LINGO2

protein-coding

leucine rich repeat and Ig domain containing 2, the group of I-set domain containing|MicroRNA protein coding host genes

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 glutamatergic synapse and synaptic membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LRRN6C

MANE transcript

NM_001258282.3

Inheritance

—

ClinVar variants

U:75B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr9:27,937,617-29,213,601

External References & Databases

Ensembl (ENSG00000174482)

Transcript & Mutation Effects

hg38 • Region Span ~1,276.0 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 LINGO2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001258282.3. 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			2 clinvar	3 clinvar		5
missense			73 clinvar	1 clinvar	1 clinvar	75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	4	1	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001258282.3	RefSeq	NP_001245211.1	1	MANE Select
ENST00000698399.1	Ensembl	ENSP00000513694.1	1	MANE Select
NM_001354574.2	RefSeq	NP_001341503.1	1	Standard
NM_001354575.2	RefSeq	NP_001341504.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
lingo2a	Danio rerio	Structure: olfactory bulb glomerulus Quality: aplastic/hypoplastic abnormal

Gene / Model

Organism

Observed Phenotype

lingo2a

Danio rerio

Structure: olfactory bulb glomerulus

Quality: aplastic/hypoplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of synapse assembly

Cellular Component

extracellular space
integral component of membrane
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379992
Coding exons: 1
Length: 722208
Individuals with no LoFs: 125667
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125677
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.674	311	346	0.898	0.0000190	3990
Missense (PolyPhen)		93	133.45	0.69688		1592
Synonymous	-2.12	166	135	1.23	0.00000705	1250
Loss of Function	3.13	2	15.2	0.132	9.78e-7	174

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000057	0.000053	rare
South Asian	0	0.0	absent
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.0589
RVIS EVS: -0.75
RVIS percentile EVS: 13.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.154

Gene Damage Prediction

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