TRIM58

tripartite motif containing 58, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 1:247857187-247880138

Links

ENSG00000162722 ∙ NCBI:25893 ∙ ∙ HGNC:24150 ∙ Uniprot:Q8NG06 ∙ 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 TRIM58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM58 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			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	0

Variants in TRIM58

This is a list of pathogenic ClinVar variants found in the TRIM58 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-247857253-T-C		not specified	Uncertain significance (Jun 18, 2021)
1-247857256-G-A		not specified	Uncertain significance (Aug 10, 2023)
1-247857265-G-C		not specified	Uncertain significance (May 24, 2023)
1-247857271-C-T		not specified	Uncertain significance (Nov 30, 2021)
1-247857349-T-A		not specified	Uncertain significance (Dec 31, 2024)
1-247857427-C-G		not specified	Uncertain significance (Nov 13, 2024)
1-247857461-A-G		not specified	Uncertain significance (Dec 27, 2023)
1-247857523-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-247857539-G-C		not specified	Uncertain significance (Dec 02, 2024)
1-247857543-C-G		not specified	Uncertain significance (Jun 03, 2024)
1-247857547-G-C		not specified	Uncertain significance (Jul 31, 2024)
1-247857559-C-G		not specified	Uncertain significance (Jan 04, 2025)
1-247857587-T-C		not specified	Uncertain significance (Jun 22, 2023)
1-247857644-A-T		not specified	Uncertain significance (Oct 19, 2024)
1-247860621-A-G		not specified	Uncertain significance (Feb 01, 2025)
1-247860629-A-T		not specified	Uncertain significance (Feb 07, 2025)
1-247860639-A-T		not specified	Uncertain significance (Feb 01, 2023)
1-247860684-A-G		not specified	Likely benign (Aug 08, 2022)
1-247860686-G-A		not specified	Uncertain significance (Apr 09, 2024)
1-247864714-G-A		not specified	Uncertain significance (Jan 23, 2025)
1-247864729-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-247864757-G-A		not specified	Uncertain significance (Oct 28, 2024)
1-247864757-G-T		not specified	Uncertain significance (Nov 26, 2024)
1-247864781-A-G		not specified	Uncertain significance (Nov 08, 2024)
1-247864805-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM58	protein_coding	protein_coding	ENST00000366481	6	21007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-10	0.0549	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.418	219	237	0.924	0.0000132	3075
Missense in Polyphen		65	63.018	1.0314		835
Synonymous	-0.755	109	99.4	1.10	0.00000549	986
Loss of Function	-0.0782	15	14.7	1.02	7.95e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00174	0.00141
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000180	0.000176
Middle Eastern	0.000599	0.000435
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin ligase induced during late erythropoiesis. Directly binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. May participate in the erythroblast enucleation process through regulation of nuclear polarization. {ECO:0000269|PubMed:25241935}.

Recessive Scores

• pRec: 0.0997

Intolerance Scores

• loftool: 0.833
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.17

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.208
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim58

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;biological_process;protein autoubiquitination;positive regulation of erythrocyte enucleation;regulation of nuclear migration along microtubule
• Molecular function: molecular_function;zinc ion binding;dynein heavy chain binding;dynein intermediate chain binding;ubiquitin protein ligase activity