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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

ENSG00000110171NCBI:10612OMIM:605493HGNC:10064Uniprot:O75382AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM3 gene.

  • Inborn genetic diseases (16 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.

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
1
clinvar
1
missense
16
clinvar
16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 16 1 0

Variants in TRIM3

This is a list of pathogenic ClinVar variants found in the TRIM3 region.

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

Position Type Phenotype Significance ClinVar
11-6449042-G-A not specified Uncertain significance (Jan 30, 2024)3182361
11-6449349-T-C not specified Uncertain significance (Feb 27, 2023)2460098
11-6450946-C-T not specified Uncertain significance (Nov 10, 2021)2260382
11-6451288-G-A not specified Uncertain significance (Apr 22, 2022)2216477
11-6451309-G-T not specified Uncertain significance (Dec 22, 2023)3182359
11-6456110-G-A not specified Uncertain significance (Aug 02, 2021)2404645
11-6456410-C-G TRIM3-related condition • not specified Conflicting classifications of pathogenicity (Mar 29, 2023)2357516
11-6456480-C-A not specified Uncertain significance (Oct 03, 2022)3182358
11-6456545-G-A not specified Uncertain significance (Jul 09, 2021)2235815
11-6456586-G-A Likely benign (Mar 28, 2018)739716
11-6456813-G-C not specified Uncertain significance (Feb 05, 2024)3182367
11-6456816-C-A not specified Uncertain significance (Dec 28, 2023)3182366
11-6456816-C-T not specified Uncertain significance (Dec 13, 2022)2390271
11-6457014-G-T not specified Uncertain significance (Oct 06, 2022)2225399
11-6457442-C-G not specified Uncertain significance (Jul 12, 2022)2301049
11-6457442-C-T not specified Uncertain significance (Sep 12, 2023)2602599
11-6457460-C-T not specified Uncertain significance (Nov 21, 2023)3182363
11-6457720-C-T not specified Uncertain significance (Nov 17, 2022)2259510
11-6457741-T-C not specified Uncertain significance (Jan 09, 2024)3182362
11-6457790-C-T not specified Uncertain significance (Feb 10, 2022)2387835
11-6457796-G-A not specified Uncertain significance (Jul 26, 2021)2347959
11-6457825-G-C not specified Uncertain significance (Dec 28, 2022)2228020
11-6458234-G-A not specified Uncertain significance (Nov 20, 2023)3182360
11-6465613-C-T not specified Uncertain significance (Jul 05, 2023)2592518
11-6465620-G-C not specified Uncertain significance (Dec 20, 2023)3182365

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRIM3protein_codingprotein_codingENST00000525074 1125847
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9890.0107125742051257470.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.712695030.5350.00003424823
Missense in Polyphen83224.170.370252183
Synonymous-0.07382072061.010.00001381563
Loss of Function4.52431.30.1280.00000179318

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00009310.0000924
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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