TNFRSF10A
Basic information
Region (hg38): 8:23190452-23225102
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (85 variants)
- not_provided (16 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF10A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003844.4. 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 | 8 | |||||
missense | 79 | 88 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 79 | 11 | 6 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TNFRSF10A | protein_coding | protein_coding | ENST00000221132 | 10 | 34675 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.07e-15 | 0.00708 | 125580 | 0 | 168 | 125748 | 0.000668 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.645 | 291 | 262 | 1.11 | 0.0000139 | 2984 |
Missense in Polyphen | 51 | 44.885 | 1.1362 | 560 | ||
Synonymous | -1.06 | 120 | 106 | 1.13 | 0.00000606 | 954 |
Loss of Function | -0.342 | 21 | 19.4 | 1.08 | 9.32e-7 | 223 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000578 | 0.0000578 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000326 | 0.000326 |
Finnish | 0.000601 | 0.000601 |
European (Non-Finnish) | 0.00125 | 0.00125 |
Middle Eastern | 0.000326 | 0.000326 |
South Asian | 0.00 | 0.00 |
Other | 0.000653 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for the cytotoxic ligand TNFSF10/TRAIL (PubMed:26457518). 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. {ECO:0000269|PubMed:26457518, ECO:0000269|PubMed:9430227}.;
- Pathway
- 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);Apoptosis Modulation and Signaling;miR-targeted genes in lymphocytes - TarBase;TP53 Regulates Transcription of Cell Death Genes;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)
Recessive Scores
- pRec
- 0.0662
Intolerance Scores
- loftool
- 0.280
- rvis_EVS
- 0.51
- rvis_percentile_EVS
- 80.3
Haploinsufficiency Scores
- pHI
- 0.101
- hipred
- N
- hipred_score
- 0.402
- ghis
- 0.423
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0357
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;signal transduction;cell surface receptor signaling pathway;activation of NF-kappaB-inducing kinase activity;extrinsic apoptotic signaling pathway via death domain receptors;TRAIL-activated apoptotic signaling pathway;regulation of apoptotic process;positive regulation of apoptotic process;leukocyte migration;cellular response to mechanical stimulus;extrinsic apoptotic signaling pathway;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
- protease binding;death receptor activity;protein binding;transcription factor binding;signaling receptor activity;TRAIL binding