TRAF1
TNF receptor associated factor 1, the group of TNF receptor associated factors
Basic information
Region (hg38): 9:120902393-120929173
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005658.5. 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 | 2 | |||||
| missense | 40 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 4 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRAF1 | protein_coding | protein_coding | ENST00000373887 | 7 | 26781 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00356 | 0.988 | 125727 | 0 | 21 | 125748 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.920 | 206 | 247 | 0.835 | 0.0000145 | 2707 |
| Missense in Polyphen | 52 | 78.935 | 0.65877 | 909 | ||
| Synonymous | 1.27 | 90 | 107 | 0.843 | 0.00000653 | 835 |
| Loss of Function | 2.31 | 7 | 17.4 | 0.403 | 8.05e-7 | 205 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000202 | 0.000202 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000708 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000101 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Adapter molecule that regulates the activation of NF- kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein- ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2. {ECO:0000269|PubMed:10692572, ECO:0000269|PubMed:16323247, ECO:0000269|PubMed:18429822, ECO:0000269|PubMed:19287455, ECO:0000269|PubMed:19698991, ECO:0000269|PubMed:20385093}.;
- Pathway
- Small cell lung cancer - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway;TNF alpha Signaling Pathway;Apoptosis;EBV LMP1 signaling;Apoptosis-related network due to altered Notch3 in ovarian cancer;Apoptotic Signaling Pathway;Oxidative Damage;TWEAK;Signal Transduction;tnfr2 signaling pathway;hiv-1 nef: negative effector of fas and tnf;keratinocyte differentiation;TNFR1-induced NFkappaB signaling pathway;TNF signaling;Death Receptor Signalling;Regulation of TNFR1 signaling;TNFalpha;RANKL;HIV-1 Nef: Negative effector of Fas and TNF-alpha;CD40/CD40L signaling;TNF receptor signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.395
Intolerance Scores
- loftool
- 0.644
- rvis_EVS
- 0.09
- rvis_percentile_EVS
- 60.57
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- Y
- hipred_score
- 0.645
- ghis
- 0.531
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.869
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Traf1
- Phenotype
- cellular phenotype; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- apoptotic process;signal transduction;regulation of tumor necrosis factor-mediated signaling pathway;positive regulation of NF-kappaB transcription factor activity;protein-containing complex assembly;regulation of extrinsic apoptotic signaling pathway
- Cellular component
- cytoplasm;cytosol;protein-containing complex
- Molecular function
- tumor necrosis factor receptor binding;protein binding;zinc ion binding;ubiquitin protein ligase binding;thioesterase binding;identical protein binding