TRIM62

tripartite motif containing 62, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 1:33145399-33182059

Links

ENSG00000116525 ∙ NCBI:55223 ∙ OMIM:616755 ∙ HGNC:25574 ∙ Uniprot:Q9BVG3 ∙ 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 TRIM62 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM62 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				4	1	5
missense			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	21	5	2

Variants in TRIM62

This is a list of pathogenic ClinVar variants found in the TRIM62 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-33147184-C-T		not specified	Uncertain significance (Jun 13, 2023)
1-33147188-C-T			Benign (Jun 19, 2018)
1-33147205-G-A		not specified	Uncertain significance (Dec 01, 2023)
1-33147280-C-T		not specified	Uncertain significance (May 26, 2024)
1-33147316-T-C		not specified	Uncertain significance (Oct 16, 2023)
1-33147331-C-A		not specified	Uncertain significance (Oct 10, 2023)
1-33147455-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-33147500-G-T		not specified	Uncertain significance (May 30, 2023)
1-33147602-C-T		not specified	Uncertain significance (May 27, 2022)
1-33147603-G-A			Likely benign (Apr 20, 2018)
1-33147620-C-G		not specified	Uncertain significance (Apr 30, 2024)
1-33147703-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-33159697-A-G		not specified	Uncertain significance (Oct 20, 2021)
1-33159727-C-T		not specified	Uncertain significance (Apr 23, 2024)
1-33159731-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-33159747-C-T			Benign (Jun 29, 2018)
1-33159816-G-A			Likely benign (Apr 20, 2018)
1-33159828-C-T			Likely benign (Dec 31, 2019)
1-33159829-G-A		not specified	Uncertain significance (Apr 17, 2024)
1-33159832-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-33159833-G-A		not specified	Uncertain significance (May 15, 2023)
1-33159854-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-33159874-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-33159926-G-T			Likely benign (Apr 20, 2018)
1-33165493-T-C		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM62	protein_coding	protein_coding	ENST00000291416	5	36658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.18e-8	0.534	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	225	302	0.744	0.0000199	3057
Missense in Polyphen		84	125.84	0.66754		1274
Synonymous	0.493	130	137	0.946	0.00000945	948
Loss of Function	1.03	14	18.8	0.745	8.84e-7	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000324
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000312	0.000185
European (Non-Finnish)	0.0000918	0.0000879
Middle Eastern	0.000111	0.000109
South Asian	0.000232	0.000229
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin ligase whose activity is dependent on E2 ubiquitin-conjugating enzyme UBE2D2. {ECO:0000269|PubMed:23402750}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.581
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.495
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim62
• Phenotype: neoplasm; respiratory system phenotype; liver/biliary system phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of epithelial to mesenchymal transition;protein ubiquitination;negative regulation of viral transcription;positive regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;regulation of viral entry into host cell;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity;interferon-gamma-mediated signaling pathway;regulation of viral release from host cell
• Cellular component: cytoplasm;cytosol
• Molecular function: ubiquitin-protein transferase activity;zinc ion binding