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): 1:12166990-12209228

Previous symbols: [ "TNFR2" ]

Links

ENSG00000028137 ∙ NCBI:7133 ∙ OMIM:191191 ∙ HGNC:11917 ∙ Uniprot:P20333 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNFRSF1B gene.

• not provided (9 variants)
• Inborn genetic diseases (9 variants)

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				3	1	4
missense			9		4	13
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	9	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)
1-12192870-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)
1-12206917-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-12206937-G-A		not specified	Uncertain significance (Dec 17, 2021)
1-12207235-C-T		Susceptibility to severe coronavirus disease (COVID-19) • Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR3 • Associated with severe COVID-19 disease	Uncertain significance (Jul 01, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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