TRIM3
tripartite motif containing 3, the group of Tripartite motif family|Ring finger proteins
Basic information
Region (hg38): 11:6448612-6474459
Previous symbols: [ "RNF22" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (13 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM3 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 1 | 0 |
Variants in TRIM3
This is a list of pathogenic ClinVar variants found in the TRIM3 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-6449349-T-C | Inborn genetic diseases | Uncertain significance (Feb 27, 2023) | ||
| 11-6450946-C-T | Inborn genetic diseases | Uncertain significance (Nov 10, 2021) | ||
| 11-6451288-G-A | Inborn genetic diseases | Uncertain significance (Apr 22, 2022) | ||
| 11-6456110-G-A | Inborn genetic diseases | Uncertain significance (Aug 02, 2021) | ||
| 11-6456410-C-G | Inborn genetic diseases | Uncertain significance (Jul 06, 2021) | ||
| 11-6456545-G-A | Inborn genetic diseases | Uncertain significance (Jul 09, 2021) | ||
| 11-6456586-G-A | Likely benign (Mar 28, 2018) | |||
| 11-6456816-C-T | Inborn genetic diseases | Uncertain significance (Dec 13, 2022) | ||
| 11-6457014-G-T | Inborn genetic diseases | Uncertain significance (Oct 06, 2022) | ||
| 11-6457442-C-G | Inborn genetic diseases | Uncertain significance (Jul 12, 2022) | ||
| 11-6457442-C-T | Inborn genetic diseases | Uncertain significance (Sep 12, 2023) | ||
| 11-6457720-C-T | Inborn genetic diseases | Uncertain significance (Nov 17, 2022) | ||
| 11-6457790-C-T | Inborn genetic diseases | Uncertain significance (Feb 10, 2022) | ||
| 11-6457796-G-A | Inborn genetic diseases | Uncertain significance (Jul 26, 2021) | ||
| 11-6457825-G-C | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
| 11-6465613-C-T | Inborn genetic diseases | Uncertain significance (Jul 05, 2023) | ||
| 11-6465676-C-T | Inborn genetic diseases | Uncertain significance (Dec 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRIM3 | protein_coding | protein_coding | ENST00000525074 | 11 | 25847 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.989 | 0.0107 | 125742 | 0 | 5 | 125747 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.71 | 269 | 503 | 0.535 | 0.0000342 | 4823 |
| Missense in Polyphen | 83 | 224.17 | 0.37025 | 2183 | ||
| Synonymous | -0.0738 | 207 | 206 | 1.01 | 0.0000138 | 1563 |
| Loss of Function | 4.52 | 4 | 31.3 | 0.128 | 0.00000179 | 318 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000931 | 0.0000924 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Probably involved in vesicular trafficking via its association with the CART complex (PubMed:15772161). The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation (PubMed:15772161). Positively regulates motility of microtubule-dependent motor protein KIF21B (By similarity). {ECO:0000250|UniProtKB:Q9R1R2, ECO:0000269|PubMed:15772161}.;
- Pathway
- Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- loftool
- 0.0797
- rvis_EVS
- -1.2
- rvis_percentile_EVS
- 5.76
Haploinsufficiency Scores
- pHI
- 0.412
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.681
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.792
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trim3
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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);
Gene ontology
- Biological process
- protein polyubiquitination;nervous system development;protein transport;proteasome-mediated ubiquitin-dependent protein catabolic process
- Cellular component
- cytoplasm;early endosome;Golgi apparatus;dendrite
- Molecular function
- protein binding;protein C-terminus binding;zinc ion binding;ubiquitin protein ligase activity