TRIM4

tripartite motif containing 4, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 7:99876957-99919531

Links

ENSG00000146833 ∙ NCBI:89122 ∙ ∙ HGNC:16275 ∙ Uniprot:Q9C037 ∙ 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 TRIM4 gene.

• Inborn genetic diseases (25 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM4 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in TRIM4

This is a list of pathogenic ClinVar variants found in the TRIM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99876961-G-A		not specified	Uncertain significance (Aug 04, 2023)
7-99876967-T-A		not specified	Uncertain significance (Oct 12, 2021)
7-99877003-C-G		not specified	Uncertain significance (Oct 12, 2021)
7-99877025-C-A		not specified	Uncertain significance (Mar 13, 2023)
7-99892208-A-C		not specified	Uncertain significance (Dec 15, 2022)
7-99892215-CA-C			not provided (-)
7-99892252-A-G		not specified	Uncertain significance (Jul 09, 2021)
7-99892273-C-T		not specified	Uncertain significance (Mar 11, 2024)
7-99892279-C-T		not specified	Uncertain significance (Jun 01, 2023)
7-99892299-T-G		not specified	Uncertain significance (Jul 11, 2023)
7-99892312-G-C		not specified	Uncertain significance (Nov 03, 2023)
7-99892379-C-A		not specified	Uncertain significance (Feb 17, 2024)
7-99892447-G-A		not specified	Uncertain significance (Dec 04, 2021)
7-99892516-C-G		not specified	Uncertain significance (Oct 26, 2021)
7-99892582-T-C		not specified	Uncertain significance (Apr 20, 2023)
7-99892615-A-G		not specified	Uncertain significance (Feb 16, 2023)
7-99892675-T-C		not specified	Uncertain significance (Feb 17, 2022)
7-99903226-C-T		not specified	Likely benign (Feb 23, 2023)
7-99903255-C-G		not specified	Uncertain significance (Oct 26, 2021)
7-99903579-G-T		not specified	Uncertain significance (Apr 05, 2023)
7-99903585-A-T		not specified	Uncertain significance (May 05, 2023)
7-99908602-G-C		not specified	Uncertain significance (Sep 14, 2022)
7-99908778-G-A		not specified	Uncertain significance (Dec 13, 2022)
7-99908793-C-T		not specified	Uncertain significance (Jun 29, 2023)
7-99909579-C-T		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM4	protein_coding	protein_coding	ENST00000355947	7	42643

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.50e-12	0.0764	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	250	255	0.981	0.0000136	3232
Missense in Polyphen		55	64.482	0.85294		869
Synonymous	-0.0341	102	102	1.00	0.00000573	957
Loss of Function	0.342	18	19.6	0.917	0.00000100	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000270
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000819	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase. Mediates 'Lys-63'-linked polyubiquitination of the innate immune receptor DDX58, this linkage doesn't lead to proteasomal degradation but seems to enhance IFN induction. {ECO:0000269|PubMed:24755855}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.123
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Gene ontology

• Biological process: protein ubiquitination;innate immune response;protein trimerization
• Cellular component: cytoplasm;cytosol;plasma membrane
• Molecular function: zinc ion binding;transferase activity