TRAF4
TNF receptor associated factor 4, the group of TNF receptor associated factors|Ring finger proteins|Zinc fingers TRAF-type
Basic information
Region (hg38): 17:28744011-28750956
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 TRAF4 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 | 0 | |||||
| missense | 16 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 1 |
Variants in TRAF4
This is a list of pathogenic ClinVar variants found in the TRAF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-28744254-A-G | not specified | Uncertain significance (Jul 27, 2022) | ||
| 17-28747218-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 17-28747257-A-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-28748084-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 17-28748099-C-G | not specified | Uncertain significance (Feb 23, 2023) | ||
| 17-28748155-G-A | not specified | Uncertain significance (Jan 24, 2023) | ||
| 17-28748176-G-A | not specified | Uncertain significance (May 02, 2024) | ||
| 17-28748271-G-A | not specified | Uncertain significance (Jul 14, 2022) | ||
| 17-28748316-G-A | Benign (May 21, 2018) | |||
| 17-28748563-G-A | not specified | Uncertain significance (Jul 30, 2023) | ||
| 17-28748572-C-T | not specified | Uncertain significance (Oct 20, 2023) | ||
| 17-28748581-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 17-28748980-G-C | not specified | Uncertain significance (Jun 04, 2024) | ||
| 17-28749108-G-A | not specified | Uncertain significance (Apr 11, 2023) | ||
| 17-28749267-G-A | not specified | Uncertain significance (Sep 26, 2023) | ||
| 17-28749350-C-T | not specified | Uncertain significance (Aug 10, 2021) | ||
| 17-28749496-C-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 17-28749501-G-A | not specified | Uncertain significance (May 27, 2022) | ||
| 17-28749511-C-G | not specified | Uncertain significance (Mar 29, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRAF4 | protein_coding | protein_coding | ENST00000262395 | 7 | 6973 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.936 | 0.0640 | 125720 | 0 | 7 | 125727 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.42 | 178 | 295 | 0.603 | 0.0000183 | 3074 |
| Missense in Polyphen | 56 | 109.83 | 0.5099 | 1167 | ||
| Synonymous | -0.235 | 113 | 110 | 1.03 | 0.00000560 | 941 |
| Loss of Function | 3.75 | 3 | 22.0 | 0.137 | 0.00000117 | 231 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Adapter protein and signal transducer that links members of the tumor necrosis factor receptor (TNFR) family to different signaling pathways. Plays a role in the activation of NF-kappa-B and JNK, and in the regulation of cell survival and apoptosis. Regulates activation of NF-kappa-B in response to signaling through Toll-like receptors. Required for normal skeleton development, and for normal development of the respiratory tract (By similarity). Required for activation of RPS6KB1 in response to TNF signaling. Modulates TRAF6 functions. {ECO:0000250, ECO:0000269|PubMed:12023963, ECO:0000269|PubMed:12801526, ECO:0000269|PubMed:16052631, ECO:0000269|PubMed:16157600, ECO:0000269|PubMed:18953416, ECO:0000269|PubMed:19937093}.;
- Pathway
- Small cell lung cancer - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);ApoE and miR-146 in inflammation and atherosclerosis;Validated transcriptional targets of TAp63 isoforms;TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.202
Intolerance Scores
- loftool
- 0.429
- rvis_EVS
- -0.4
- rvis_percentile_EVS
- 26.53
Haploinsufficiency Scores
- pHI
- 0.351
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.873
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Traf4
- Phenotype
- limbs/digits/tail 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); skeleton phenotype; immune system phenotype; respiratory system phenotype; embryo phenotype; pigmentation phenotype; growth/size/body region 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); reproductive system phenotype; cellular phenotype;
Gene ontology
- Biological process
- apoptotic process;signal transduction;activation of NF-kappaB-inducing kinase activity;respiratory gaseous exchange;respiratory tube development;regulation of apoptotic process;positive regulation of protein kinase activity;positive regulation of JNK cascade;positive regulation of protein homodimerization activity
- Cellular component
- nucleus;cytoplasm;cytoskeleton;plasma membrane;bicellular tight junction;protein-containing complex;perinuclear region of cytoplasm
- Molecular function
- DNA binding;tumor necrosis factor receptor binding;protein binding;zinc ion binding;protein kinase binding;ubiquitin protein ligase binding;thioesterase binding;identical protein binding;WW domain binding