{"gene":"NLGN4X","run_date":"2026-04-29T11:37:57","timeline":{"discoveries":[{"year":2003,"finding":"NLGN4X (neuroligin 4) is a cell-adhesion molecule localized at the synapse; loss-of-function mutations in NLGN4 identified in siblings with autism-spectrum disorders implicate defective synaptogenesis as a pathogenic mechanism.","method":"Human genetic mutation identification in affected siblings; protein localization at synapse noted","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 — foundational paper with >1300 citations, mutation characterization in human subjects, widely replicated","pmids":["12669065"],"is_preprint":false},{"year":2004,"finding":"A 2-bp deletion in NLGN4 causing a premature stop codon is predicted to eliminate the transmembrane domain and sequences required for neuroligin dimerization and beta-neurexin binding, linking NLGN4X loss-of-function to defective cell-cell interaction at excitatory synapses.","method":"Sequencing of human family with X-linked mental retardation/autism; protein domain analysis of truncation","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 — mutation characterization in human pedigree, mechanistic inference from domain structure, >550 citations","pmids":["14963808"],"is_preprint":false},{"year":2020,"finding":"NLGN4X maturation, surface expression, and synaptogenic activity are regulated by a single critical amino acid that distinguishes it from NLGN4Y; a cluster of ASD-associated mutations surrounding this residue causes NLGN4X to phenocopy NLGN4Y's severe deficits, and NLGN4Y cannot compensate for these NLGN4X mutant deficits.","method":"Biochemistry (protein maturation/surface expression assays), electrophysiology, and imaging in heterologous cells and neurons; mutagenesis of critical amino acid","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 1 — multiple orthogonal methods (biochemistry, electrophysiology, imaging, mutagenesis) in a single rigorous study","pmids":["32243781"],"is_preprint":false},{"year":2013,"finding":"Nlgn4 knockout in mice results in decreased network response to stimulation in both excitatory and inhibitory circuits of somatosensory cortex and a decreased excitation-inhibition ratio, demonstrating that Nlgn4 regulates the balance of excitatory and inhibitory circuit activity.","method":"Multi-electrode array recording of cortical slices and patch-clamp electrophysiology in Nlgn4 knock-out versus wild-type juvenile mice","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — clean KO with defined electrophysiological phenotype using two complementary methods","pmids":["24104404"],"is_preprint":false},{"year":2013,"finding":"NLGN4X knockdown in human neural stem cells delays neuronal development and impairs neurite formation during differentiation, and reduces expression of postsynaptic genes including DLG4, NLGN1, and NLGN3, placing NLGN4X upstream of multiple synaptic and neurogenic pathways.","method":"shRNAmir-based knockdown in neural stem cells differentiated into neurons; morphological analysis and whole-genome gene expression profiling at multiple time points","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — KD with defined cellular and molecular phenotypes using morphological and transcriptomic readouts","pmids":["23710042"],"is_preprint":false},{"year":2025,"finding":"NLGN4X is phosphorylated at serine 712 by PKA (exclusively on NLGN4X) and by Cdk5 (on both NLGN4X and NLGN4Y); S712 phosphorylation reduces mature mushroom spine density, while unphosphorylated S712 increases spine density and enhances miniature excitatory postsynaptic current frequency.","method":"Phosphorylation site characterization by mutagenesis; kinase specificity assays with PKA and Cdk5; spine density analysis and mEPSC recordings in neurons expressing phospho-mimetic and phospho-null mutants","journal":"eNeuro","confidence":"High","confidence_rationale":"Tier 1 — in vitro kinase assays with mutagenesis, functional readouts of spinogenesis and synaptic transmission","pmids":["40032531"],"is_preprint":false},{"year":2012,"finding":"Nlgn4 null mutant mice display reduced social interaction, deficits in ultrasonic communication, altered aggression, nest-building, self-grooming, and circling behaviors in both males and females, establishing NLGN4X loss-of-function as sufficient to produce autism-relevant behavioral phenotypes.","method":"Loss-of-function mouse model (Nlgn4 null mutants); behavioral battery including social interaction tests, ultrasonic vocalization recording, and stereotypy measures in both sexes","journal":"Behavioural brain research","confidence":"Medium","confidence_rationale":"Tier 2 — clean KO with multiple behavioral phenotypic readouts across sexes, consistent with prior work","pmids":["23183221"],"is_preprint":false},{"year":2024,"finding":"In melanoma cells, NLGN4X suppression downregulates the prefoldin member VBP1, leading to HIF1A accumulation and HIF1A-dependent acquisition of migratory properties; re-expression of NLGN4X in late-stage melanoma lines reduces tumour growth in human skin organoid models.","method":"Loss- and gain-of-function experiments in vitro; whole-genome expression analysis; tumorsphere grafting to human skin organoids derived from pluripotent stem cells","journal":"British journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (KD, OE, organoid model, transcriptomics) in a single study","pmids":["38902533"],"is_preprint":false}],"current_model":"NLGN4X is a postsynaptic cell-adhesion molecule that binds presynaptic neurexins to regulate synapse formation and maturation; its surface expression and synaptogenic function are controlled by a critical amino acid distinguishing it from NLGN4Y, it undergoes PKA- and Cdk5-mediated phosphorylation at S712 that bidirectionally regulates spine density and excitatory synaptic transmission, and its loss in neurons disrupts the excitation-inhibition balance and impairs neurite formation with downstream effects on multiple postsynaptic scaffold genes."},"narrative":{"teleology":[{"year":2003,"claim":"Identification of loss-of-function NLGN4X mutations in siblings with autism established this synaptic cell-adhesion molecule as a causative gene for neurodevelopmental disease, raising the question of how its molecular function at synapses relates to pathogenesis.","evidence":"Mutation screening in affected human siblings; protein localization at synapse","pmids":["12669065"],"confidence":"High","gaps":["No functional characterization of how the identified mutations disrupt synaptogenesis","Expression pattern and synaptic subtype specificity of NLGN4X not defined"]},{"year":2004,"claim":"A truncating frameshift in NLGN4X was predicted to ablate the transmembrane domain and sequences required for dimerization and neurexin binding, providing the first structural rationale for how NLGN4X mutations disrupt trans-synaptic adhesion.","evidence":"Sequencing of X-linked intellectual disability/autism pedigree; protein domain analysis of truncation","pmids":["14963808"],"confidence":"Medium","gaps":["Functional effect of truncation not tested experimentally in cells or neurons","Whether partial protein products are expressed and exert dominant-negative effects was unknown"]},{"year":2012,"claim":"Nlgn4 knockout mice recapitulated core autism-relevant behaviors—reduced social interaction, communication deficits, and stereotypies—in both sexes, confirming that NLGN4X loss of function is sufficient to produce behavioral phenotypes.","evidence":"Behavioral battery in Nlgn4-null mice including social interaction, ultrasonic vocalization, and repetitive behavior assays","pmids":["23183221"],"confidence":"Medium","gaps":["Circuit-level and synaptic mechanisms underlying the behavioral deficits were not identified","Mouse Nlgn4 diverges from human NLGN4X, limiting direct translation"]},{"year":2013,"claim":"Electrophysiological analysis of Nlgn4-knockout cortex revealed decreased network responses and a reduced excitation-inhibition ratio, establishing that NLGN4X regulates the E/I balance rather than solely excitatory or inhibitory synaptogenesis.","evidence":"Multi-electrode array and patch-clamp recordings in somatosensory cortical slices from Nlgn4-KO versus wild-type juvenile mice","pmids":["24104404"],"confidence":"Medium","gaps":["Whether the E/I imbalance arises from selective loss of specific synapse types was not resolved","Developmental versus acute contributions of Nlgn4 loss were not distinguished"]},{"year":2013,"claim":"NLGN4X knockdown in human neural stem cells impaired neurite formation and reduced expression of key postsynaptic scaffold genes (DLG4, NLGN1, NLGN3), placing NLGN4X upstream of broader synaptogenic transcriptional programs during neuronal differentiation.","evidence":"shRNA knockdown in differentiating human neural stem cells; morphological analysis and genome-wide expression profiling","pmids":["23710042"],"confidence":"Medium","gaps":["Whether the transcriptional changes are direct or secondary to failed neurite outgrowth is unknown","Rescue experiments with wild-type NLGN4X were not reported"]},{"year":2020,"claim":"A single critical amino acid distinguishing NLGN4X from NLGN4Y was shown to control protein maturation, surface trafficking, and synaptogenic activity, and ASD-associated mutations near this residue phenocopied NLGN4Y's severe deficits, explaining why the Y paralog cannot compensate for NLGN4X loss.","evidence":"Protein maturation/surface expression assays, electrophysiology, and imaging in heterologous cells and neurons with site-directed mutagenesis","pmids":["32243781"],"confidence":"High","gaps":["Structural basis for how this residue controls folding and ER exit is not resolved","In vivo confirmation of NLGN4Y non-compensation in a mammalian model is lacking"]},{"year":2024,"claim":"In melanoma, NLGN4X suppression was found to downregulate VBP1, causing HIF1A accumulation and HIF1A-dependent migration, revealing an unexpected non-neuronal role for NLGN4X in tumor biology.","evidence":"Loss- and gain-of-function in melanoma cells; transcriptomics; tumorsphere grafting to human skin organoids","pmids":["38902533"],"confidence":"Medium","gaps":["Mechanism linking NLGN4X to VBP1 regulation is undefined","Relevance to in vivo melanoma progression not established beyond organoid model","Whether this pathway operates in other cancer types is unknown"]},{"year":2025,"claim":"Phosphorylation of NLGN4X at S712 by PKA (X-specific) and Cdk5 was shown to bidirectionally regulate spine morphogenesis and excitatory synaptic transmission, providing the first post-translational mechanism for dynamic modulation of NLGN4X synaptogenic function.","evidence":"In vitro kinase assays with mutagenesis; spine density imaging and mEPSC recordings in neurons expressing phospho-mimetic and phospho-null S712 mutants","pmids":["40032531"],"confidence":"High","gaps":["In vivo relevance of S712 phosphorylation to behavior or circuit function not tested","Whether S712 phosphorylation affects neurexin binding affinity is unknown","Upstream signals triggering PKA- versus Cdk5-mediated phosphorylation at this site are not defined"]},{"year":null,"claim":"Key unresolved questions include the structural basis for the NLGN4X/NLGN4Y functional divergence, the identity of signals that dynamically regulate S712 phosphorylation in vivo, and whether the non-neuronal VBP1-HIF1A pathway represents a physiologically relevant NLGN4X function outside the nervous system.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of NLGN4X in complex with neurexin","In vivo phospho-S712 dynamics have not been measured","Non-neuronal functions lack independent replication"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,5]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,2]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[0,3,5]},{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[0,1,2]}],"complexes":[],"partners":["NRXN1","DLG4","VBP1"],"other_free_text":[]},"mechanistic_narrative":"NLGN4X is a postsynaptic cell-adhesion molecule that binds presynaptic neurexins to promote synapse formation and regulate the balance of excitatory and inhibitory circuit activity [PMID:12669065, PMID:24104404]. Its surface expression and synaptogenic function depend on a single critical amino acid that distinguishes it from its Y-linked paralog NLGN4Y, and autism-associated mutations clustering near this residue phenocopy NLGN4Y's severe functional deficits [PMID:32243781]. Phosphorylation of serine 712 by PKA and Cdk5 bidirectionally controls dendritic spine density and excitatory synaptic transmission, with the phosphorylated state reducing mushroom spines and the unphosphorylated state enhancing spine density and mEPSC frequency [PMID:40032531]. Loss-of-function mutations in NLGN4X cause X-linked autism-spectrum disorder and intellectual disability, consistent with its requirement for neurite formation and expression of downstream postsynaptic scaffold genes including DLG4 [PMID:12669065, PMID:23710042]."},"prefetch_data":{"uniprot":{"accession":"Q8N0W4","full_name":"Neuroligin-4, X-linked","aliases":["HNLX"],"length_aa":816,"mass_kda":91.9,"function":"Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members","subcellular_location":"Cell membrane; Postsynaptic density membrane; Cell projection, dendritic spine; Cell projection, dendrite; Synapse","url":"https://www.uniprot.org/uniprotkb/Q8N0W4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NLGN4X","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NLGN4X","total_profiled":1310},"omim":[{"mim_id":"300495","title":"AUTISM, SUSCEPTIBILITY TO, X-LINKED 2; AUTSX2","url":"https://www.omim.org/entry/300495"},{"mim_id":"300427","title":"NEUROLIGIN 4, X-LINKED; NLGN4X","url":"https://www.omim.org/entry/300427"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":11.8},{"tissue":"lymphoid tissue","ntpm":13.3},{"tissue":"ovary","ntpm":13.8}],"url":"https://www.proteinatlas.org/search/NLGN4X"},"hgnc":{"alias_symbol":["KIAA1260","NLGN","HLNX"],"prev_symbol":["NLGN4"]},"alphafold":{"accession":"Q8N0W4","domains":[{"cath_id":"3.40.50.1820","chopping":"46-587","consensus_level":"medium","plddt":93.9927,"start":46,"end":587}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N0W4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N0W4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N0W4-F1-predicted_aligned_error_v6.png","plddt_mean":79.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NLGN4X","jax_strain_url":"https://www.jax.org/strain/search?query=NLGN4X"},"sequence":{"accession":"Q8N0W4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N0W4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N0W4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N0W4"}},"corpus_meta":[{"pmid":"12669065","id":"PMC_12669065","title":"Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism.","date":"2003","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12669065","citation_count":1337,"is_preprint":false},{"pmid":"14963808","id":"PMC_14963808","title":"X-linked mental retardation and autism are associated with a mutation in the NLGN4 gene, a member of the neuroligin family.","date":"2004","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/14963808","citation_count":553,"is_preprint":false},{"pmid":"18231125","id":"PMC_18231125","title":"Familial deletion within NLGN4 associated with autism and Tourette syndrome.","date":"2008","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/18231125","citation_count":205,"is_preprint":false},{"pmid":"16648374","id":"PMC_16648374","title":"Novel splice isoforms for NLGN3 and NLGN4 with possible implications in autism.","date":"2006","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16648374","citation_count":131,"is_preprint":false},{"pmid":"23183221","id":"PMC_23183221","title":"Development of an autism severity score for mice using Nlgn4 null mutants as a construct-valid model of heritable monogenic autism.","date":"2012","source":"Behavioural brain research","url":"https://pubmed.ncbi.nlm.nih.gov/23183221","citation_count":98,"is_preprint":false},{"pmid":"15389766","id":"PMC_15389766","title":"NLGN3/NLGN4 gene mutations are not responsible for autism in the Quebec population.","date":"2005","source":"American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/15389766","citation_count":89,"is_preprint":false},{"pmid":"32243781","id":"PMC_32243781","title":"A Cluster of Autism-Associated Variants on X-Linked NLGN4X Functionally Resemble NLGN4Y.","date":"2020","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/32243781","citation_count":63,"is_preprint":false},{"pmid":"17391250","id":"PMC_17391250","title":"Deletions of VCX-A and NLGN4: a variable phenotype including normal intellect.","date":"2007","source":"Journal of intellectual disability research : JIDR","url":"https://pubmed.ncbi.nlm.nih.gov/17391250","citation_count":52,"is_preprint":false},{"pmid":"19645625","id":"PMC_19645625","title":"A substitution involving the NLGN4 gene associated with autistic behavior in the Greek population.","date":"2009","source":"Genetic testing and molecular biomarkers","url":"https://pubmed.ncbi.nlm.nih.gov/19645625","citation_count":40,"is_preprint":false},{"pmid":"18189281","id":"PMC_18189281","title":"No evidence for involvement of genetic variants in the X-linked neuroligin genes NLGN3 and NLGN4X in probands with autism spectrum disorder on high functioning level.","date":"2008","source":"American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18189281","citation_count":38,"is_preprint":false},{"pmid":"24570023","id":"PMC_24570023","title":"Variations analysis of NLGN3 and NLGN4X gene in Chinese autism patients.","date":"2014","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/24570023","citation_count":33,"is_preprint":false},{"pmid":"18194880","id":"PMC_18194880","title":"Normal intelligence and social interactions in a male patient despite the deletion of NLGN4X and the VCX genes.","date":"2007","source":"European journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18194880","citation_count":29,"is_preprint":false},{"pmid":"21569590","id":"PMC_21569590","title":"A sex-specific association of common variants of neuroligin genes (NLGN3 and NLGN4X) with autism spectrum disorders in a Chinese Han cohort.","date":"2011","source":"Behavioral and brain functions : BBF","url":"https://pubmed.ncbi.nlm.nih.gov/21569590","citation_count":26,"is_preprint":false},{"pmid":"23468870","id":"PMC_23468870","title":"Lack of association between NLGN3, NLGN4, SHANK2 and SHANK3 gene variants and autism spectrum disorder in a Chinese population.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23468870","citation_count":24,"is_preprint":false},{"pmid":"23710042","id":"PMC_23710042","title":"The functional genetic link of NLGN4X knockdown and neurodevelopment in neural stem cells.","date":"2013","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23710042","citation_count":23,"is_preprint":false},{"pmid":"24104404","id":"PMC_24104404","title":"Nlgn4 knockout induces network hypo-excitability in juvenile mouse somatosensory cortex in vitro.","date":"2013","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/24104404","citation_count":23,"is_preprint":false},{"pmid":"23851596","id":"PMC_23851596","title":"Mutation screening in the Greek population and evaluation of NLGN3 and NLGN4X genes causal factors for autism.","date":"2013","source":"Psychiatric genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23851596","citation_count":14,"is_preprint":false},{"pmid":"23431752","id":"PMC_23431752","title":"Analysis of the genes encoding neuroligins NLGN3 and NLGN4 in Bulgarian patients with autism.","date":"2012","source":"Genetic counseling (Geneva, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/23431752","citation_count":13,"is_preprint":false},{"pmid":"33636238","id":"PMC_33636238","title":"Effects of chronic exposure to haloperidol, olanzapine or lithium on SV2A and NLGN synaptic puncta in the rat frontal cortex.","date":"2021","source":"Behavioural brain research","url":"https://pubmed.ncbi.nlm.nih.gov/33636238","citation_count":12,"is_preprint":false},{"pmid":"37715782","id":"PMC_37715782","title":"NLGN4X TCR transgenic T cells to treat gliomas.","date":"2024","source":"Neuro-oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37715782","citation_count":12,"is_preprint":false},{"pmid":"38739110","id":"PMC_38739110","title":"Rare heterozygous genetic variants of NRXN and NLGN gene families involved in synaptic function and their association with neurodevelopmental disorders.","date":"2024","source":"Developmental neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/38739110","citation_count":9,"is_preprint":false},{"pmid":"31852540","id":"PMC_31852540","title":"Novel human sex-typing strategies based on the autism candidate gene NLGN4X and its male-specific gametologue NLGN4Y.","date":"2019","source":"Biology of sex differences","url":"https://pubmed.ncbi.nlm.nih.gov/31852540","citation_count":8,"is_preprint":false},{"pmid":"38902533","id":"PMC_38902533","title":"Late stage melanoma is hallmarked by low NLGN4X expression leading to HIF1A accumulation.","date":"2024","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38902533","citation_count":7,"is_preprint":false},{"pmid":"33369065","id":"PMC_33369065","title":"Pathogenic paternally inherited NLGN4X deletion in a female with autism spectrum disorder: Clinical, cytogenetic, and molecular characterization.","date":"2020","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/33369065","citation_count":6,"is_preprint":false},{"pmid":"20714171","id":"PMC_20714171","title":"Gender differences in cognitive ability associated with genetic variants of NLGN4.","date":"2010","source":"Neuropsychobiology","url":"https://pubmed.ncbi.nlm.nih.gov/20714171","citation_count":5,"is_preprint":false},{"pmid":"30298512","id":"PMC_30298512","title":"[Role of NRXN-NLGN-SHANK pathway gene variations in the pathogenesis of autism spectrum disorders].","date":"2018","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30298512","citation_count":4,"is_preprint":false},{"pmid":"40032531","id":"PMC_40032531","title":"Phosphorylation of NLGN4X Regulates Spinogenesis and Synaptic Function.","date":"2025","source":"eNeuro","url":"https://pubmed.ncbi.nlm.nih.gov/40032531","citation_count":4,"is_preprint":false},{"pmid":"31139237","id":"PMC_31139237","title":"Analysis of the SNP rs3747333 and rs3747334 in NLGN4X gene in autism spectrum disorder: a meta-analysis.","date":"2019","source":"Annals of general psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/31139237","citation_count":1,"is_preprint":false},{"pmid":"40034542","id":"PMC_40034542","title":"The association between NLGN4 gene variants and the incidence of autism spectrum disorders in Guilan, Iran.","date":"2025","source":"IBRO neuroscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/40034542","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.18.689032","title":"DNMT1 Coordinates PV Interneuron–Glia Coupling to Maintain Cortical Network Stability and Regulate Behavior","date":"2025-11-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.18.689032","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.05.24313143","title":"Neuroligin fragments as blood-based biomarkers for early detection of Alzheimer’s disease","date":"2024-09-06","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.05.24313143","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.07.25329125","title":"Genetically determined ancestry associates with morphological and molecular carotid plaque features","date":"2025-06-08","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.07.25329125","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.24.620138","title":"NLGN3 contributes to angiogenesis in myocardial infarction via activation of the Gαi1/3-Akt Pathway","date":"2024-10-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.24.620138","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.07.617121","title":"Longitudinal multi-omics reveals pathogenic<i>TSC2</i>variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex","date":"2024-10-11","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.07.617121","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.06.11.598408","title":"High-affinity detection of endogenously biotinylated neuroligin-1 at excitatory and inhibitory synapses using a tagged knock-in mouse strain","date":"2024-06-11","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.11.598408","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17849,"output_tokens":1884,"usd":0.040904},"stage2":{"model":"claude-opus-4-6","input_tokens":5157,"output_tokens":2313,"usd":0.125415},"total_usd":0.166319,"stage1_batch_id":"msgbatch_012ZiiCUBfB62NCTQd4Bk1Jo","stage2_batch_id":"msgbatch_01Xuqq9aUHoQouS7UVGZNStZ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"NLGN4X (neuroligin 4) is a cell-adhesion molecule localized at the synapse; loss-of-function mutations in NLGN4 identified in siblings with autism-spectrum disorders implicate defective synaptogenesis as a pathogenic mechanism.\",\n      \"method\": \"Human genetic mutation identification in affected siblings; protein localization at synapse noted\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — foundational paper with >1300 citations, mutation characterization in human subjects, widely replicated\",\n      \"pmids\": [\"12669065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"A 2-bp deletion in NLGN4 causing a premature stop codon is predicted to eliminate the transmembrane domain and sequences required for neuroligin dimerization and beta-neurexin binding, linking NLGN4X loss-of-function to defective cell-cell interaction at excitatory synapses.\",\n      \"method\": \"Sequencing of human family with X-linked mental retardation/autism; protein domain analysis of truncation\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutation characterization in human pedigree, mechanistic inference from domain structure, >550 citations\",\n      \"pmids\": [\"14963808\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NLGN4X maturation, surface expression, and synaptogenic activity are regulated by a single critical amino acid that distinguishes it from NLGN4Y; a cluster of ASD-associated mutations surrounding this residue causes NLGN4X to phenocopy NLGN4Y's severe deficits, and NLGN4Y cannot compensate for these NLGN4X mutant deficits.\",\n      \"method\": \"Biochemistry (protein maturation/surface expression assays), electrophysiology, and imaging in heterologous cells and neurons; mutagenesis of critical amino acid\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple orthogonal methods (biochemistry, electrophysiology, imaging, mutagenesis) in a single rigorous study\",\n      \"pmids\": [\"32243781\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Nlgn4 knockout in mice results in decreased network response to stimulation in both excitatory and inhibitory circuits of somatosensory cortex and a decreased excitation-inhibition ratio, demonstrating that Nlgn4 regulates the balance of excitatory and inhibitory circuit activity.\",\n      \"method\": \"Multi-electrode array recording of cortical slices and patch-clamp electrophysiology in Nlgn4 knock-out versus wild-type juvenile mice\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined electrophysiological phenotype using two complementary methods\",\n      \"pmids\": [\"24104404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NLGN4X knockdown in human neural stem cells delays neuronal development and impairs neurite formation during differentiation, and reduces expression of postsynaptic genes including DLG4, NLGN1, and NLGN3, placing NLGN4X upstream of multiple synaptic and neurogenic pathways.\",\n      \"method\": \"shRNAmir-based knockdown in neural stem cells differentiated into neurons; morphological analysis and whole-genome gene expression profiling at multiple time points\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with defined cellular and molecular phenotypes using morphological and transcriptomic readouts\",\n      \"pmids\": [\"23710042\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NLGN4X is phosphorylated at serine 712 by PKA (exclusively on NLGN4X) and by Cdk5 (on both NLGN4X and NLGN4Y); S712 phosphorylation reduces mature mushroom spine density, while unphosphorylated S712 increases spine density and enhances miniature excitatory postsynaptic current frequency.\",\n      \"method\": \"Phosphorylation site characterization by mutagenesis; kinase specificity assays with PKA and Cdk5; spine density analysis and mEPSC recordings in neurons expressing phospho-mimetic and phospho-null mutants\",\n      \"journal\": \"eNeuro\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro kinase assays with mutagenesis, functional readouts of spinogenesis and synaptic transmission\",\n      \"pmids\": [\"40032531\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Nlgn4 null mutant mice display reduced social interaction, deficits in ultrasonic communication, altered aggression, nest-building, self-grooming, and circling behaviors in both males and females, establishing NLGN4X loss-of-function as sufficient to produce autism-relevant behavioral phenotypes.\",\n      \"method\": \"Loss-of-function mouse model (Nlgn4 null mutants); behavioral battery including social interaction tests, ultrasonic vocalization recording, and stereotypy measures in both sexes\",\n      \"journal\": \"Behavioural brain research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with multiple behavioral phenotypic readouts across sexes, consistent with prior work\",\n      \"pmids\": [\"23183221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In melanoma cells, NLGN4X suppression downregulates the prefoldin member VBP1, leading to HIF1A accumulation and HIF1A-dependent acquisition of migratory properties; re-expression of NLGN4X in late-stage melanoma lines reduces tumour growth in human skin organoid models.\",\n      \"method\": \"Loss- and gain-of-function experiments in vitro; whole-genome expression analysis; tumorsphere grafting to human skin organoids derived from pluripotent stem cells\",\n      \"journal\": \"British journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (KD, OE, organoid model, transcriptomics) in a single study\",\n      \"pmids\": [\"38902533\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NLGN4X is a postsynaptic cell-adhesion molecule that binds presynaptic neurexins to regulate synapse formation and maturation; its surface expression and synaptogenic function are controlled by a critical amino acid distinguishing it from NLGN4Y, it undergoes PKA- and Cdk5-mediated phosphorylation at S712 that bidirectionally regulates spine density and excitatory synaptic transmission, and its loss in neurons disrupts the excitation-inhibition balance and impairs neurite formation with downstream effects on multiple postsynaptic scaffold genes.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"NLGN4X is a postsynaptic cell-adhesion molecule that binds presynaptic neurexins to promote synapse formation and regulate the balance of excitatory and inhibitory circuit activity [PMID:12669065, PMID:24104404]. Its surface expression and synaptogenic function depend on a single critical amino acid that distinguishes it from its Y-linked paralog NLGN4Y, and autism-associated mutations clustering near this residue phenocopy NLGN4Y's severe functional deficits [PMID:32243781]. Phosphorylation of serine 712 by PKA and Cdk5 bidirectionally controls dendritic spine density and excitatory synaptic transmission, with the phosphorylated state reducing mushroom spines and the unphosphorylated state enhancing spine density and mEPSC frequency [PMID:40032531]. Loss-of-function mutations in NLGN4X cause X-linked autism-spectrum disorder and intellectual disability, consistent with its requirement for neurite formation and expression of downstream postsynaptic scaffold genes including DLG4 [PMID:12669065, PMID:23710042].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Identification of loss-of-function NLGN4X mutations in siblings with autism established this synaptic cell-adhesion molecule as a causative gene for neurodevelopmental disease, raising the question of how its molecular function at synapses relates to pathogenesis.\",\n      \"evidence\": \"Mutation screening in affected human siblings; protein localization at synapse\",\n      \"pmids\": [\"12669065\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No functional characterization of how the identified mutations disrupt synaptogenesis\",\n        \"Expression pattern and synaptic subtype specificity of NLGN4X not defined\"\n      ]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"A truncating frameshift in NLGN4X was predicted to ablate the transmembrane domain and sequences required for dimerization and neurexin binding, providing the first structural rationale for how NLGN4X mutations disrupt trans-synaptic adhesion.\",\n      \"evidence\": \"Sequencing of X-linked intellectual disability/autism pedigree; protein domain analysis of truncation\",\n      \"pmids\": [\"14963808\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional effect of truncation not tested experimentally in cells or neurons\",\n        \"Whether partial protein products are expressed and exert dominant-negative effects was unknown\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Nlgn4 knockout mice recapitulated core autism-relevant behaviors—reduced social interaction, communication deficits, and stereotypies—in both sexes, confirming that NLGN4X loss of function is sufficient to produce behavioral phenotypes.\",\n      \"evidence\": \"Behavioral battery in Nlgn4-null mice including social interaction, ultrasonic vocalization, and repetitive behavior assays\",\n      \"pmids\": [\"23183221\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Circuit-level and synaptic mechanisms underlying the behavioral deficits were not identified\",\n        \"Mouse Nlgn4 diverges from human NLGN4X, limiting direct translation\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Electrophysiological analysis of Nlgn4-knockout cortex revealed decreased network responses and a reduced excitation-inhibition ratio, establishing that NLGN4X regulates the E/I balance rather than solely excitatory or inhibitory synaptogenesis.\",\n      \"evidence\": \"Multi-electrode array and patch-clamp recordings in somatosensory cortical slices from Nlgn4-KO versus wild-type juvenile mice\",\n      \"pmids\": [\"24104404\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the E/I imbalance arises from selective loss of specific synapse types was not resolved\",\n        \"Developmental versus acute contributions of Nlgn4 loss were not distinguished\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"NLGN4X knockdown in human neural stem cells impaired neurite formation and reduced expression of key postsynaptic scaffold genes (DLG4, NLGN1, NLGN3), placing NLGN4X upstream of broader synaptogenic transcriptional programs during neuronal differentiation.\",\n      \"evidence\": \"shRNA knockdown in differentiating human neural stem cells; morphological analysis and genome-wide expression profiling\",\n      \"pmids\": [\"23710042\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the transcriptional changes are direct or secondary to failed neurite outgrowth is unknown\",\n        \"Rescue experiments with wild-type NLGN4X were not reported\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A single critical amino acid distinguishing NLGN4X from NLGN4Y was shown to control protein maturation, surface trafficking, and synaptogenic activity, and ASD-associated mutations near this residue phenocopied NLGN4Y's severe deficits, explaining why the Y paralog cannot compensate for NLGN4X loss.\",\n      \"evidence\": \"Protein maturation/surface expression assays, electrophysiology, and imaging in heterologous cells and neurons with site-directed mutagenesis\",\n      \"pmids\": [\"32243781\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for how this residue controls folding and ER exit is not resolved\",\n        \"In vivo confirmation of NLGN4Y non-compensation in a mammalian model is lacking\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"In melanoma, NLGN4X suppression was found to downregulate VBP1, causing HIF1A accumulation and HIF1A-dependent migration, revealing an unexpected non-neuronal role for NLGN4X in tumor biology.\",\n      \"evidence\": \"Loss- and gain-of-function in melanoma cells; transcriptomics; tumorsphere grafting to human skin organoids\",\n      \"pmids\": [\"38902533\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism linking NLGN4X to VBP1 regulation is undefined\",\n        \"Relevance to in vivo melanoma progression not established beyond organoid model\",\n        \"Whether this pathway operates in other cancer types is unknown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Phosphorylation of NLGN4X at S712 by PKA (X-specific) and Cdk5 was shown to bidirectionally regulate spine morphogenesis and excitatory synaptic transmission, providing the first post-translational mechanism for dynamic modulation of NLGN4X synaptogenic function.\",\n      \"evidence\": \"In vitro kinase assays with mutagenesis; spine density imaging and mEPSC recordings in neurons expressing phospho-mimetic and phospho-null S712 mutants\",\n      \"pmids\": [\"40032531\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"In vivo relevance of S712 phosphorylation to behavior or circuit function not tested\",\n        \"Whether S712 phosphorylation affects neurexin binding affinity is unknown\",\n        \"Upstream signals triggering PKA- versus Cdk5-mediated phosphorylation at this site are not defined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis for the NLGN4X/NLGN4Y functional divergence, the identity of signals that dynamically regulate S712 phosphorylation in vivo, and whether the non-neuronal VBP1-HIF1A pathway represents a physiologically relevant NLGN4X function outside the nervous system.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No high-resolution structure of NLGN4X in complex with neurexin\",\n        \"In vivo phospho-S712 dynamics have not been measured\",\n        \"Non-neuronal functions lack independent replication\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"NRXN1\",\n      \"DLG4\",\n      \"VBP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}