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GeneE
25 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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NRXN1
neurexin 1
Chromosome 2 · 2p16.3
NCBI Gene: 9378Ensembl: ENSG00000179915.25HGNC: HGNC:8008UniProt: A0A0D9SEM5
173PubMed Papers
22Diseases
0Drugs
97Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub Gene
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
vocalization behaviorprotein bindingneuromuscular process controlling balancecell surfacePitt-Hopkins-like syndrome 2autism spectrum disordergenetic disorderAbnormality of the skeletal system
✦AI Summary

NRXN1 is a presynaptic cell-adhesion protein that functions as a critical synaptic organizer in the brain 1. The gene encodes both long α-neurexin and short β-neurexin isoforms through alternative splicing, generating diverse protein variants that establish distinct neurocircuitry 23. NRXN1 regulates synaptic transmission primarily through trans-synaptic complexes with postsynaptic proteins including neuroligins, cerebellins, and GRID1, modulating glutamatergic and GABAergic neurotransmission 2. Cell-type-specific splicing patterns across interneurons, pyramidal neurons, and glia are established during development and remain stable through maturation 3. Heterozygous NRXN1 deletions cause neuropsychiatric disease through both loss-of-function and gain-of-function mechanisms: decreased synaptic activity in glutamatergic neurons contrasts with increased activity in GABAergic neurons 1. Deletions are associated with autism spectrum disorder, schizophrenia, intellectual disability, seizures, and speech/language delays, with reduced penetrance and variable expressivity complicating genetic counseling 45. Genome-wide analysis of 41,321 subjects identified NRXN1 (2p16.3) as a genome-wide significant schizophrenia susceptibility locus with CNV burden enriched for synaptic function genes 5. Precision medicine approaches require stratifying patients by loss-of-function versus gain-of-function mechanisms to tailor therapeutic restoration of NRXN1 isoform repertoires 1.

Sources cited
1
NRXN1 is a presynaptic cell-adhesion protein and synaptic organizer; heterozygous deletions cause opposing effects in glutamatergic (decreased) vs GABAergic (increased) neurons through aberrant splicing
PMID: 40205044
2
Neurexins form trans-synaptic complexes with neuroligins and cerebellins; essential for neurotransmission and synapse differentiation; mutations linked to autism and schizophrenia
PMID: 24083347
3
NRXN1 undergoes extensive cell-type-specific alternative splicing across interneurons, pyramidal neurons, and glia; isoform profiles established during development and stable through maturation
PMID: 41293024
4
Heterozygous NRXN1 deletions show diverse phenotypes including autism, ADHD, intellectual disability, seizures, schizophrenia, and speech/language delay with variable expressivity
PMID: 30031152
5
2p16.3 NRXN1 identified as genome-wide significant schizophrenia susceptibility locus; CNV burden enriched for synaptic function genes
PMID: 27869829
6
NRXN1 plays important roles in synaptic formation, organization, transmission and plasticity; genetic variations associated with schizophrenia, autism, and developmental abnormalities
PMID: 31138894
Disease Associationsⓘ22
Pitt-Hopkins-like syndrome 2Open Targets
0.74Strong
autism spectrum disorderOpen Targets
0.57Moderate
genetic disorderOpen Targets
0.51Moderate
Abnormality of the skeletal systemOpen Targets
0.50Moderate
chromosome 2p16.3 deletion syndromeOpen Targets
0.47Moderate
autismOpen Targets
0.42Moderate
Pitt-Hopkins-like syndromeOpen Targets
0.42Moderate
complex neurodevelopmental disorderOpen Targets
0.40Weak
Intellectual disabilityOpen Targets
0.39Weak
alcohol drinkingOpen Targets
0.39Weak
major depressive disorderOpen Targets
0.38Weak
mathematical abilityOpen Targets
0.35Weak
smoking initiationOpen Targets
0.34Weak
osteoarthritisOpen Targets
0.33Weak
risk-taking behaviourOpen Targets
0.33Weak
intelligenceOpen Targets
0.32Weak
hemolytic anemiaOpen Targets
0.31Weak
diabetes mellitusOpen Targets
0.31Weak
respiratory system diseaseOpen Targets
0.31Weak
adolescent idiopathic scoliosisOpen Targets
0.30Weak
Pitt-Hopkins-like syndrome 2UniProt
Schizophrenia 17UniProt
Pathogenic Variants97
NM_001330078.2(NRXN1):c.832+1G>ALikely pathogenic
Pitt-Hopkins-like syndrome 2|not provided
★★☆☆2026
NM_001330078.2(NRXN1):c.3430C>T (p.Arg1144Ter)Pathogenic
not provided|Pitt-Hopkins-like syndrome 2|Autism spectrum disorder
★★☆☆2025→ Residue 1144
NM_001330078.2(NRXN1):c.471dup (p.Leu158fs)Pathogenic
Autism spectrum disorder|Pitt-Hopkins-like syndrome 2
★★☆☆2025→ Residue 158
NM_001330078.2(NRXN1):c.2239C>T (p.Arg747Ter)Likely pathogenic
Pitt-Hopkins-like syndrome 2|not provided
★★☆☆2024→ Residue 747
NM_001330078.2(NRXN1):c.3778C>T (p.Arg1260Ter)Pathogenic
Pitt-Hopkins-like syndrome 2|Inborn genetic diseases
★★☆☆2024→ Residue 1260
NM_001330078.2(NRXN1):c.772+1128_772+1129delPathogenic
Pitt-Hopkins-like syndrome 2|not provided
★★☆☆2024
NM_001330078.2(NRXN1):c.2792del (p.Phe931fs)Pathogenic
Pitt-Hopkins-like syndrome 2|Inborn genetic diseases|not provided
★★☆☆2023→ Residue 931
NM_001330078.2(NRXN1):c.2563C>T (p.Arg855Ter)Pathogenic
Pitt-Hopkins-like syndrome 2|not provided
★★☆☆2023→ Residue 855
NM_001330078.2(NRXN1):c.3757C>T (p.Arg1253Ter)Pathogenic
not provided|Pitt-Hopkins-like syndrome 2
★★☆☆2022→ Residue 1253
NM_001330078.2(NRXN1):c.772+1102delPathogenic
not provided|Pitt-Hopkins-like syndrome 2
★★☆☆2022
GRCh38/hg38 2p16.3(chr2:50727462-51004961)x1Pathogenic
not provided
★☆☆☆2025
NM_001330078.2(NRXN1):c.1327dup (p.Tyr443fs)Likely pathogenic
Complex neurodevelopmental disorder
★☆☆☆2025→ Residue 443
NM_001330078.2(NRXN1):c.3417G>A (p.Trp1139Ter)Pathogenic
Pitt-Hopkins-like syndrome 2
★☆☆☆2025→ Residue 1139
NM_001330078.2(NRXN1):c.1607_1608dup (p.Lys537Ter)Pathogenic
Inborn genetic diseases
★☆☆☆2025→ Residue 537
NM_001330078.2(NRXN1):c.151G>T (p.Glu51Ter)Pathogenic
Pitt-Hopkins-like syndrome 2
★☆☆☆2025→ Residue 51
NM_001330078.2(NRXN1):c.1990del (p.Ser664fs)Pathogenic
Pitt-Hopkins-like syndrome 2
★☆☆☆2025→ Residue 664
NM_001330078.2(NRXN1):c.2094T>G (p.Tyr698Ter)Pathogenic
Pitt-Hopkins-like syndrome 2
★☆☆☆2025→ Residue 698
NM_001330078.2(NRXN1):c.3244+1G>TLikely pathogenic
Pitt-Hopkins-like syndrome 2
★☆☆☆2025
NM_001330078.2(NRXN1):c.4164T>A (p.Cys1388Ter)Likely pathogenic
not provided
★☆☆☆2025→ Residue 1388
NM_001330078.2(NRXN1):c.2427G>A (p.Trp809Ter)Pathogenic
Inborn genetic diseases
★☆☆☆2025→ Residue 809
View on ClinVar ↗
Related Genes
CBLN1Protein interaction99%GRID2Protein interaction99%ACHEProtein interaction92%DLG2Protein interaction92%DLG3Protein interaction92%GLUD1Protein interaction92%
Tissue Expression6 tissues
Brain
100%
Heart
18%
Bone Marrow
13%
Ovary
1%
Liver
0%
Lung
0%
Gene Interaction Network
Click a node to explore
NRXN1CBLN1GRID2ACHEDLG2DLG3GLUD1
PROTEIN STRUCTURE
Preparing viewer…
PDB6NID · 1.86 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.32Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.23 [0.17–0.32]
RankingsWhere NRXN1 stands among ~20K protein-coding genes
  • #2,550of 20,598
    Most Researched173 · top quartile
  • #799of 5,498
    Most Pathogenic Variants97 · top quartile
  • #1,264of 17,882
    Most Constrained (LOEUF)0.32 · top 10%
Genes detectedNRXN1
Sources retrieved25 papers
Response time—
📄 Sources
25▼
1
Autism spectrum disorder: neuropathology and animal models.
PMID: 28584888
Acta Neuropathol · 2017
1.00
2
Risk factors, diagnosis, prognosis and treatment of autism.
PMID: 32472753
Front Biosci (Landmark Ed) · 2020
0.90
3
NRXN1 deletion syndrome; phenotypic and penetrance data from 34 families.
PMID: 30031152
Eur J Med Genet · 2019
0.80
4
Phenotypic complexities of rare heterozygous neurexin-1 deletions.
PMID: 40205044
Nature · 2025
0.70
5
Neurexins and neuropsychiatric disorders.
PMID: 29221905
Neurosci Res · 2018
0.64