TRIM38
Basic information
Region (hg38): 6:25962802-25991231
Previous symbols: [ "RNF15" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (44 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM38 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006355.5. 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 | 0 | |||||
| missense | 39 | 44 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 39 | 5 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRIM38 | protein_coding | protein_coding | ENST00000357085 | 6 | 24355 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.39e-8 | 0.597 | 125662 | 2 | 84 | 125748 | 0.000342 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.593 | 227 | 254 | 0.895 | 0.0000133 | 3063 |
| Missense in Polyphen | 56 | 66.467 | 0.84252 | 879 | ||
| Synonymous | 1.47 | 79 | 97.5 | 0.811 | 0.00000524 | 875 |
| Loss of Function | 1.16 | 15 | 20.7 | 0.724 | 9.60e-7 | 250 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00114 | 0.00114 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000150 | 0.000149 |
| Middle Eastern | 0.00114 | 0.00114 |
| South Asian | 0.00138 | 0.00131 |
| Other | 0.000491 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase. Mediates 'Lys-48'-linked polyubiquitination and proteasomal degradation of the critical TLR adapter TICAM1, inhibiting TLR3-mediated type I interferon signaling. {ECO:0000269|PubMed:23056470}.;
- Pathway
- Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.0902
Intolerance Scores
- loftool
- 0.922
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.6
Haploinsufficiency Scores
- pHI
- 0.0897
- hipred
- N
- hipred_score
- 0.148
- ghis
- 0.483
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.782
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trim38
- Phenotype
- immune system 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of interferon-beta production;positive regulation of I-kappaB kinase/NF-kappaB signaling;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of viral genome replication;positive regulation of viral entry into host cell;negative regulation of defense response to virus;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity;interferon-gamma-mediated signaling pathway;protein K48-linked ubiquitination
- Cellular component
- cellular_component;cytosol
- Molecular function
- protein binding;zinc ion binding;transferase activity