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

ENSG00000110171 ∙ NCBI:10612 ∙ OMIM:605493 ∙ HGNC:10064 ∙ Uniprot:O75382 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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		1
missense			16			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)
11-6449349-T-C		not specified	Uncertain significance (Feb 27, 2023)
11-6450946-C-T		not specified	Uncertain significance (Nov 10, 2021)
11-6451288-G-A		not specified	Uncertain significance (Apr 22, 2022)
11-6451309-G-T		not specified	Uncertain significance (Dec 22, 2023)
11-6456110-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-6456410-C-G		TRIM3-related disorder • not specified	Conflicting classifications of pathogenicity (Mar 29, 2023)
11-6456480-C-A		not specified	Uncertain significance (Oct 03, 2022)
11-6456545-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-6456586-G-A			Likely benign (Mar 28, 2018)
11-6456813-G-C		not specified	Uncertain significance (Feb 05, 2024)
11-6456816-C-A		not specified	Uncertain significance (Dec 28, 2023)
11-6456816-C-T		not specified	Uncertain significance (Dec 13, 2022)
11-6457014-G-T		not specified	Uncertain significance (Oct 06, 2022)
11-6457442-C-G		not specified	Uncertain significance (Jul 12, 2022)
11-6457442-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-6457460-C-T		not specified	Uncertain significance (Nov 21, 2023)
11-6457720-C-T		not specified	Uncertain significance (Nov 17, 2022)
11-6457741-T-C		not specified	Uncertain significance (Jan 09, 2024)
11-6457790-C-T		not specified	Uncertain significance (Feb 10, 2022)
11-6457796-G-A		not specified	Uncertain significance (Jul 26, 2021)
11-6457825-G-C		not specified	Uncertain significance (Dec 28, 2022)
11-6458234-G-A		not specified	Uncertain significance (Nov 20, 2023)
11-6465613-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-6465620-G-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM3	protein_coding	protein_coding	ENST00000525074	11	25847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0107	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.71	269	503	0.535	0.0000342	4823
Missense in Polyphen		83	224.17	0.37025		2183
Synonymous	-0.0738	207	206	1.01	0.0000138	1563
Loss of Function	4.52	4	31.3	0.128	0.00000179	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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
• gene_indispensability_pred: E
• gene_indispensability_score: 0.792

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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