LRRC52

protein-coding

leucine rich repeat containing 52

Gene summary

Enables potassium channel activator activity; transmembrane transporter binding activity; and voltage-gated potassium channel activity. Involved in positive regulation of voltage-gated potassium channel activity and potassium ion transmembrane transport. Part of voltage-gated potassium channel complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001005214.4

Inheritance

—

ClinVar variants

U:42B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr1:165,544,000-165,563,957

External References & Databases

Ensembl (ENSG00000162763)

Transcript & Mutation Effects

hg38 • Region Span ~20.0 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 LRRC52 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001005214.4. 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					1 clinvar	1
missense			42 clinvar	2 clinvar	1 clinvar	45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	2	2	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001005214.4	RefSeq	NP_001005214.2	2	MANE Select
ENST00000294818.2	Ensembl	ENSP00000294818.2	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

reproductive process
potassium ion transmembrane transport
positive regulation of voltage-gated potassium channel activity

Molecular Function

voltage-gated potassium channel activity
ion channel binding
potassium channel activator activity

Cellular Component

integral component of plasma membrane
voltage-gated potassium channel complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000294818
Coding exons: 2
Length: 19955
Individuals with no LoFs: 125680
Homozygous LoFs: 0
Heterozygous LoFs: 68
Defined: 125748
p: 0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0365	173	174	0.992	0.0000101	2034
Missense (PolyPhen)		42	48.77	0.86119		647
Synonymous	-1.27	93	78.6	1.18	0.00000488	654
Loss of Function	0.126	8	8.39	0.953	5.15e-7	94

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00051	0.00051	rare
European (Non-Finnish)	0.00033	0.00032	rare
South Asian	0.000065	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Auxiliary protein of the large-conductance, voltage and calcium-activated potassium channel (BK alpha). Modulates gating properties by producing a marked shift in the BK channel's voltage dependence of activation in the hyperpolarizing direction, and in the absence of calcium. KCNU1 channel auxiliary protein. May modulate KCNU1 gating properties. {ECO:0000269|PubMed:22547800, ECO:0000269|PubMed:23129643}.;

Intolerance Scores

LoFtool: 0.585
RVIS EVS: -0.09
RVIS percentile EVS: 46.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.228

Gene Damage Prediction

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