LRRC41

protein-coding

leucine rich repeat containing 41

Gene summary

Predicted to enable identical protein binding activity. Predicted to be involved in protein ubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006369.5

Inheritance

—

ClinVar variants

U:122B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr1:46,261,196-46,303,616

External References & Databases

Ensembl (ENSG00000132128)

Transcript & Mutation Effects

hg38 • Region Span ~42.4 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 LRRC41 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006369.5. 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			3 clinvar			3
missense			111 clinvar	3 clinvar		114
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	122	3	0	125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006369.5	RefSeq	NP_006360.3	10	MANE Select
ENST00000617190.5	Ensembl	ENSP00000477792.1	10	MANE Select
ENST00000343304.10	Ensembl	ENSP00000343298.6	10	Standard
ENST00000343304.11	Ensembl	ENSP00000343298.6	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
Immune System
Adaptive Immune System
Antigen processing: Ubiquitination & Proteasome degradation

Biological Process

protein ubiquitination
post-translational protein modification

Molecular Function

protein homodimerization activity

Cellular Component

nucleus
cytoplasm
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000343304
Coding exons: 10
Length: 42413
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.08	300	492	0.609	0.0000305	5137
Missense (PolyPhen)		22	59.816	0.3678		660
Synonymous	0.867	173	188	0.920	0.00000934	1827
Loss of Function	5.09	2	34.1	0.0587	0.00000213	336

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000067	0.000058	rare
Ashkenazi Jewish	0.00034	0.00030	rare
East Asian	0.000058	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000089	0.000070	rare
South Asian	0.000072	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable substrate recognition component of an ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000269|PubMed:15601820}.;

Intolerance Scores

LoFtool: 0.213
RVIS EVS: -0.44
RVIS percentile EVS: 24.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.973

Gene Damage Prediction

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