NRXN2
neurexin 2, the group of Neurexins
Basic information
Region (hg38): 11:64606174-64723197
Links
Phenotypes
GenCC
Source:
- autism (Strong), mode of inheritance: AD
- autism (Limited), mode of inheritance: AD
- neurodevelopmental disorder (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (225 variants)
- not_provided (60 variants)
- NRXN2-related_disorder (24 variants)
- Intellectual_disability (6 variants)
- NRXN2-associated_Neurodevelopmental_disorder (1 variants)
- Epilepsy (1 variants)
- Autism_spectrum_disorder (1 variants)
- Schizophrenia (1 variants)
- NRXN2-related_autism_spectrum_disorder (1 variants)
- See_cases (1 variants)
- Severe_intellectual_deficiency (1 variants)
- NRXN2-related_Austism_Spectrum_Disorder (1 variants)
- Developmental_and_epileptic_encephalopathy,_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRXN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015080.4. 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 | 25 | 38 | ||||
| missense | 216 | 19 | 236 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 226 | 44 | 9 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NRXN2 | protein_coding | protein_coding | ENST00000265459 | 22 | 117015 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000660 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.02 | 646 | 1.00e+3 | 0.643 | 0.0000694 | 10943 |
| Missense in Polyphen | 140 | 263.82 | 0.53067 | 2569 | ||
| Synonymous | 0.233 | 444 | 450 | 0.986 | 0.0000335 | 3652 |
| Loss of Function | 6.16 | 9 | 60.8 | 0.148 | 0.00000358 | 649 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000658 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.204
- rvis_EVS
- -2.16
- rvis_percentile_EVS
- 1.43
Haploinsufficiency Scores
- pHI
- 0.242
- hipred
- Y
- hipred_score
- 0.651
- ghis
- 0.603
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.861
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nrxn2
- Phenotype
- growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory 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); normal phenotype; 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);
Zebrafish Information Network
- Gene name
- nrxn2a
- Affected structure
- CaP motoneuron
- Phenotype tag
- abnormal
- Phenotype quality
- truncated
Gene ontology
- Biological process
- neuron cell-cell adhesion;signal transduction;chemical synaptic transmission;neurotransmitter secretion;synapse assembly;adult behavior;social behavior;vocal learning;vocalization behavior;postsynaptic membrane assembly;gephyrin clustering involved in postsynaptic density assembly;neuroligin clustering involved in postsynaptic membrane assembly;postsynaptic density protein 95 clustering
- Cellular component
- plasma membrane;integral component of membrane;presynapse
- Molecular function
- transmembrane signaling receptor activity;calcium channel regulator activity;metal ion binding;cell adhesion molecule binding;neuroligin family protein binding