LRFN2
protein-codingleucine rich repeat and fibronectin type III domain containing 2, the group of Ig-like cell adhesion molecule family|Fibronectin type III domain containing|I-set domain containing
Gene summary
Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- KIAA1246
- SALM1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~195.8 kbGenCC 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 LRFN2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020737.3. 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 | 1 | 3 | 1 | 5 | ||
| missense | 108 | 1 | 109 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 110 | 4 | 1 | 115 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065788.1 | 2 | MANE Select | |
| Ensembl | ENSP00000345985.6 | 2 | MANE Select | |
| Ensembl | ENSP00000514953.1 | 2 | Standard | |
| Ensembl | ENSP00000776515.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neuronal System
- Synaptic adhesion-like molecules
- Protein-protein interactions at synapses
Biological Process
- modulation of chemical synaptic transmission
- regulation of postsynapse organization
Cellular Component
- plasma membrane
- cell surface
- integral component of membrane
- cell junction
- postsynaptic membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000338305
- Coding exons
- 2
- Length
- 195880
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125747
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.60 | 406 | 508 | 0.800 | 0.0000336 | 5064 |
| Missense (PolyPhen) | 107 | 194.72 | 0.54951 | 2082 | ||
| Synonymous | -1.02 | 252 | 232 | 1.09 | 0.0000162 | 1755 |
| Loss of Function | 2.41 | 6 | 16.6 | 0.362 | 8.61e-7 | 181 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000059 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000064 | 0.000062 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.299
- RVIS EVS
- -1.24
- RVIS percentile EVS
- 5.46
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.230
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |