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GeneBe

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:O75382AlphaFoldGenCCjaxSfariGnomADPubmed

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 (13 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 1
missense 13 13
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 0
Total 0 0 13 1 0

Variants in TRIM3

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

Position Type Phenotype Significance ClinVar
11-6449349-T-C Inborn genetic diseases Uncertain significance (Feb 27, 2023)link
11-6450946-C-T Inborn genetic diseases Uncertain significance (Nov 10, 2021)link
11-6451288-G-A Inborn genetic diseases Uncertain significance (Apr 22, 2022)link
11-6456110-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2021)link
11-6456410-C-G Inborn genetic diseases Uncertain significance (Jul 06, 2021)link
11-6456545-G-A Inborn genetic diseases Uncertain significance (Jul 09, 2021)link
11-6456586-G-A Likely benign (Mar 28, 2018)link
11-6456816-C-T Inborn genetic diseases Uncertain significance (Dec 13, 2022)link
11-6457014-G-T Inborn genetic diseases Uncertain significance (Oct 06, 2022)link
11-6457442-C-G Inborn genetic diseases Uncertain significance (Jul 12, 2022)link
11-6457442-C-T Inborn genetic diseases Uncertain significance (Sep 12, 2023)link
11-6457720-C-T Inborn genetic diseases Uncertain significance (Nov 17, 2022)link
11-6457790-C-T Inborn genetic diseases Uncertain significance (Feb 10, 2022)link
11-6457796-G-A Inborn genetic diseases Uncertain significance (Jul 26, 2021)link
11-6457825-G-C Inborn genetic diseases Uncertain significance (Dec 28, 2022)link
11-6465613-C-T Inborn genetic diseases Uncertain significance (Jul 05, 2023)link
11-6465676-C-T Inborn genetic diseases Uncertain significance (Dec 01, 2022)link

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