TRIM22

tripartite motif containing 22, the group of Minor histocompatibility antigens|Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 11:5689609-5737089

Links

ENSG00000132274 ∙ NCBI:10346 ∙ OMIM:606559 ∙ HGNC:16379 ∙ Uniprot:Q8IYM9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inflammatory bowel disease (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM22 gene.

• Inborn genetic diseases (10 variants)
• not specified (9 variants)
• not provided (2 variants)
• TRIM22-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM22 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					3	3
missense			10	2	2	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					5	5
Total	0	0	10	2	10

Variants in TRIM22

This is a list of pathogenic ClinVar variants found in the TRIM22 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5696339-A-G		not specified	Uncertain significance (Sep 09, 2021)
11-5696347-A-T		not specified	Uncertain significance (Dec 18, 2023)
11-5696351-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-5696414-C-A		TRIM22-related disorder	Likely benign (Jan 17, 2023)
11-5696440-C-A		not specified	Uncertain significance (Dec 15, 2022)
11-5696441-C-A		not specified	Uncertain significance (May 24, 2023)
11-5696479-G-A			Uncertain significance (-)
11-5696532-T-C		not specified	Benign (Jan 24, 2024)
11-5696550-C-T			Benign (Jun 14, 2018)
11-5697287-G-A		not specified	Benign (Jan 24, 2024)
11-5698315-A-G		not specified	Uncertain significance (Feb 17, 2022)
11-5698387-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-5698414-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-5698415-A-T		not specified	Uncertain significance (Feb 13, 2024)
11-5698433-T-C		not specified	Uncertain significance (May 18, 2022)
11-5698437-T-C		not specified	Benign (Jan 24, 2024)
11-5698490-C-T		not specified	Uncertain significance (Sep 20, 2023)
11-5698520-G-C		not specified	Benign (Jan 24, 2024)
11-5698547-T-C		TRIM22-related disorder	Likely benign (Jan 08, 2021)
11-5698558-A-G		not specified	Benign (Jan 24, 2024)
11-5698605-T-C		not specified	Benign (Jan 24, 2024)
11-5698618-C-T		not specified	Benign (Jan 24, 2024)
11-5708197-G-C		TRIM22-related disorder • not specified	Uncertain significance (Oct 10, 2023)
11-5708210-T-C		not specified	Likely benign (Jun 01, 2023)
11-5708265-T-A		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM22	protein_coding	protein_coding	ENST00000379965	7	47401

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000213	0.911	125326	2	405	125733	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	256	262	0.977	0.0000132	3271
Missense in Polyphen		65	70.451	0.92262		988
Synonymous	-0.0910	103	102	1.01	0.00000564	934
Loss of Function	1.60	10	17.1	0.584	8.98e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0213	0.0198
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000578	0.000563
Middle Eastern	0.000221	0.000217
South Asian	0.000400	0.000392
Other	0.000513	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced antiviral protein involved in cell innate immunity. The antiviral activity could in part be mediated by TRIM22-dependent ubiquitination of viral proteins. Plays a role in restricting the replication of HIV-1, encephalomyocarditis virus (EMCV) and hepatitis B virus (HBV). Acts as a transcriptional repressor of HBV core promoter. May have E3 ubiquitin-protein ligase activity. {ECO:0000269|PubMed:18389079, ECO:0000269|PubMed:18656448, ECO:0000269|PubMed:19218198, ECO:0000269|PubMed:19585648}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0703

Intolerance Scores

• loftool: 0.586
• rvis_EVS: 1.78
• rvis_percentile_EVS: 96.84

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.148
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;immune response;response to virus;positive regulation of autophagy;viral process;protein ubiquitination;regulation of protein localization;positive regulation of I-kappaB kinase/NF-kappaB signaling;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 trimerization;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytoplasm;Golgi apparatus;cytosol;Cajal body;nuclear body;nuclear speck
• Molecular function: DNA-binding transcription factor activity;transcription corepressor activity;protein binding;zinc ion binding;transferase activity;protein kinase binding;protein binding, bridging