NLGN2
neuroligin 2, the group of Neuroligins
Basic information
Region (hg38): 17:7404874-7419860
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (143 variants)
- not_specified (70 variants)
- NLGN2-related_disorder (7 variants)
- Autism (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLGN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020795.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 48 | 55 | ||||
| missense | 125 | 129 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 133 | 51 | 8 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NLGN2 | protein_coding | protein_coding | ENST00000302926 | 7 | 14987 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000259 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.47 | 225 | 508 | 0.442 | 0.0000367 | 5271 |
| Missense in Polyphen | 83 | 300.88 | 0.27585 | 3091 | ||
| Synonymous | 0.278 | 234 | 239 | 0.977 | 0.0000194 | 1807 |
| Loss of Function | 4.50 | 0 | 23.6 | 0.00 | 0.00000102 | 277 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transmembrane scaffolding protein involved in cell-cell interactions via its interactions with neurexin family members. Mediates cell-cell interactions both in neurons and in other types of cells, such as Langerhans beta cells. Plays a role in synapse function and synaptic signal transmission, especially via gamma- aminobutyric acid receptors (GABA(A) receptors). Functions by recruiting and clustering synaptic proteins. Promotes clustering of postsynaptic GABRG2 and GPHN. Modulates signaling by inhibitory synapses, and thereby plays a role in controlling the ratio of signaling by excitatory and inhibitory synapses and information processing. Required for normal signal amplitude from inhibitory synapses, but is not essential for normal signal frequency. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. Mediates cell-cell interactions between Langerhans beta cells and modulates insulin secretion (By similarity). {ECO:0000250}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 7.94
Haploinsufficiency Scores
- pHI
- 0.310
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.767
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nlgn2
- Phenotype
- growth/size/body region phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- regulation of respiratory gaseous exchange by neurological system process;neuron cell-cell adhesion;synapse assembly;sensory perception of pain;positive regulation of insulin secretion;positive regulation of synaptic transmission, GABAergic;protein localization to synapse;locomotory exploration behavior;cell-cell junction maintenance;synaptic vesicle endocytosis;modulation of chemical synaptic transmission;synapse organization;neuromuscular process controlling balance;positive regulation of synapse assembly;positive regulation of synaptic transmission, glutamatergic;terminal button organization;postsynaptic membrane assembly;presynaptic membrane assembly;gephyrin clustering involved in postsynaptic density assembly;postsynaptic density protein 95 clustering;positive regulation of inhibitory postsynaptic potential;cell-cell adhesion;presynapse assembly;positive regulation of protein localization to synapse;inhibitory synapse assembly;regulation of AMPA receptor activity;positive regulation of excitatory postsynaptic potential;positive regulation of synaptic vesicle clustering
- Cellular component
- plasma membrane;integral component of plasma membrane;cell surface;membrane;cell junction;presynaptic membrane;synapse;postsynaptic membrane;inhibitory synapse;spanning component of membrane;glycinergic synapse;dopaminergic synapse;symmetric, GABA-ergic, inhibitory synapse;integral component of postsynaptic membrane;integral component of postsynaptic specialization membrane
- Molecular function
- signaling receptor activity;neurexin family protein binding;identical protein binding;cell adhesion molecule binding