TNFRSF6B
protein-codingTNF receptor superfamily member 6b, the group of Tumor necrosis factor receptor superfamily
Gene summary
This gene belongs to the tumor necrosis factor receptor superfamily. The encoded protein is postulated to play a regulatory role in suppressing FasL- and LIGHT-mediated cell death. It acts as a decoy receptor that competes with death receptors for ligand binding. Over-expression of this gene has been noted in gastrointestinal tract tumors. Read-through transcription into this gene from the neighboring upstream gene, which encodes regulator of telomere elongation helicase 1 (RTEL1), generates a non-coding transcript. [provided by RefSeq, Feb 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TNFRSF6B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003823.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 124 | 6 | 132 | ||
| missense | 271 | 14 | 1 | 286 | ||
| nonsense | 8 | 8 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 11 | 11 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 294 | 138 | 7 | 439 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003814.1 | 3 | MANE Select | |
| Ensembl | ENSP00000359013.1 | 3 | MANE Select | |
| Ensembl | ENSP00000548561.1 | 3 | Standard | |
| Ensembl | ENSP00000548562.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cytokine-cytokine receptor interaction - Homo sapiens (human)
- Apoptosis Modulation and Signaling
- HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
- DNA Repair
- DNA Double-Strand Break Repair
Biological Process
- apoptotic process
- tumor necrosis factor-mediated signaling pathway
- negative regulation of apoptotic process
Molecular Function
- protein binding
- signaling receptor activity
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369996
- Coding exons
- 3
- Length
- 2017
- Individuals with no LoFs
- 123602
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 212
- Defined
- 123814
- p
- 0.000856
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.30 | 250 | 199 | 1.26 | 0.0000138 | 1845 |
| Missense (PolyPhen) | 50 | 51.187 | 0.9768 | 540 | ||
| Synonymous | -4.41 | 145 | 91.4 | 1.59 | 0.00000650 | 669 |
| Loss of Function | -0.145 | 8 | 7.57 | 1.06 | 3.75e-7 | 79 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.0011 | notable |
| Latino/Admixed American | 0.00094 | 0.00093 | rare |
| Ashkenazi Jewish | 0.00041 | 0.00040 | rare |
| East Asian | 0.0011 | 0.0010 | notable |
| Finnish | 0.0014 | 0.0014 | notable |
| European (Non-Finnish) | 0.00085 | 0.00081 | rare |
| South Asian | 0.00053 | 0.00052 | rare |
| Other | 0.00069 | 0.00066 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Decoy receptor that can neutralize the cytotoxic ligands TNFS14/LIGHT, TNFSF15 and TNFSF6/FASL. Protects against apoptosis. {ECO:0000269|PubMed:21300286}.;
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- LoFtool
- 0.370
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.88
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |