TRIM6

tripartite motif containing 6, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 11:5596108-5612958

Links

ENSG00000121236 ∙ NCBI:117854 ∙ OMIM:607564 ∙ HGNC:16277 ∙ Uniprot:Q9C030 ∙ 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 TRIM6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM6 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	2		18
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	3	0

Variants in TRIM6

This is a list of pathogenic ClinVar variants found in the TRIM6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5603734-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-5604536-G-T			Likely benign (Jun 18, 2018)
11-5604572-G-A			Likely benign (Jun 18, 2018)
11-5610798-A-G		not specified	Uncertain significance (Sep 27, 2021)
11-5610801-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-5610816-T-C		not specified	Uncertain significance (Dec 16, 2022)
11-5610875-T-C		not specified	Uncertain significance (Sep 26, 2022)
11-5610891-A-G			Likely benign (Mar 01, 2023)
11-5610949-G-C		not specified	Uncertain significance (May 23, 2023)
11-5610976-G-C		not specified	Uncertain significance (May 11, 2022)
11-5611062-A-G		not specified	Uncertain significance (Aug 28, 2023)
11-5611077-A-G		not specified	Uncertain significance (May 23, 2024)
11-5611163-C-T		not specified	Uncertain significance (Mar 12, 2024)
11-5611167-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-5611182-T-C		not specified	Uncertain significance (Apr 04, 2023)
11-5611218-A-C		not specified	Uncertain significance (Oct 04, 2022)
11-5611295-C-A		not specified	Uncertain significance (Aug 12, 2021)
11-5611314-C-G		not specified	Uncertain significance (Feb 17, 2024)
11-5611325-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-5611329-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM6	protein_coding	protein_coding	ENST00000380097	8	16850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-12	0.290	125536	0	211	125747	0.000839

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.02	324	276	1.17	0.0000150	3358
Missense in Polyphen		90	67.937	1.3247		987
Synonymous	0.288	101	105	0.964	0.00000517	1028
Loss of Function	1.10	22	28.3	0.776	0.00000182	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00315	0.00303
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.000489	0.000489
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000957	0.000651
Middle Eastern	0.000489	0.000489
South Asian	0.000458	0.000425
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which ubiquitinates MYC and inhibits its transcription activation activity, maintaining the pluripotency of embryonic stem cells (By similarity). Involved in the synthesis of unanchored K48-linked polyubiquitin chains which interact with and activate the serine/threonine kinase IKBKE, leading to phosphorylation of STAT1 and stimulation of an antiviral response (PubMed:24882218). {ECO:0000250|UniProtKB:Q8BGE7, ECO:0000269|PubMed:24882218}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0811

Intolerance Scores

• loftool: 0.639
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.131
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim6

Gene ontology

• Biological process: protein polyubiquitination;positive regulation of defense response to virus by host;positive regulation of cytokine secretion involved in immune response;positive regulation of gene expression;negative regulation of gene expression;positive regulation of peptidyl-threonine phosphorylation;free ubiquitin chain polymerization;viral process;response to lipopolysaccharide;positive regulation of peptidyl-serine phosphorylation;cellular response to interferon-beta;negative regulation of viral genome replication;negative regulation of transcription, DNA-templated;positive regulation of type I interferon-mediated signaling pathway;protein trimerization;cellular response to virus;regulation of NIK/NF-kappaB signaling;positive regulation of transcription regulatory region DNA binding;negative regulation of stem cell differentiation
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: protein binding;transcription factor binding;zinc ion binding;protein kinase binding;protein binding, bridging;ubiquitin protein ligase activity;protein tyrosine kinase binding