TRIM58

protein-coding

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

Gene summary

Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response and regulation of gene expression. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015431.4

Inheritance

—

ClinVar variants

U:72B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr1:247,857,187-247,880,138

External References & Databases

Ensembl (ENSG00000162722)

Transcript & Mutation Effects

hg38 • Region Span ~23.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRIM58 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 69

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015431.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			70 clinvar	2 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	2	0	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015431.4	RefSeq	NP_056246.3	6	MANE Select
ENST00000366481.4	Ensembl	ENSP00000355437.3	6	MANE Select
ENST00001144783.1	Ensembl	ENSP00000809070.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein polyubiquitination
ubiquitin-dependent protein catabolic process
biological_process
protein autoubiquitination
positive regulation of erythrocyte enucleation

Molecular Function

molecular_function
zinc ion binding
dynein heavy chain binding
dynein intermediate chain binding
ubiquitin protein ligase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366481
Coding exons: 6
Length: 21007
Individuals with no LoFs: 125689
Homozygous LoFs: 0
Heterozygous LoFs: 59
Defined: 125748
p: 0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.418	219	237	0.924	0.0000132	3075
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0012	notable
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00044	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0900

Gene Damage Prediction

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