TRIM59

tripartite motif containing 59, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 3:160432445-160485773

Previous symbols: [ "TRIM57" ]

Links

ENSG00000213186 ∙ NCBI:286827 ∙ OMIM:616148 ∙ HGNC:30834 ∙ Uniprot:Q8IWR1 ∙ 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 TRIM59 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM59 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			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	3	0

Variants in TRIM59

This is a list of pathogenic ClinVar variants found in the TRIM59 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-160433064-A-G		not specified	Uncertain significance (Sep 06, 2022)
3-160433150-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-160433156-A-C		not specified	Uncertain significance (Apr 09, 2024)
3-160433163-C-T		not specified	Uncertain significance (Nov 23, 2024)
3-160433205-T-C		not specified	Uncertain significance (Jul 22, 2024)
3-160433697-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-160433791-A-T			Uncertain significance (-)
3-160437976-T-C		not specified	Likely benign (Nov 09, 2023)
3-160437995-C-T		not specified	Likely benign (Jun 06, 2023)
3-160438009-A-G		not specified	Uncertain significance (Aug 02, 2021)
3-160438013-A-T		not specified	Uncertain significance (Oct 27, 2023)
3-160438027-A-G		not specified	Uncertain significance (Jan 05, 2022)
3-160438054-T-C		not specified	Uncertain significance (Jul 06, 2021)
3-160438060-A-G		not specified	Uncertain significance (May 02, 2024)
3-160438087-T-C		not specified	Uncertain significance (Oct 01, 2024)
3-160438100-T-C		not specified	Likely benign (Jul 26, 2023)
3-160438127-T-C		not specified	Uncertain significance (Mar 28, 2024)
3-160438169-A-G		not specified	Uncertain significance (Mar 29, 2023)
3-160438177-G-A		not specified	Uncertain significance (Feb 11, 2022)
3-160438201-T-C		not specified	Uncertain significance (Mar 14, 2023)
3-160438254-T-A		not specified	Uncertain significance (Mar 17, 2023)
3-160438258-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-160438343-C-G		not specified	Uncertain significance (Oct 12, 2024)
3-160438355-T-C		not specified	Uncertain significance (Jul 20, 2021)
3-160438404-A-T		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM59	protein_coding	protein_coding	ENST00000309784	1	53329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00146	0.969	125049	6	664	125719	0.00267

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.504	182	202	0.900	0.00000945	2675
Missense in Polyphen		53	55.619	0.95292		729
Synonymous	0.403	66	70.3	0.939	0.00000344	732
Loss of Function	1.92	7	15.0	0.466	8.99e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00645	0.00639
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00333	0.00332
Finnish	0.00111	0.00111
European (Non-Finnish)	0.00247	0.00244
Middle Eastern	0.00333	0.00332
South Asian	0.00448	0.00422
Other	0.00199	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May serve as a multifunctional regulator for innate immune signaling pathways. {ECO:0000250|UniProtKB:Q922Y2}.
• Pathway: Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.0870

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.395
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.369

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim59

Gene ontology

• Biological process: protein ubiquitination;negative regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;negative regulation of viral entry into host cell
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;centrosome;cilium;integral component of membrane;intraciliary transport particle B
• Molecular function: protein binding;zinc ion binding;ubiquitin protein ligase activity