TNFRSF10B
TNF receptor superfamily member 10b, the group of CD molecules|Tumor necrosis factor receptor superfamily
Basic information
Region (hg38): 8:23020133-23069031
Links
Phenotypes
GenCC
Source:
- head and neck squamous cell carcinoma (Limited), mode of inheritance: AD
- head and neck squamous cell carcinoma (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Squamous cell carcinoma, head and neck | AD | Oncologic | Surveillance and early diagnosis could potentially be beneficial to allow prompt management of detected neoplasms | Oncologic | 9721851 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (55 variants)
- not_provided (7 variants)
- TNFRSF10B-related_disorder (6 variants)
- Squamous_cell_carcinoma_of_the_head_and_neck (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF10B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003842.5. 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 | 8 | |||||
| missense | 49 | 57 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 1 | 49 | 15 | 1 |
Highest pathogenic variant AF is 0.000229247
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TNFRSF10B | protein_coding | protein_coding | ENST00000276431 | 9 | 49047 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000199 | 0.979 | 125648 | 0 | 100 | 125748 | 0.000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.670 | 270 | 241 | 1.12 | 0.0000128 | 2826 |
| Missense in Polyphen | 48 | 53.824 | 0.89179 | 721 | ||
| Synonymous | -0.224 | 102 | 99.2 | 1.03 | 0.00000584 | 892 |
| Loss of Function | 2.05 | 9 | 18.5 | 0.486 | 8.95e-7 | 221 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000796 | 0.000796 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.000571 | 0.000571 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000232 | 0.000229 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for the cytotoxic ligand TNFSF10/TRAIL (PubMed:10549288). The adapter molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. Promotes the activation of NF-kappa-B. Essential for ER stress-induced apoptosis. {ECO:0000269|PubMed:10542098, ECO:0000269|PubMed:10549288, ECO:0000269|PubMed:15322075}.;
- Disease
- DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
- Pathway
- p53 signaling pathway - Homo sapiens (human);Influenza A - 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);miRNA Regulation of DNA Damage Response;Apoptosis Modulation and Signaling;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Apoptosis;Apoptosis-related network due to altered Notch3 in ovarian cancer;Apoptotic Signaling Pathway;TP53 Regulates Transcription of Cell Death Genes;miRNA regulation of p53 pathway in prostate cancer;DNA Damage Response;Signal Transduction;Gene expression (Transcription);induction of apoptosis through dr3 and dr4/5 death receptors;Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;Regulation of necroptotic cell death;Dimerization of procaspase-8;Regulation by c-FLIP;Ligand-dependent caspase activation;RNA Polymerase II Transcription;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;CASP8 activity is inhibited;Regulated Necrosis;Programmed Cell Death;RIPK1-mediated regulated necrosis;TRAIL signaling;Cell surface interactions at the vascular wall;Hemostasis;Death Receptor Signalling;Transcriptional Regulation by TP53;Direct p53 effectors;Caspase Cascade in Apoptosis;TRAIL signaling pathway;TP53 Regulates Transcription of Death Receptors and Ligands
(Consensus)
Intolerance Scores
- loftool
- 0.196
- rvis_EVS
- 0.64
- rvis_percentile_EVS
- 84.05
Haploinsufficiency Scores
- pHI
- 0.172
- hipred
- N
- hipred_score
- 0.327
- ghis
- 0.452
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.479
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tnfrsf10b
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; immune 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); hematopoietic system phenotype; neoplasm;
Gene ontology
- Biological process
- apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;cell surface receptor signaling pathway;activation of NF-kappaB-inducing kinase activity;extrinsic apoptotic signaling pathway via death domain receptors;response to endoplasmic reticulum stress;TRAIL-activated apoptotic signaling pathway;regulation of apoptotic process;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;leukocyte migration;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;cellular response to mechanical stimulus;regulation of extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
- Cellular component
- plasma membrane;cell surface;integral component of membrane
- Molecular function
- protein binding;signaling receptor activity;TRAIL binding