LRRC53

protein-coding

leucine rich repeat containing 53

Gene summary

Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001382280.1

Inheritance

—

ClinVar variants

U:3B:7

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr1:74,469,376-74,512,611

External References & Databases

Ensembl (ENSG00000162621)

NCBI Gene (105378803)

Transcript & Mutation Effects

hg38 • Region Span ~43.2 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 LRRC53 variants in ClinVar

7 Conditions Cataloged

not providedTotal: 131

not specifiedTotal: 18

Inborn genetic diseasesTotal: 14

Atrial conduction diseaseTotal: 13

Cardiovascular phenotypeTotal: 2

TNNI3K-related disorderTotal: 2

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001382280.1. 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 clinvar	2
missense			1 clinvar	5 clinvar		6
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	3	6	1	10

Highest pathogenic variant AF is 0.0000068472327

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001382280.1	RefSeq	NP_001369209.1	4	MANE Select
ENST00000294635.5	Ensembl	ENSP00000294635.4	4	MANE Select
NM_001364666.2	RefSeq	NP_001351595.1	3	Standard
XM_011542512.4	RefSeq	XP_011540814.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000294635
Coding exons: 4
Length: 42737
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.893	231	273	0.848	0.0000139	8182
Missense (PolyPhen)		42	58.772	0.71463		1243
Synonymous	1.72	92	115	0.797	0.00000632	2373
Loss of Function	0.333	16	17.5	0.914	0.00000101	509

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0293

Gene Damage Prediction

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