NLGN3 Gene: Neuroligin 3 - Function, Mutations, and Associated Disorders
Comprehensive biomedical overview of NLGN3, including gene structure, expression, mutations, and clinical significance.
Gene Information Card
| Symbol | NLGN3 |
|---|---|
| Full Name | Neuroligin 3 |
| Gene Type | Protein coding |
| Chromosomal Location | Xq13.1 |
| NCBI Gene ID | 6458 ncbi.nlm.nih.gov/gene/6458 |
| Ensembl ID | ENSG00000196338 |
| UniProt ID | Q9NZ94 |
| OMIM ID | 300336 |
| HGNC ID | 14287 |
| Aliases | HNL3, neuroligin 3 |
Description
NLGN3 encodes neuroligin 3, a postsynaptic cell-adhesion molecule involved in synapse formation and function. It interacts with neurexins to mediate synaptic transmission and is implicated in neurodevelopmental disorders, particularly autism spectrum disorder (ASD).
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Autism spectrum disorder (ASD) | Missense mutations (e.g., R451C) alter synaptic function and may affect neuroligin-neurexin interactions. | ClinVar, OMIM, multiple studies |
| Intellectual disability | Rare variants and chromosomal rearrangements involving NLGN3 have been reported in patients with intellectual disability. | OMIM, ClinVar |
| Asperger syndrome | Some studies associate NLGN3 mutations with Asperger syndrome, though evidence is limited. | OMIM, literature |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | High | High expression in cerebral cortex, hippocampus, and cerebellum |
| Testis | Low | Low expression |
| Other tissues | Very low | Minimal expression outside nervous system |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y (neuroblastoma) | High | Neuronal-like cells show high NLGN3 expression |
| SK-N-SH (neuroblastoma) | Moderate | Moderate expression |
| HeLa (cervical carcinoma) | Low | Low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| R451C | Missense | Rare | Alters synaptic function; associated with autism in some families |
| R473C | Missense | Rare | Reported in autism; affects protein folding and trafficking |
| c.2134C>T (p.R712C) | Missense | Rare | Potential pathogenic variant; functional impact unclear |
Mutation functional classification
Loss of Function (LOF)
Some variants may reduce protein stability or synaptic localization, leading to loss of function.
Gain of Function (GOF)
R451C has been suggested to cause gain-of-function effects in certain synaptic assays.
Dominant Negative (DN)
Potential dominant-negative effects due to altered protein interactions.
View complete mutation data：
Gene Ontology (GO)
| • synaptic cell adhesion | • protein binding |
| • cell adhesion molecule binding | • neurexin binding |
| • synapse organization | • chemical synaptic transmission |
Pathways
• Neurexin-neuroligin signaling
• Synaptic adhesion and organization
• Postsynaptic density assembly
Protein Summary
Neuroligin 3 is a type I membrane protein localized to the postsynaptic membrane. It binds to presynaptic neurexins, promoting synapse formation and maturation. It is involved in both excitatory and inhibitory synaptic transmission. Mutations in NLGN3 are rare but can contribute to autism and intellectual disability.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| NLGN3 Knockout HEK293 Cell Line | EDJ-KQ3891 | Human | 54413 | Details Get a Quote |
| NLGN3 Knockout HeLa Cell Line | EDJ-KQ56411 | Human | 54413 | Details Get a Quote |
| NLGN3 Knockout A-549 Cell Line | EDJ-KQ64906 | Human | 54413 | Details Get a Quote |
| NLGN3 Knockout HCT 116 Cell Line | EDJ-KQ73349 | Human | 54413 | Details Get a Quote |
