LRRN4

protein-coding

leucine rich repeat neuronal 4, the group of Fibronectin type III domain containing

Gene summary

Predicted to be involved in long-term memory. Predicted to act upstream of or within visual learning. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf75

MANE transcript

NM_152611.5

Inheritance

—

ClinVar variants

U:126B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr20:6,040,546-6,054,060

External References & Databases

Ensembl (ENSG00000125872)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 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 LRRN4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 130

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152611.5. 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			1 clinvar	3 clinvar		4
missense			123 clinvar	8 clinvar		131
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	126	11	0	137

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152611.5	RefSeq	NP_689824.2	4	MANE Select
ENST00000378858.5	Ensembl	ENSP00000368135.4	4	MANE Select
ENST00000698795.1	Ensembl	ENSP00000513938.1	4	Standard
ENST00000698795.2	Ensembl	ENSP00000513938.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

long-term memory
visual learning

Cellular Component

integral component of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378858
Coding exons: 4
Length: 13272
Individuals with no LoFs: 125581
Homozygous LoFs: 0
Heterozygous LoFs: 167
Defined: 125748
p: 0.000664

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.989	375	433	0.866	0.0000265	4579
Missense (PolyPhen)		82	106.24	0.77181		1287
Synonymous	1.10	202	223	0.906	0.0000156	1664
Loss of Function	0.504	15	17.3	0.869	8.29e-7	172

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00057	0.00049	rare
Latino/Admixed American	0.00077	0.00075	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0050	0.0044	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00030	0.00028	rare
South Asian	0.00056	0.00052	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play an important role in hippocampus-dependent long-lasting memory. {ECO:0000250}.;

Recessive Scores

pRec: 0.0964

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.433

Gene Damage Prediction

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