tumor necrosis factor superfamily
Basic information
Region (hg38): 3:172505508-172523475
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (27 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003810.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 27 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 27 | 1 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TNFSF10 | protein_coding | protein_coding | ENST00000241261 | 5 | 18000 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.135 | 0.861 | 125714 | 0 | 33 | 125747 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.166 | 142 | 148 | 0.962 | 0.00000715 | 1871 |
| Missense in Polyphen | 39 | 45.131 | 0.86414 | 622 | ||
| Synonymous | 0.154 | 51 | 52.4 | 0.973 | 0.00000268 | 496 |
| Loss of Function | 2.51 | 4 | 14.2 | 0.281 | 6.67e-7 | 176 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000552 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000238 | 0.000237 |
| Middle Eastern | 0.0000552 | 0.0000544 |
| South Asian | 0.0000983 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that binds to TNFRSF10A/TRAILR1, TNFRSF10B/TRAILR2, TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and possibly also to TNFRSF11B/OPG (PubMed:26457518, PubMed:10549288). Induces apoptosis. Its activity may be modulated by binding to the decoy receptors TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and TNFRSF11B/OPG that cannot induce apoptosis. {ECO:0000269|PubMed:10549288, ECO:0000269|PubMed:26457518}.;
- Pathway
- Influenza A - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Measles - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);TP53 Network;Apoptosis Modulation and Signaling;Apoptosis;Photodynamic therapy-induced AP-1 survival signaling.;Apoptotic Signaling Pathway;Protein alkylation leading to liver fibrosis;Signal Transduction;induction of apoptosis through dr3 and dr4/5 death receptors;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;Regulation of necroptotic cell death;GPCR signaling-cholera toxin;Dimerization of procaspase-8;GPCR signaling-pertussis toxin;Regulation by c-FLIP;Ligand-dependent caspase activation;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;CASP8 activity is inhibited;Regulated Necrosis;Programmed Cell Death;RIPK1-mediated regulated necrosis;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;TRAIL signaling;JAK STAT pathway and regulation;Death Receptor Signalling;GPCR signaling-G alpha i;Caspase Cascade in Apoptosis;TRAIL signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.671
Intolerance Scores
- loftool
- 0.331
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.92
Haploinsufficiency Scores
- pHI
- 0.0960
- hipred
- Y
- hipred_score
- 0.598
- ghis
- 0.427
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.516
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tnfsf10
- Phenotype
- skeleton phenotype; immune system phenotype; neoplasm; 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; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- tnfsf10
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;immune response;signal transduction;cell surface receptor signaling pathway;cell-cell signaling;male gonad development;regulation of signaling receptor activity;response to insulin;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of release of cytochrome c from mitochondria;regulation of extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of extrinsic apoptotic signaling pathway
- Cellular component
- extracellular region;integral component of plasma membrane;extracellular exosome
- Molecular function
- signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;protein binding;zinc ion binding;identical protein binding;TRAIL binding