Affinage

NRXN3

Neurexin-3-beta · UniProt Q9HDB5

Length
637 aa
Mass
69.3 kDa
Annotated
2026-06-10
26 papers in source corpus 12 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NRXN3 encodes neurexin-3, a presynaptic cell adhesion molecule that organizes and matures synaptic connections across multiple neural circuits (PMID:38358390, PMID:39254120, PMID:38410471). At hippocampal mossy fiber–CA3 synapses, a specific splice variant, Nrxn3(25b+), directly binds C1ql2 to regulate synaptic vesicle recruitment and long-term potentiation, acting downstream of a Bcl11b/C1ql2 transcriptional pathway (PMID:38358390). Acting as a transsynaptic adhesion molecule, Nrxn3 is required for ribbon-synapse maturation in hair cells, where loss causes synapses to fail to pair over time and reduces pre- and postsynaptic responses in mouse and zebrafish (PMID:39254120, PMID:38410471). Neurexin-3 also forms a complex with its ligand neuroligin-1 in the hippocampus linked to synaptic plasticity (PMID:40286836), and its expression in the central amygdala attenuates nociceptive orofacial pain by limiting neuronal activity in the pain pathway (PMID:41466820). Loss-of-function variants in NRXN3 cause an autosomal recessive neurodevelopmental syndrome with developmental delay, movement disorder, and behavioral problems, consistent with Nrxn3α/β knockout mice (PMID:36898513). NRXN3 transcription is repressed by FoxQ1 and positively regulated by ZNF582, linking its expression to tumor proliferation, migration, and metastasis (PMID:23383267, PMID:33038291); a distinct non-neuronal role has it competitively block RSK1-mediated phosphorylation of caspase-3 to promote caspase-3/GSDME pyroptosis in cholangiocarcinoma (PMID:40324630). Beyond these contexts, the molecular determinants of its broad non-neuronal expression remain uncharacterized in the available corpus.

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2002 Medium

    Established that NRXN3 expression is not restricted to neurons and that tissue-specific splice variants exist, raising the question of non-synaptic adhesion roles.

    Evidence RT-PCR tissue panel and characterization of heart-specific splicing variants

    PMID:12379233

    Open questions at the time
    • Dystroglycan/ECM complex participation inferred, not shown by co-IP or pulldown
    • Functional role of cardiac isoforms not tested
  2. 2013 Medium

    Identified NRXN3 as a transcriptional target whose repression has cellular consequences, showing FoxQ1 directly binds and silences the NRXN3 promoter to promote glioma proliferation and migration.

    Evidence ChIP and luciferase reporter assays with knockdown/overexpression and proliferation/migration readouts in glioma cells

    PMID:23383267

    Open questions at the time
    • Does not establish which NRXN3 protein function mediates the tumor phenotype
    • Single lab
  3. 2020 Medium

    Extended NRXN3 transcriptional control by showing ZNF582 directly activates NRXN3, and that restoring NRXN3 reverses pro-metastatic effects, linking NRXN3 expression to metastasis suppression.

    Evidence ChIP-seq/ChIP-qPCR, luciferase, bisulfite pyrosequencing, migration/invasion and in vivo metastasis rescue in nasopharyngeal carcinoma

    PMID:33038291

    Open questions at the time
    • Mechanism by which NRXN3 suppresses metastasis not resolved
    • Single lab
  4. 2023 Medium

    Connected NRXN3 to human disease, demonstrating that biallelic loss-of-function variants cause an autosomal recessive neurodevelopmental syndrome consistent with knockout mice.

    Evidence Whole exome sequencing, CRISPR-edited cell functional studies, and phenotype comparison to Nrxn3α/β KO mice

    PMID:36898513

    Open questions at the time
    • Molecular consequence of variants on synaptic function not directly assayed
    • Limited functional mechanistic detail
  5. 2024 High

    Defined a precise splice-variant-specific molecular interaction, showing Nrxn3(25b+) directly binds C1ql2 to control synaptic vesicle recruitment and LTP downstream of the Bcl11b/C1ql2 pathway.

    Evidence Conditional mouse KO, LTP electrophysiology, non-binding C1ql2 mutant recapitulation, and epistasis analysis at mossy fiber–CA3 synapses

    PMID:38358390

    Open questions at the time
    • Structural basis of the C1ql2-Nrxn3(25b+) interaction not resolved
    • Generalizability to other circuits unknown
  6. 2024 High

    Established a transsynaptic role in synapse maturation, showing Nrxn3 is required for hair-cell ribbon-synapse pairing across two vertebrate models.

    Evidence Mouse and zebrafish KO with confocal imaging, electrophysiology, and behavioral assays

    PMID:38410471 PMID:39254120

    Open questions at the time
    • Identity of the postsynaptic partner mediating pairing not defined
    • Splice-variant dependence in hair cells not resolved
  7. 2025 Medium

    Revealed an unexpected non-neuronal, non-adhesion function, showing NRXN3 competitively blocks RSK1-caspase-3 binding to stabilize caspase-3 and promote GSDME-dependent pyroptosis.

    Evidence Genome-scale CRISPR screen, IP-MS, and in vitro/in vivo functional experiments in intrahepatic cholangiocarcinoma

    PMID:40324630

    Open questions at the time
    • Which NRXN3 isoform mediates this cytoplasmic interaction unknown
    • Reconciliation with extracellular adhesion role not addressed
    • Single lab
  8. 2025 Medium

    Linked NRXN3 to behavioral plasticity, indicating Nrxn3 in the central amygdala attenuates nociceptive orofacial pain and that a hippocampal NRXN3-NLGN1 complex tracks stress-induced depression susceptibility.

    Evidence Rat central amygdala shRNA knockdown with von Frey and c-Fos readouts; maternal separation model with Western blot and morphological analysis

    PMID:40286836 PMID:41466820

    Open questions at the time
    • NRXN3-NLGN1 complex inferred from co-expression, not direct co-IP
    • Causal directionality in depression model not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How NRXN3 splice-variant selection is coordinated across tissues, and how its presynaptic adhesion activity relates mechanistically to its non-neuronal cytoplasmic functions, remains unresolved.
  • No unified model linking adhesion and pyroptosis functions
  • Postsynaptic partners for many circuits not mapped
  • Structural basis of ligand interactions unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098631 cell adhesion mediator activity 3
Localization
GO:0005886 plasma membrane 2
Pathway
R-HSA-112316 Neuronal System 3 R-HSA-1500931 Cell-Cell communication 2

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2024 C1ql2 directly interacts with a specific splice variant of neurexin-3, Nrxn3(25b+), at hippocampal mossy fiber-CA3 synapses. This C1ql2-Nrxn3(25b+) interaction regulates synaptic vesicle recruitment and long-term potentiation. Disruption of this interaction (via non-binding C1ql2 mutant or dentate gyrus-specific Nrxn3 deletion) recapitulates the Bcl11b and C1ql2 mutant synaptic phenotypes, placing Nrxn3(25b+) downstream of the Bcl11b/C1ql2 transcriptional pathway. In vivo mouse genetics (conditional KO), in vitro electrophysiology (LTP recording), expression of non-binding C1ql2 mutant, direct interaction assay, epistasis analysis eLife High 38358390
2024 Nrxn3, functioning as a presynaptic adhesion molecule, is essential for ribbon-synapse maturation in hair cells. Loss of Nrxn3 in both mouse and zebrafish leads to significantly fewer intact ribbon synapses; in zebrafish, initial pre- and postsynapse numbers are normal but synapses fail to pair over time, resulting in postsynapse loss. A 60% loss of ribbon synapses in nrxn3 zebrafish mutants dramatically reduces pre- and postsynaptic responses. Mouse and zebrafish genetic KO, confocal imaging of synaptic markers, electrophysiology (pre- and postsynaptic response recording), behavioral assays (acoustic startle response) Development (Cambridge, England) High 38410471 39254120
2002 NRXN3 is expressed not only in neurons but also in heart, lung, pancreas, placenta, liver, and kidney. Heart-specific splicing variants of NRXN3 were identified and characterized, and cardiac isoforms of NRXN3 likely participate in a complex involving dystroglycan and extracellular matrix proteins involved in intercellular connections. RT-PCR, tissue expression panel, characterization of alternative splicing variants Biochemical and biophysical research communications Medium 12379233
2013 FoxQ1 directly binds the NRXN3 promoter region and suppresses its transcriptional activity, leading to downregulation of NRXN3 expression. This FoxQ1-mediated repression of NRXN3 promotes glioma cell proliferation and migration, as depletion of FoxQ1 reduces these capacities. Chromatin immunoprecipitation (ChIP), luciferase reporter assay, stable knockdown/overexpression clones, MTT proliferation assay, transwell migration assay PloS one Medium 23383267
2020 The transcription factor ZNF582 directly regulates transcription of NRXN3 (and Nectin-3). Hypermethylation of the ZNF582 promoter reduces ZNF582 expression, leading to downregulation of NRXN3. Restoration of NRXN3 reverses the pro-metastatic effect of ZNF582 loss in nasopharyngeal carcinoma. ChIP-seq, ChIP-qPCR, luciferase reporter assay, bisulfite pyrosequencing, in vitro migration/invasion assays, in vivo metastasis models, rescue experiments Cancer communications (London, England) Medium 33038291
2008 Nrxn3beta mRNA expression is upregulated in the globus pallidus of mice developing short-term cocaine appetence, implicating NRXN3 adhesion molecules in synaptic plasticity of basal ganglia neurons involved in indirect pathways of reward-related learning. mRNA quantification in dissected brain regions after cocaine exposure in mice Neuroreport Low 18418251
2025 NRXN3 competitively blocks caspase-3 binding to RSK1, thereby inhibiting RSK1-dependent phosphorylation of caspase-3 at T152. Inhibition of this phosphorylation impairs caspase-3 interaction with the ubiquitin ligase component FBXO1, enhancing caspase-3 stability and facilitating caspase-3/GSDME-dependent pyroptotic cell death and chemosensitivity in intrahepatic cholangiocarcinoma. Genome-scale CRISPR-Cas9 screen, RNA-seq, immunoprecipitation-mass spectrometry (IP-MS), in vitro and in vivo functional experiments Journal of advanced research Medium 40324630
2025 NRXN3 forms a complex with its ligand neuroligin 1 (NLGN1) in the hippocampus. Downregulation of both NRXN3 and NLGN1 precedes synaptic plasticity alterations (reduced dendritic branch and spine lengths) and depression-related behaviors induced by maternal separation stress in rats, suggesting the NRXN3-NLGN1 complex mediates synaptic plasticity changes underlying stress-induced depression susceptibility. Rat maternal separation model, Western blot, behavioral assays, hippocampal morphological analysis (branch and spine quantification) Brain research Low 40286836
2025 Knockdown of Nrxn3 in the central amygdala of rats significantly increased the nociceptive pain response to inflammatory orofacial pain (myofascial pain model) and increased c-Fos levels in the central amygdala, lateral parabrachial nucleus, trigeminal ganglia, and trigeminal nucleus caudalis, indicating that Nrxn3 expression in the central amygdala attenuates nociceptive orofacial pain by reducing neuronal activity in the orofacial pain pathway. shRNA knockdown (stereotaxic infusion), von Frey filament testing, c-Fos immunostaining, meal duration measurement Neurobiology of pain (Cambridge, Mass.) Medium 41466820
2023 A circular RNA originating from the Nrxn3 locus (circNrxn3) binds the splicing factor SAM68 (RNA immunoprecipitation), and its knockdown alters splicing of Nrxn3 mRNA and expression of genes in learning/memory pathways, enhancing sucrose self-administration and motivation for reward in the orbitofrontal cortex. RNA immunoprecipitation, RNA sequencing, qPCR, in vivo shRNA knockdown, sucrose self-administration behavioral assay Progress in neurobiology Low 38036039
2023 Loss-of-function variants in NRXN3 (including homozygous and compound heterozygous missense/splice-site mutations validated by CRISPR-edited cell functional studies) cause a novel autosomal recessive neurodevelopmental syndrome with developmental delay, movement disorder, and behavioral problems, phenotypically consistent with homozygous Nrxn3α/β knockout mice. Whole exome sequencing, CRISPR-edited cell lines, in-silico analysis, phenotype-genotype correlation with mouse KO model Gene Medium 36898513

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. PLoS genetics 205 19557197
2013 FoxQ1 promotes glioma cells proliferation and migration by regulating NRXN3 expression. PloS one 47 23383267
2018 Low expression of aging-related NRXN3 is associated with Alzheimer disease: A systematic review and meta-analysis. Medicine 40 29995770
2009 Association of a polymorphism in the NRXN3 gene with the degree of smoking in schizophrenia: a preliminary study. The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry 38 19658047
2011 Influence of genomic variation in FTO at 16q12.2, MC4R at 18q22 and NRXN3 at 14q31 genes on breast cancer risk. Molecular biology reports 36 21688152
2011 Implications of central obesity-related variants in LYPLAL1, NRXN3, MSRA, and TFAP2B on quantitative metabolic traits in adult Danes. PloS one 35 21674055
2021 Circ_0001367 inhibits glioma proliferation, migration and invasion by sponging miR-431 and thus regulating NRXN3. Cell death & disease 34 34035217
2014 Association study of common polymorphisms in MSRA, TFAP2B, MC4R, NRXN3, PPARGC1A, TMEM18, SEC16B, HOXB5 and OLFM4 genes with obesity-related traits among Portuguese children. Journal of human genetics 34 24670271
2010 Polymorphisms in NRXN3, TFAP2B, MSRA, LYPLAL1, FTO and MC4R and their effect on visceral fat area in the Japanese population. Journal of human genetics 32 20703240
2013 Association study of NRXN3 polymorphisms with schizophrenia and risperidone-induced bodyweight gain in Chinese Han population. Progress in neuro-psychopharmacology & biological psychiatry 31 23306218
2020 ZNF582 hypermethylation promotes metastasis of nasopharyngeal carcinoma by regulating the transcription of adhesion molecules Nectin-3 and NRXN3. Cancer communications (London, England) 30 33038291
2018 A rare exonic NRXN3 deletion segregating with neurodevelopmental and neuropsychiatric conditions in a three-generation Chinese family. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 25 30076746
2008 Nrxn3 upregulation in the globus pallidus of mice developing cocaine addiction. Neuroreport 25 18418251
2002 Identification and characterization of heart-specific splicing of human neurexin 3 mRNA (NRXN3). Biochemical and biophysical research communications 19 12379233
2023 NRXN3 mutations cause developmental delay, movement disorder, and behavioral problems: CRISPR edited cells based WES results. Gene 17 36898513
2024 Regulation of hippocampal mossy fiber-CA3 synapse function by a Bcl11b/C1ql2/Nrxn3(25b+) pathway. eLife 16 38358390
2013 DNA pooling base genome-wide association study identifies variants at NRXN3 associated with delayed encephalopathy after acute carbon monoxide poisoning. PloS one 13 24265751
2012 Examining the association of NRXN3 SNPs with borderline personality disorder phenotypes in heroin dependent cases and socio-economically disadvantaged controls. Drug and alcohol dependence 9 23245376
2024 Presynaptic Nrxn3 is essential for ribbon-synapse maturation in hair cells. Development (Cambridge, England) 8 39254120
2023 Case Report-An Inherited Loss-of-Function NRXN3 Variant Potentially Causes a Neurodevelopmental Disorder with Autism Consistent with Previously Described 14q24.3-31.1 Deletions. Genes 7 37372397
2023 Orbitofrontal intronic circular RNA from Nrxn3 mediates reward learning and motivation for reward. Progress in neurobiology 6 38036039
2025 NRXN3 regulates pyroptosis in intrahepatic cholangiocarcinoma via mediating the phospho-dependent ubiquitination and degradation of caspase-3. Journal of advanced research 3 40324630
2025 Nrxn3 reduces myofascial nociceptive pain. Neurobiology of pain (Cambridge, Mass.) 2 41466820
2024 Presynaptic Nrxn3 is essential for ribbon-synapse assembly in hair cells. bioRxiv : the preprint server for biology 2 38410471
2026 Robo2-Nrxn3 Deficiency: A Molecular Hub Linking Excitation-Inhibition Imbalance to the Pathogenesis of Schizophrenia. Schizophrenia bulletin 0 41863359
2025 NRXN3-NLGN1 complex influences the development of depression induced by maternal separation in rats. Brain research 0 40286836

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