TRIM40
protein-codingtripartite motif containing 40, the group of Tripartite motif family|Ring finger proteins
Gene summary
This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.6 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 TRIM40 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001286633.2. 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 | 0 | |||||
| missense | 31 | 5 | 36 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 1 | 3 | |||
| Total | 0 | 0 | 33 | 6 | 1 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001273562.1 | 5 | MANE Select | |
| Ensembl | ENSP00000379826.1 | 5 | MANE Select | |
| RefSeq | NP_619645.1 | 5 | Standard | |
| Ensembl | ENSP00000308310.4 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of cell growth
- negative regulation of NF-kappaB transcription factor activity
- negative regulation of protein catabolic process
- protein neddylation
- negative regulation of protein localization to nucleus
Molecular Function
- protein binding
- zinc ion binding
Cellular Component
- IkappaB kinase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000307859
- Coding exons
- 5
- Length
- 12628
- Individuals with no LoFs
- 123348
- Homozygous LoFs
- 31
- Heterozygous LoFs
- 2369
- Defined
- 125748
- p
- 0.00959
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.147 | 117 | 122 | 0.963 | 0.00000613 | 1487 |
| Missense (PolyPhen) | 32 | 29.308 | 1.0919 | 358 | ||
| Synonymous | 0.315 | 46 | 48.8 | 0.943 | 0.00000247 | 443 |
| Loss of Function | -0.799 | 14 | 11.1 | 1.26 | 6.12e-7 | 117 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.011 | 0.011 | notable |
| Latino/Admixed American | 0.018 | 0.018 | notable |
| Ashkenazi Jewish | 0.046 | 0.046 | notable |
| East Asian | 0.0029 | 0.0029 | notable |
| Finnish | 0.00088 | 0.00083 | rare |
| European (Non-Finnish) | 0.0083 | 0.0082 | notable |
| South Asian | 0.0024 | 0.0024 | notable |
| Other | 0.014 | 0.014 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway. Promotes neddylation of IKBKG/NEMO, stabilizing NFKBIA, and inhibiting of NF-kappaB nuclear translocation and activity. {ECO:0000269|PubMed:21474709}.;
Intolerance Scores
- LoFtool
- 0.802
- RVIS EVS
- 1.44
- RVIS percentile EVS
- 95.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.700
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |