LRRN3

protein-coding

leucine rich repeat neuronal 3, the group of Fibronectin type III domain containing|I-set domain containing

Gene summary

Predicted to enable signaling receptor activity. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001099658.2

Inheritance

—

ClinVar variants

U:88B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr7:111,091,006-111,125,454

External References & Databases

Ensembl (ENSG00000173114)

Transcript & Mutation Effects

hg38 • Region Span ~34.4 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 LRRN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099658.2. 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			1 clinvar		3 clinvar	4
missense			87 clinvar	1 clinvar	1 clinvar	89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	88	1	4	93

Loading ClinVar variants...

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_001099658.2	RefSeq	NP_001093128.1	1	MANE Select
ENST00000308478.10	Ensembl	ENSP00000312001.5	1	MANE Select
NM_001099660.2	RefSeq	NP_001093130.1	1	Standard
NM_018334.5	RefSeq	NP_060804.3	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of synapse assembly

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000451085
Coding exons: 1
Length: 34449
Individuals with no LoFs: 125671
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125694
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	311	367	0.847	0.0000175	4676
Missense (PolyPhen)		98	145.66	0.67282		1910
Synonymous	0.533	126	134	0.941	0.00000650	1404
Loss of Function	2.75	6	18.9	0.317	0.00000118	236

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.468
RVIS EVS: -0.33
RVIS percentile EVS: 30.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.623

Gene Damage Prediction

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