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TRIM38

tripartite motif containing 38, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 6:25962801-25991231

Previous symbols: [ "RNF15" ]

Links

ENSG00000112343NCBI:10475HGNC:10059Uniprot:O00635AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM38 gene.

  • Inborn genetic diseases (18 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.

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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
18
clinvar
18
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 18 0 0

Variants in TRIM38

This is a list of pathogenic ClinVar variants found in the TRIM38 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
6-25966593-C-T not specified Uncertain significance (Aug 02, 2023)2598584
6-25966633-C-G not specified Uncertain significance (Mar 21, 2023)2527580
6-25966724-A-G not specified Uncertain significance (Sep 15, 2021)2351632
6-25966838-G-A not specified Uncertain significance (Feb 22, 2023)2465296
6-25966899-C-T not specified Uncertain significance (Dec 17, 2021)2209197
6-25969374-G-C not specified Uncertain significance (Feb 17, 2024)3182421
6-25969374-G-T not specified Uncertain significance (Oct 18, 2021)2369096
6-25971899-C-T not specified Uncertain significance (Nov 01, 2022)2321960
6-25971953-C-A not specified Uncertain significance (Nov 29, 2023)3182422
6-25971963-T-C not specified Uncertain significance (Mar 06, 2023)2494689
6-25972033-T-A not specified Uncertain significance (Aug 21, 2023)2596798
6-25972068-A-G not specified Uncertain significance (Jun 03, 2022)2293622
6-25973175-G-A not specified Uncertain significance (Nov 30, 2021)2221034
6-25983186-T-A not specified Uncertain significance (Sep 28, 2022)2314158
6-25983199-G-A not specified Uncertain significance (Jul 13, 2022)2301357
6-25983235-C-T not specified Uncertain significance (Dec 21, 2023)3182423
6-25983344-A-G not specified Uncertain significance (Jun 26, 2023)2606494
6-25983356-G-T not specified Uncertain significance (Dec 13, 2022)2334154
6-25983376-G-A not specified Uncertain significance (Jun 17, 2022)2350324
6-25983485-C-T not specified Uncertain significance (Dec 18, 2023)3182418
6-25983539-A-G not specified Uncertain significance (Dec 19, 2023)3182419
6-25983605-A-G not specified Uncertain significance (Jan 04, 2024)3182420
6-25983629-G-A not specified Uncertain significance (Nov 30, 2021)2262992
6-25983676-C-G not specified Uncertain significance (Mar 13, 2023)2495788

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRIM38protein_codingprotein_codingENST00000357085 624355
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.39e-80.5971256622841257480.000342
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5932272540.8950.00001333063
Missense in Polyphen5666.4670.84252879
Synonymous1.477997.50.8110.00000524875
Loss of Function1.161520.70.7249.60e-7250

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001480.000148
Ashkenazi Jewish0.000.00
East Asian0.001140.00114
Finnish0.000.00
European (Non-Finnish)0.0001500.000149
Middle Eastern0.001140.00114
South Asian0.001380.00131
Other0.0004910.000489

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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