TRIM5

tripartite motif containing 5, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 11:5663195-5938619

Links

ENSG00000132256 ∙ NCBI:85363 ∙ OMIM:608487 ∙ HGNC:16276 ∙ Uniprot:Q9C035 ∙ 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 TRIM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM5 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			25	6	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			145	18	17	180
Total	0	0	170	24	19

Variants in TRIM5

This is a list of pathogenic ClinVar variants found in the TRIM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5664855-G-A			Benign (Aug 20, 2018)
11-5664906-T-C		not specified	Uncertain significance (Aug 20, 2023)
11-5664933-T-C		not specified	Uncertain significance (Jan 10, 2022)
11-5664981-C-T		not specified	Uncertain significance (Feb 12, 2024)
11-5664983-A-C		not specified	Uncertain significance (Jul 09, 2021)
11-5665044-C-G		not specified	Uncertain significance (Jul 26, 2022)
11-5665164-C-T		not specified	Likely benign (Aug 10, 2021)
11-5665170-C-T		not specified	Uncertain significance (Sep 17, 2021)
11-5665236-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-5665237-G-C		not specified	Uncertain significance (Jan 24, 2023)
11-5665251-C-T		not specified	Uncertain significance (Oct 13, 2023)
11-5665276-A-T		not specified	Uncertain significance (Sep 16, 2021)
11-5665317-G-T		not specified	Uncertain significance (Jun 23, 2023)
11-5665369-T-C		not specified	Uncertain significance (Sep 27, 2022)
11-5665384-C-A		not specified	Likely benign (Aug 21, 2023)
11-5666001-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-5666028-C-G		not specified	Uncertain significance (Jan 24, 2023)
11-5667699-C-T		not specified	Likely benign (Dec 19, 2023)
11-5667718-A-G			Benign (Jul 16, 2018)
11-5678194-C-T			Benign (Feb 16, 2018)
11-5678221-C-T		not specified	Likely benign (Aug 28, 2023)
11-5678235-C-T		not specified	Uncertain significance (Feb 15, 2023)
11-5678261-T-C			Benign (Aug 20, 2018)
11-5678280-T-A		not specified	Uncertain significance (Jun 16, 2023)
11-5678298-G-C		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM5	protein_coding	protein_coding	ENST00000380034	7	275425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000597	0.902	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.475	290	268	1.08	0.0000140	3235
Missense in Polyphen		65	76.41	0.85068		947
Synonymous	-0.463	107	101	1.06	0.00000533	939
Loss of Function	1.53	9	15.5	0.580	7.24e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000870	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.000870	0.000870
South Asian	0.0000664	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses. Blocks viral replication early in the life cycle, after viral entry but before reverse transcription. In addition to acting as a capsid-specific restriction factor, also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Binding to the viral capsid triggers its E3 ubiquitin ligase activity, and in concert with the heterodimeric ubiquitin conjugating enzyme complex UBE2V1-UBE2N (also known as UBC13-UEV1A complex) generates 'Lys-63'-linked polyubiquitin chains, which in turn are catalysts in the autophosphorylation of the MAP3K7/TAK1 complex (includes TAK1, TAB2, and TAB3). Activation of the MAP3K7/TAK1 complex by autophosphorylation results in the induction and expression of NF- kappa-B and MAPK-responsive inflammatory genes, thereby leading to an innate immune response in the infected cell. Restricts infection by N-tropic murine leukemia virus (N-MLV), equine infectious anemia virus (EIAV), simian immunodeficiency virus of macaques (SIVmac), feline immunodeficiency virus (FIV), and bovine immunodeficiency virus (BIV) (PubMed:17156811). Plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2 (PubMed:25127057). Also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction (PubMed:25127057). {ECO:0000269|PubMed:12878161, ECO:0000269|PubMed:17156811, ECO:0000269|PubMed:18312418, ECO:0000269|PubMed:21035162, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:21632761, ECO:0000269|PubMed:22291694, ECO:0000269|PubMed:25127057}.
• Pathway: Mesodermal Commitment Pathway;Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0951

Intolerance Scores

• loftool: 0.531
• rvis_EVS: 1.2
• rvis_percentile_EVS: 93.01

Haploinsufficiency Scores

• pHI: 0.0571
• hipred: N
• hipred_score: 0.491
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.329

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim5

Gene ontology

• Biological process: activation of innate immune response;pattern recognition receptor signaling pathway;autophagy;viral process;regulation of lipopolysaccharide-mediated signaling pathway;regulation of protein localization;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of MAPK cascade;innate immune response;negative regulation of viral entry into host cell;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity;defense response to virus;interferon-gamma-mediated signaling pathway;protein K63-linked ubiquitination;negative regulation of viral release from host cell
• Cellular component: P-body;nucleus;cytoplasm;cytosol;omegasome
• Molecular function: ubiquitin-protein transferase activity;protein binding;zinc ion binding;signaling pattern recognition receptor activity;protein kinase binding;protein binding, bridging;identical protein binding;protein homodimerization activity