TRIM3
protein-codingtripartite motif containing 3, the group of Tripartite motif family|Ring finger proteins
Gene summary
The protein encoded by this gene is a member of the tripartite motif (TRIM) family, also called the 'RING-B-box-coiled-coil' (RBCC) subgroup of RING finger proteins. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein localizes to cytoplasmic filaments. It is similar to a rat protein which is a specific partner for the tail domain of myosin V, a class of myosins which are involved in the targeted transport of organelles. The rat protein can also interact with alpha-actinin-4. Thus it is suggested that this human protein may play a role in myosin V-mediated cargo transport. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]
- RNF22
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.8 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 TRIM3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033278.4. 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 | 1 | 1 | ||||
| missense | 69 | 69 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 75 | 1 | 0 | 76 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_150594.2 | 11 | MANE Select | |
| Ensembl | ENSP00000340797.3 | 11 | MANE Select | |
| RefSeq | NP_001234935.1 | 11 | Standard | |
| RefSeq | NP_001234936.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cytokine Signaling in Immune system
- Immune System
- Interferon gamma signaling
- Interferon Signaling
Biological Process
- protein polyubiquitination
- nervous system development
- protein transport
- proteasome-mediated ubiquitin-dependent protein catabolic process
Molecular Function
- protein binding
- protein C-terminus binding
- zinc ion binding
- ubiquitin protein ligase activity
Cellular Component
- cytoplasm
- early endosome
- Golgi apparatus
- dendrite
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000525074
- Coding exons
- 11
- Length
- 25847
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125747
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.71 | 269 | 503 | 0.535 | 0.0000342 | 4823 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- LoFtool
- 0.0797
- RVIS EVS
- -1.2
- RVIS percentile EVS
- 5.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.792
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |