TNFRSF10D
protein-codingTNF receptor superfamily member 10d, the group of CD molecules|Tumor necrosis factor receptor superfamily
Gene summary
The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contains an extracellular TRAIL-binding domain, a transmembrane domain, and a truncated cytoplamic death domain. This receptor does not induce apoptosis, and has been shown to play an inhibitory role in TRAIL-induced cell apoptosis. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.4 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 TNFRSF10D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003840.5. 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 | 1 | 3 | |||
| missense | 59 | 9 | 2 | 70 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 62 | 9 | 3 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003831.2 | 9 | MANE Select | |
| Ensembl | ENSP00000310263.3 | 9 | MANE Select | |
| Ensembl | ENSP00000540349.1 | 9 | Standard | |
| Ensembl | ENSP00000710593.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- apoptotic process
- signal transduction
- cell surface receptor signaling pathway
- regulation of apoptotic process
- negative regulation of apoptotic process
Molecular Function
- transmembrane signaling receptor activity
- TRAIL binding
Cellular Component
- plasma membrane
- cell surface
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312584
- Coding exons
- 9
- Length
- 28443
- Individuals with no LoFs
- 125723
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 24
- Defined
- 125747
- p
- 0.0000954
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.00939 | 218 | 218 | 1.00 | 0.0000122 | 2409 |
| Missense (PolyPhen) | 36 | 46.404 | 0.77579 | 587 | ||
| Synonymous | 0.401 | 82 | 86.8 | 0.945 | 0.00000494 | 792 |
| Loss of Function | 1.01 | 14 | 18.7 | 0.748 | 8.93e-7 | 227 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00076 | 0.00076 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for the cytotoxic ligand TRAIL. Contains a truncated death domain and hence is not capable of inducing apoptosis but protects against TRAIL-mediated apoptosis. Reports are contradictory with regards to its ability to induce the NF- kappa-B pathway. According to PubMed:9382840, it cannot but according to PubMed:9430226, it can induce the NF-kappa-B pathway.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.206
- RVIS EVS
- 3.11
- RVIS percentile EVS
- 99.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00884
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |