LRRC58

protein-coding

leucine rich repeat containing 58

Gene summary

Enables ubiquitin-like ligase-substrate adaptor activity. Involved in proteasome-mediated ubiquitin-dependent protein catabolic process and regulation of taurine biosynthetic process. Part of Cul5-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001099678.2

Inheritance

—

ClinVar variants

U:56B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr3:120,324,509-120,349,354

External References & Databases

Ensembl (ENSG00000163428)

Transcript & Mutation Effects

hg38 • Region Span ~24.8 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 LRRC58 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099678.2. 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						0
missense			55 clinvar	4 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	56	4	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099678.2	RefSeq	NP_001093148.1	4	MANE Select
ENST00000295628.4	Ensembl	ENSP00000295628.3	4	MANE Select
ENST00000886041.1	Ensembl	ENSP00000556100.1	3	Standard
ENST00000886041.2	Ensembl	ENSP00000556100.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295628
Coding exons: 4
Length: 24831
Individuals with no LoFs: 124624
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124638
p: 0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	119	175	0.681	0.00000871	2302
Missense (PolyPhen)		44	70.1	0.62767		854
Synonymous	1.23	58	71.2	0.814	0.00000323	794
Loss of Function	1.82	6	13.1	0.457	7.80e-7	171

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000078	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000058	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000073	0.000062	rare
South Asian	0.00013	0.00013	rare
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.111

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.581

Gene Damage Prediction

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