TNFRSF1B
TNF receptor superfamily member 1B, the group of CD molecules|Tumor necrosis factor receptor superfamily|MicroRNA protein coding host genes
Basic information
Region (hg38): 1:12166991-12209228
Previous symbols: [ "TNFR2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF1B 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 | 4 | |||||
| missense | 13 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 3 | 5 |
Variants in TNFRSF1B
This is a list of pathogenic ClinVar variants found in the TNFRSF1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-12188797-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 1-12188855-T-C | Likely benign (Mar 31, 2018) | |||
| 1-12192470-C-G | not specified | Uncertain significance (Nov 09, 2021) | ||
| 1-12192470-C-T | not specified | Uncertain significance (Aug 30, 2022) | ||
| 1-12192516-C-T | Benign (Feb 20, 2018) | |||
| 1-12192865-G-C | not specified | Uncertain significance (May 21, 2024) | ||
| 1-12192870-G-A | Benign (Dec 31, 2019) | |||
| 1-12192898-T-G | Susceptibility to severe coronavirus disease (COVID-19) • Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR2 • Associated with severe COVID-19 disease | Uncertain significance (Jul 01, 2023) | ||
| 1-12192913-C-G | not specified | Uncertain significance (Mar 23, 2022) | ||
| 1-12192919-C-T | Benign (May 21, 2018) | |||
| 1-12192981-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 1-12193009-C-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 1-12193079-C-T | Likely benign (Aug 09, 2018) | |||
| 1-12193105-C-A | Likely benign (Dec 20, 2017) | |||
| 1-12193958-T-C | Benign (Dec 31, 2019) | |||
| 1-12201985-A-G | Benign (Jul 31, 2018) | |||
| 1-12201991-C-T | not specified | Uncertain significance (Jun 26, 2023) | ||
| 1-12202021-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
| 1-12202038-G-C | Likely benign (Aug 08, 2018) | |||
| 1-12202107-G-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-12202128-G-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 1-12202150-C-T | not specified | Uncertain significance (Sep 22, 2022) | ||
| 1-12206823-T-G | not specified | Uncertain significance (May 02, 2024) | ||
| 1-12206917-G-A | not specified | Uncertain significance (Jul 12, 2022) | ||
| 1-12206937-G-A | not specified | Uncertain significance (Dec 17, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TNFRSF1B | protein_coding | protein_coding | ENST00000376259 | 10 | 42226 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.502 | 0.498 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.930 | 235 | 279 | 0.843 | 0.0000174 | 2948 |
| Missense in Polyphen | 42 | 75.47 | 0.55651 | 813 | ||
| Synonymous | 0.642 | 114 | 123 | 0.926 | 0.00000883 | 951 |
| Loss of Function | 3.22 | 4 | 19.2 | 0.208 | 9.15e-7 | 228 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000105 | 0.0000992 |
| East Asian | 0.000116 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000371 | 0.0000352 |
| Middle Eastern | 0.000116 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000174 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor with high affinity for TNFSF2/TNF-alpha and approximately 5-fold lower affinity for homotrimeric TNFSF1/lymphotoxin-alpha. The TRAF1/TRAF2 complex recruits the apoptotic suppressors BIRC2 and BIRC3 to TNFRSF1B/TNFR2. This receptor mediates most of the metabolic effects of TNF-alpha. Isoform 2 blocks TNF-alpha-induced apoptosis, which suggests that it regulates TNF-alpha function by antagonizing its biological activity. {ECO:0000269|PubMed:12370298}.;
- Pathway
- Adipocytokine signaling pathway - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Apoptosis Modulation and Signaling;TNF alpha Signaling Pathway;Apoptosis;Apoptotic Signaling Pathway;Oxidative Damage;TYROBP Causal Network;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Inflammatory Response Pathway;Neutrophil degranulation;tnfr2 signaling pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Innate Immune System;Immune System;TNFs bind their physiological receptors;TNFalpha;TNF receptor signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.728
Intolerance Scores
- loftool
- 0.0807
- rvis_EVS
- 0.09
- rvis_percentile_EVS
- 60.47
Haploinsufficiency Scores
- pHI
- 0.586
- hipred
- Y
- hipred_score
- 0.669
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.842
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tnfrsf1b
- 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; normal 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; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; muscle phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- tnfrsf1b
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- increased accumulation
Gene ontology
- Biological process
- regulation of T cell cytokine production;regulation of cytokine secretion involved in immune response;aortic valve development;pulmonary valve development;negative regulation of extracellular matrix constituent secretion;inflammatory response;aging;intrinsic apoptotic signaling pathway in response to DNA damage;negative regulation of cardiac muscle hypertrophy;cytokine-mediated signaling pathway;regulation of myelination;tumor necrosis factor-mediated signaling pathway;regulation of T cell proliferation;neutrophil degranulation;negative regulation of inflammatory response;RNA destabilization;positive regulation of membrane protein ectodomain proteolysis;cellular response to lipopolysaccharide;cellular response to growth factor stimulus;extrinsic apoptotic signaling pathway;regulation of neuroinflammatory response;positive regulation of apoptotic process involved in morphogenesis
- Cellular component
- tumor necrosis factor receptor superfamily complex;extracellular region;nucleus;plasma membrane;membrane;integral component of membrane;specific granule membrane;neuronal cell body;varicosity;membrane raft;perinuclear region of cytoplasm
- Molecular function
- tumor necrosis factor-activated receptor activity;protein binding;ubiquitin protein ligase binding;tumor necrosis factor binding