TNFAIP1
Basic information
Region (hg38): 17:28335602-28347009
Previous symbols: [ "EDP1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFAIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021137.5. 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 | 1 | |||||
| missense | 39 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 39 | 0 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TNFAIP1 | protein_coding | protein_coding | ENST00000226225 | 6 | 11408 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.135 | 0.861 | 125718 | 0 | 30 | 125748 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.53 | 143 | 205 | 0.698 | 0.0000140 | 2067 |
| Missense in Polyphen | 50 | 81.48 | 0.61365 | 822 | ||
| Synonymous | -0.110 | 83 | 81.7 | 1.02 | 0.00000513 | 616 |
| Loss of Function | 2.51 | 4 | 14.2 | 0.281 | 7.74e-7 | 170 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000173 | 0.000173 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000160 | 0.000158 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex involved in regulation of cytoskeleton structure. The BCR(TNFAIP1) E3 ubiquitin ligase complex mediates the ubiquitination of RHOA, leading to its degradation by the proteasome, thereby regulating the actin cytoskeleton and cell migration. Its interaction with RHOB may regulate apoptosis. May enhance the PCNA-dependent DNA polymerase delta activity. {ECO:0000269|PubMed:19637314, ECO:0000269|PubMed:19782033}.;
Recessive Scores
- pRec
- 0.493
Intolerance Scores
- loftool
- 0.489
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.434
- hipred
- Y
- hipred_score
- 0.703
- ghis
- 0.524
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tnfaip1
- Phenotype
- homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype;
Gene ontology
- Biological process
- DNA replication;apoptotic process;immune response;cell migration;protein ubiquitination;negative regulation of Rho protein signal transduction;stress fiber assembly;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of DNA replication;protein homooligomerization
- Cellular component
- nucleolus;cytoplasm;endosome;Cul3-RING ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;GTP-Rho binding;protein domain specific binding;identical protein binding