TRIM56

tripartite motif containing 56, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 7:101085480-101097967

Links

ENSG00000169871 ∙ NCBI:81844 ∙ OMIM:616996 ∙ HGNC:19028 ∙ Uniprot:Q9BRZ2 ∙ 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 TRIM56 gene.

• Inborn genetic diseases (37 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM56 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	2
missense			34	3	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	4	2

Variants in TRIM56

This is a list of pathogenic ClinVar variants found in the TRIM56 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-101087317-T-A		not specified	Uncertain significance (Dec 19, 2023)
7-101087349-G-A		not specified	Uncertain significance (Jan 04, 2024)
7-101087466-G-A		not specified	Likely benign (Jul 12, 2023)
7-101087472-G-A		not specified	Likely benign (May 27, 2022)
7-101087490-C-T		not specified	Uncertain significance (May 25, 2022)
7-101087493-G-A		not specified	Uncertain significance (May 27, 2022)
7-101087547-G-A		not specified	Uncertain significance (Feb 07, 2023)
7-101087592-C-G		not specified	Uncertain significance (Jan 24, 2023)
7-101087641-C-T		not specified	Uncertain significance (Feb 03, 2022)
7-101087680-G-A		not specified	Uncertain significance (Jun 29, 2022)
7-101087711-C-T			Benign (Dec 31, 2019)
7-101087746-G-A		not specified	Uncertain significance (Nov 21, 2022)
7-101087796-C-T		not specified	Uncertain significance (Jan 17, 2024)
7-101087831-C-T			Likely benign (Feb 01, 2023)
7-101087941-G-A		not specified	Uncertain significance (Jan 26, 2023)
7-101087947-G-A		not specified	Uncertain significance (Jan 04, 2024)
7-101087973-G-A		not specified	Uncertain significance (Aug 30, 2022)
7-101088010-C-T		not specified	Uncertain significance (Jul 17, 2023)
7-101088082-A-G		not specified	Uncertain significance (Jun 29, 2023)
7-101088093-G-T		not specified	Uncertain significance (Feb 21, 2024)
7-101088105-G-A		not specified	Uncertain significance (Nov 18, 2022)
7-101088119-G-T		not specified	Uncertain significance (Dec 15, 2022)
7-101088177-C-T		not specified	Uncertain significance (Jul 14, 2021)
7-101088231-G-A		not specified	Uncertain significance (Oct 18, 2021)
7-101088240-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM56	protein_coding	protein_coding	ENST00000306085	1	6298

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000136	0.965	124773	0	32	124805	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	397	474	0.838	0.0000330	4731
Missense in Polyphen		131	200.34	0.65387		1998
Synonymous	-0.887	235	218	1.08	0.0000152	1698
Loss of Function	1.89	9	17.5	0.513	8.99e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000234	0.000212
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that plays a key role in innate antiviral immunity (PubMed:21289118). In response to pathogen- and host-derived double-stranded DNA (dsDNA), targets TMEM173/STING to 'Lys-63'-linked ubiquitination, thereby promoting its homodimerization, a step required for the production of type I interferon IFN-beta (By similarity). Independently of its E3 ubiquitin ligase activity, positive regulator of TLR3 signaling. Potentiates extracellular double stranded RNA (dsRNA)-induced expression of IFNB1 and interferon-stimulated genes ISG15, IFIT1/ISG56, CXCL10, OASL and CCL5/RANTES. Promotes establishment of an antiviral state by TLR3 ligand and TLR3-mediated chemokine induction following infection by hepatitis C virus (PubMed:22948160). {ECO:0000250|UniProtKB:Q80VI1, ECO:0000269|PubMed:21289118, ECO:0000269|PubMed:22948160}.
• Pathway: Regulation of innate immune responses to cytosolic DNA;Innate Immune System;Immune System;Cytosolic sensors of pathogen-associated DNA (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.77

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.655
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim56
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of type I interferon production;interferon-beta production;response to type I interferon;defense response to virus;protein K63-linked ubiquitination
• Cellular component: cytoplasm;cytosol
• Molecular function: RNA binding;ubiquitin-protein transferase activity;zinc ion binding