{"gene":"CBLN4","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":2007,"finding":"Cbln4 is secreted as an N-linked glycoprotein and forms both homomeric and heteromeric complexes with other Cbln family members (Cbln1–Cbln3) in vitro; when co-expressed with Cbln1, heteromeric Cbln1/Cbln4 complexes alter each other's trafficking and secretion levels, suggesting that heteromerization modulates Cbln4 signaling pathways.","method":"Heterologous cell expression, co-immunoprecipitation, secretion assays, glycoprotein characterization","journal":"The European journal of neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal co-IP and secretion assay in single study, moderate evidence","pmids":["17331201"],"is_preprint":false},{"year":2011,"finding":"Cbln4 does not bind to neurexin α or β isoforms carrying the splice site 4 insert [NRXs(S4+)] at levels sufficient to induce synaptogenesis in cerebellar, hippocampal, or cortical neurons in vitro, distinguishing it functionally from Cbln1 and Cbln2.","method":"Cell-based synaptogenesis assay, binding assays with neurexin isoforms in cultured neurons","journal":"The European journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — replicated in two independent studies (PMID 21410790, 21356198) with binding and functional synaptogenesis assays","pmids":["21410790","21356198"],"is_preprint":false},{"year":2011,"finding":"Cbln4 shows only weak interaction with NRXN1α and β-NRXNs, selective for splice segment S4-containing variants; affinities measured by surface plasmon resonance are much lower than those of Cbln1 or Cbln2, and Cbln4 exhibits little synaptogenic activity in cortical neuron cultures.","method":"Surface plasmon resonance, cell-based presynaptic differentiation assay with cortical neurons","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 — quantitative SPR binding assay plus functional synaptogenesis readout, consistent with independent replication","pmids":["21356198"],"is_preprint":false},{"year":2012,"finding":"Cbln4 (but not Cbln1 or Cbln2) binds selectively to the netrin receptor DCC in a netrin-displaceable fashion, identified in a candidate receptor-screening assay; Cbln1/Cbln4 heteromeric complexes show greatly reduced DCC affinity but increased neurexin affinity compared with Cbln4 alone, demonstrating subunit composition-dependent receptor specificity.","method":"Candidate receptor-screening binding assay, co-immunoprecipitation of heteromeric complexes, Cbln4-null mouse generation and phenotypic analysis","journal":"Journal of neurochemistry","confidence":"High","confidence_rationale":"Tier 2 — binding assay with competition, heteromer co-IP, and in vivo KO validation in single study with multiple orthogonal methods","pmids":["22220752"],"is_preprint":false},{"year":2014,"finding":"CBLN4 binds to DCC within the membrane-proximal fibronectin domains (FN4-6), competing with Netrin-1 at an overlapping binding site but with ~5-fold lower affinity; CBLN4 also binds DCC homolog Neogenin-1 with lower affinity. CBLN4-null mice show a transient increase in wandering axons in the brachial plexus, consistent with a role in axon guidance.","method":"Extracellular protein microarray interaction screen, immunofluorescence, radio-ligand binding competition assay, CBLN4-null mouse analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1-2 — quantitative radio-ligand competition binding plus domain mapping plus in vivo KO phenotype","pmids":["24400119"],"is_preprint":false},{"year":2014,"finding":"Cbln4 promotes the formation and maintenance of inhibitory GABAergic synapses in cultured hippocampal neurons; overexpression or exogenous application increases GABAergic varicosities, while Cbln4 knockdown reduces GABAergic connections reversible by exogenous Cbln4. Cbln4 expression is downstream of the Hes1 transcription factor (itself NGF-regulated) and is associated with GABAergic synapses in CA1 pyramidal neurons in vivo.","method":"Gain-of-function (overexpression, recombinant protein), loss-of-function (shRNA knockdown), immunocytochemistry, in vivo immunostaining in AD mouse model","journal":"Neurobiology of aging","confidence":"Medium","confidence_rationale":"Tier 2 — multiple complementary gain/loss-of-function experiments in single study with defined synaptic phenotype","pmids":["25534236"],"is_preprint":false},{"year":2017,"finding":"Crystal structures of the homotrimeric C1q domains of Cbln1 (2.2 Å) and Cbln4 (2.3 Å) reveal that structural divergence in loop CD explains why Cbln4 cannot bind GluD2 despite ~70% sequence identity with Cbln1. Negative-stain EM reconstruction of the Cbln4/Nrxn1β complex (~19 Å) shows that Nrxn1β binds to the N-terminal region of Cbln4 through strand β10 of the S4 insert, and Cbln4 forms a stable complex with the LNS domain of Nrxn1β.","method":"X-ray crystallography, negative-stain electron microscopy, in vitro binding assay (SPR/pull-down with Nrxn1β LNS domain)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — crystal structures plus EM reconstruction plus in vitro binding validation in single study","pmids":["28877468"],"is_preprint":false},{"year":2018,"finding":"Glycosylation of Cbln4 at two N-linked sites attenuates receptor binding: mutation of the N-terminal glycosylation site increases neurexin binding, while mutation of the C1q-domain site markedly increases GluD2 binding. Transgenic expression of glycosylation mutants of Cbln4 completely rescued ataxia in Cbln1-null mice, demonstrating that native Cbln4 has intrinsic GluD2-binding activity that is masked by glycosylation.","method":"Site-directed mutagenesis of glycosylation sites, in vitro receptor binding assays, in vivo transgenic rescue of Cbln1-null phenotype","journal":"Brain research","confidence":"High","confidence_rationale":"Tier 1 — mutagenesis + in vitro binding + in vivo rescue, multiple orthogonal methods","pmids":["29782851"],"is_preprint":false},{"year":2018,"finding":"Genetic ablation of Cbln4 in combination with Cbln1 and Cbln2 (triple KO mice) results in salience-induced seizures and delayed loss of excitatory synapse density in hippocampus, striatum, and retrosplenial cortex, indicating that Cbln4 contributes to long-term synapse maintenance but is not required for initial synapse formation.","method":"Constitutive single, double, and triple KO mouse generation; behavioral phenotyping; synapse density quantification by electron microscopy/immunofluorescence","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — systematic KO combinatorics with quantified synaptic and behavioral phenotypes across multiple brain regions","pmids":["29691328"],"is_preprint":false},{"year":2016,"finding":"In parvalbumin-positive (PV+) interneurons of the mouse hippocampus, Cbln4 is co-expressed with a specific neurexin splice isoform (lacking Slm2-dependent S4 insert), forming a ligand-receptor pair that is cell-type specific. Conditional ablation of neurexin alternative splice insertions selectively in PV+ cells elevates hippocampal network activity and impairs learning, placing Cbln4/neurexin alternative splicing in a circuit-function pathway.","method":"Cell-type-specific RNA profiling, conditional neurexin splice-site ablation in PV+ cells, electrophysiology, behavioral testing","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — cell-type-specific KO with electrophysiology and behavioral phenotypes plus molecular expression data","pmids":["27960072"],"is_preprint":false},{"year":2022,"finding":"Presynaptic Cbln4 (expressed in entorhinal cortex neurons and bound to neurexins) forms transcellular complexes with postsynaptic neogenin-1 (expressed in dentate gyrus granule cells) and is essential for long-term potentiation (LTP) at entorhinal cortex→dentate gyrus synapses without affecting basal synaptic transmission; conditional deletion of neogenin-1 in dentate granule cells phenocopies Cbln4 deletion, establishing a Cbln4–neogenin-1 trans-synaptic signaling axis for LTP.","method":"Conditional KO mice (presynaptic Cbln4, postsynaptic neogenin-1), in vivo LTP recordings at EC→DG synapses, epistasis/phenocopy analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with presynaptic and postsynaptic conditional KOs plus electrophysiological LTP readout","pmids":["35544694"],"is_preprint":false},{"year":2024,"finding":"METTL14-mediated m6A methylation stabilizes CBLN4 mRNA; knockdown of METTL14 reduces CBLN4 mRNA stability and expression in Aβ1-42-treated SK-N-SH cells, and upregulation of CBLN4 protects neurons from Aβ1-42-induced apoptosis, inflammation, oxidative stress, and ER stress.","method":"MeRIP (methylated RNA immunoprecipitation), dual-luciferase reporter assay, siRNA knockdown, overexpression, MTT/flow cytometry apoptosis assay, ELISA, Western blot","journal":"Journal of bioenergetics and biomembranes","confidence":"Medium","confidence_rationale":"Tier 2 — MeRIP plus reporter assay validate m6A site; functional rescue in cell model; single lab study","pmids":["39235700"],"is_preprint":false},{"year":2009,"finding":"Cbln4 expression in Sertoli cells of the developing gonad is directly regulated by SRY and SOX9 transcription factors; chromatin immunoprecipitation identified a SRY-binding site 7.5 kb upstream of the Cbln4 transcriptional start site, and overexpression or reduction of Sox9 correspondingly upregulates or downregulates Cbln4 expression in vivo.","method":"Chromatin immunoprecipitation (ChIP), transgenic mouse overexpression and reduction of Sox9, in vivo ectopic SRY expression","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP identifies direct binding, in vivo gain/loss-of-function confirms regulatory relationship","pmids":["19211811"],"is_preprint":false},{"year":2024,"finding":"A variant in the GRID1 distal amino-terminal domain at a position predicted to contact Cbln2/Cbln4 disrupts complex formation between GluD1 and Cbln2 in biochemical assays, demonstrating that the GRID1 amino-terminal domain mediates physical interaction with Cbln family members including Cbln4.","method":"Biochemical co-immunoprecipitation/pull-down assay, electrophysiology, site-directed mutagenesis","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — direct binding disruption assay with mutagenesis in single study; specific to Cbln2 but implicates Cbln4 interaction site","pmids":["37944084"],"is_preprint":false},{"year":2026,"finding":"Single-cell transcriptomic atlas analysis across 17 mouse developmental stages identifies NEOGENIN-1 as the principal postsynaptic receptor for CBLN4 during the perinatal period, mediating synapse formation between somatostatin-expressing interneurons and glutamatergic neurons in the cortex.","method":"Single-cell RNA sequencing across developmental stages, ligand-receptor interaction inference, conditional genetic strategy","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 3 — transcriptomic ligand-receptor inference supported by conditional genetics, consistent with PMID 35544694 but cortical context is new; single study","pmids":["41565644"],"is_preprint":false}],"current_model":"CBLN4 is a secreted hexameric glycoprotein that functions as a trans-synaptic organizer: it binds presynaptic neurexins (with selectivity for S4-containing isoforms but lower affinity than Cbln1/2) and postsynaptic neogenin-1 (and DCC) to form transcellular complexes that are essential for long-term potentiation at entorhinal cortex→dentate gyrus synapses and for promoting inhibitory GABAergic synapse formation; its intrinsic GluD2-binding activity is masked by N-linked glycosylation, its mRNA stability is regulated by METTL14-mediated m6A methylation, its expression is directly controlled by SRY/SOX9 in the developing testis, and it heterodimerizes with other Cbln family members to modulate receptor-binding specificity in a subunit composition-dependent manner."},"narrative":{"teleology":[{"year":2007,"claim":"Establishing that CBLN4 is a secreted glycoprotein capable of heteromerizing with other cerebellin family members answered whether CBLN4 acts as a soluble signaling molecule and whether its function could be modulated by co-expression with paralogues.","evidence":"Heterologous cell expression, co-immunoprecipitation, and secretion assays in cultured cells","pmids":["17331201"],"confidence":"Medium","gaps":["Stoichiometry and assembly mechanism of heteromeric complexes not determined","In vivo relevance of heteromerization not tested","Receptor binding of heteromers not assessed"]},{"year":2009,"claim":"Demonstrating direct SRY/SOX9 transcriptional regulation of Cbln4 in Sertoli cells revealed a non-neuronal role and identified the first upstream regulators of Cbln4 expression.","evidence":"Chromatin immunoprecipitation identifying SRY binding site, in vivo Sox9 gain/loss-of-function in transgenic mice","pmids":["19211811"],"confidence":"High","gaps":["Downstream function of Cbln4 in gonadal development remains unknown","Whether DCC/neogenin-1 signaling is relevant in Sertoli cells not tested"]},{"year":2011,"claim":"Quantitative binding measurements showed that CBLN4 interacts with neurexins carrying the S4 splice insert but with much lower affinity than CBLN1/2, and lacks synaptogenic activity in standard assays, distinguishing it functionally from other family members.","evidence":"Surface plasmon resonance with neurexin isoforms, cell-based synaptogenesis assays in cerebellar/hippocampal/cortical neurons","pmids":["21410790","21356198"],"confidence":"High","gaps":["Why CBLN4 retains weak neurexin binding despite poor synaptogenic activity unclear","Alternative postsynaptic receptors not yet identified"]},{"year":2012,"claim":"Identification of DCC as a selective receptor for CBLN4 (but not CBLN1/2) that competes with netrin, combined with the finding that heteromerization with CBLN1 shifts binding from DCC toward neurexin, established subunit composition–dependent receptor specificity as a key regulatory principle.","evidence":"Candidate receptor screen, competition binding, heteromeric co-IP, Cbln4-null mouse generation","pmids":["22220752"],"confidence":"High","gaps":["Functional consequence of DCC engagement by CBLN4 at synapses not determined","In vivo validation of subunit-dependent receptor switching not performed"]},{"year":2014,"claim":"Domain mapping of the CBLN4–DCC interaction to fibronectin domains FN4-6 and demonstration that CBLN4-null mice show transient axon guidance defects linked CBLN4/DCC binding to an in vivo developmental role, while parallel work showed CBLN4 promotes GABAergic synapse formation and maintenance in hippocampal neurons.","evidence":"Radio-ligand competition binding, extracellular protein microarray, CBLN4-null mouse phenotyping, shRNA knockdown and rescue in cultured hippocampal neurons","pmids":["24400119","25534236"],"confidence":"High","gaps":["Molecular mechanism by which CBLN4 promotes inhibitory synapse formation not defined","Whether DCC and neogenin-1 mediate the GABAergic synaptogenic effect unknown"]},{"year":2016,"claim":"Cell-type-specific expression profiling revealed that Cbln4 is co-expressed in parvalbumin-positive interneurons with a specific neurexin splice isoform, placing the Cbln4–neurexin pair in a molecularly defined circuit element whose disruption elevates network activity and impairs learning.","evidence":"PV+ cell-specific RNA profiling, conditional neurexin splice-site ablation, electrophysiology, behavioral testing in mice","pmids":["27960072"],"confidence":"High","gaps":["Direct demonstration that Cbln4 is the functional ligand in PV+ interneurons (rather than other Cbln family members) not provided","Postsynaptic receptor in this circuit not identified"]},{"year":2017,"claim":"Crystal structures of the Cbln4 C1q trimer and an EM reconstruction of the Cbln4/Nrxn1β complex resolved why Cbln4 cannot bind GluD2 (structural divergence in loop CD) and how neurexin engages the N-terminal region of Cbln4 via strand β10 of the S4 insert.","evidence":"X-ray crystallography at 2.3 Å, negative-stain EM at ~19 Å, SPR/pull-down validation","pmids":["28877468"],"confidence":"High","gaps":["High-resolution structure of the ternary neurexin–Cbln4–postsynaptic receptor complex not obtained","Structural basis for DCC/neogenin-1 binding to Cbln4 not resolved"]},{"year":2018,"claim":"Mutagenesis of two N-linked glycosylation sites unmasked intrinsic GluD2-binding and enhanced neurexin-binding activities of CBLN4, and glycosylation-deficient CBLN4 fully rescued ataxia in Cbln1-null mice, establishing glycosylation as the principal mechanism that restricts CBLN4's receptor engagement in vivo.","evidence":"Site-directed glycosylation-site mutagenesis, in vitro receptor binding, transgenic rescue of Cbln1-null ataxia","pmids":["29782851"],"confidence":"High","gaps":["Physiological conditions under which glycosylation is dynamically regulated are unknown","Whether deglycosylation occurs in vivo at specific synapses not tested"]},{"year":2018,"claim":"Combinatorial knockout of Cbln1/2/4 demonstrated that the cerebellin family collectively maintains excitatory synapse density long-term and prevents seizures, with CBLN4 contributing to synapse maintenance but not initial formation.","evidence":"Single, double, and triple constitutive KO mice; EM and immunofluorescence synapse quantification; behavioral seizure phenotyping","pmids":["29691328"],"confidence":"High","gaps":["Individual contribution of CBLN4 versus redundancy with CBLN1/2 not fully dissected","Molecular mechanism of delayed synapse loss not identified"]},{"year":2022,"claim":"Conditional deletion experiments established that presynaptic CBLN4 and postsynaptic neogenin-1 form a trans-synaptic signaling axis essential for LTP at entorhinal cortex→dentate gyrus synapses, resolving the long-sought postsynaptic receptor for CBLN4 in this circuit.","evidence":"Conditional KO of Cbln4 (presynaptic) and neogenin-1 (postsynaptic) in mice, in vivo LTP recordings, epistasis analysis","pmids":["35544694"],"confidence":"High","gaps":["Downstream signaling cascade activated by neogenin-1 upon CBLN4 binding not characterized","Whether this LTP mechanism generalizes beyond EC→DG synapses unknown"]},{"year":2024,"claim":"Identification of METTL14-mediated m6A methylation as a stabilizer of CBLN4 mRNA linked epitranscriptomic regulation to CBLN4 expression levels and neuroprotective function in an Aβ-toxicity model, while a GRID1 amino-terminal domain variant confirmed that GluD1 physically contacts the Cbln2/4 interaction surface.","evidence":"MeRIP and dual-luciferase reporter assays in SK-N-SH cells; co-IP/mutagenesis of GRID1–Cbln complex","pmids":["39235700","37944084"],"confidence":"Medium","gaps":["In vivo relevance of m6A regulation of CBLN4 not demonstrated","Whether CBLN4 directly binds GluD1 under native glycosylation conditions not tested","Neuroprotective mechanism downstream of CBLN4 not defined"]},{"year":null,"claim":"Key unresolved questions include: (1) the structural basis of the CBLN4–neogenin-1/DCC interaction, (2) the intracellular signaling cascade triggered by this trans-synaptic complex to enable LTP, (3) whether CBLN4 glycosylation is dynamically regulated at specific synapses, and (4) the functional role of CBLN4 in non-neuronal tissues such as the developing gonad.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of CBLN4 bound to neogenin-1 or DCC","Intracellular signaling downstream of neogenin-1 upon CBLN4 binding uncharacterized","Dynamic regulation of CBLN4 glycosylation in vivo not studied"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[3,4,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,7,8]}],"localization":[{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[0,3,4]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[5,9,10]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,12]}],"complexes":[],"partners":["NRXN1","DCC","NEO1","CBLN1","CBLN2","CBLN3","GRID1","GRID2"],"other_free_text":[]},"mechanistic_narrative":"CBLN4 is a secreted glycoprotein of the cerebellin family that functions as a trans-synaptic organizer, bridging presynaptic neurexins and postsynaptic netrin receptors (DCC and neogenin-1) to regulate synapse specificity, maintenance, and plasticity. CBLN4 binds neurexins with low affinity through S4-containing splice variants and selectively engages DCC and neogenin-1 via their membrane-proximal fibronectin domains; N-linked glycosylation at two sites masks an intrinsic GluD2-binding capacity, and heteromerization with other Cbln family members shifts receptor-binding specificity in a subunit composition–dependent manner [PMID:28877468, PMID:29782851, PMID:22220752, PMID:17331201]. At entorhinal cortex→dentate gyrus synapses, a presynaptic CBLN4–postsynaptic neogenin-1 trans-synaptic complex is essential for long-term potentiation without affecting basal transmission, while CBLN4 also promotes inhibitory GABAergic synapse formation in hippocampal neurons and contributes to long-term excitatory synapse maintenance as revealed by combinatorial knockout analyses [PMID:35544694, PMID:25534236, PMID:29691328]. Outside the nervous system, CBLN4 expression in Sertoli cells is directly regulated by SRY and SOX9 during gonadal development [PMID:19211811]."},"prefetch_data":{"uniprot":{"accession":"Q9NTU7","full_name":"Cerebellin-4","aliases":["Cerebellin-like glycoprotein 1"],"length_aa":201,"mass_kda":21.8,"function":"Acts as a synaptic organizer in specific subsets of neurons in the brain (By similarity). Essential for the formation and maintenance of inhibitory GABAergic synapses (By similarity). Promotes the development of dendrite-targeting inhibitory GABAergic synapses made by somatostatin-positive interneurons (By similarity). May contribute to the function of ventral medial habenula region of the brain implicated in the regulation of anxiety-related behaviors (By similarity). May play a role in CBLN3 export from the endoplasmic reticulum and secretion (By similarity)","subcellular_location":"Secreted; Synapse","url":"https://www.uniprot.org/uniprotkb/Q9NTU7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CBLN4","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/CBLN4","total_profiled":1310},"omim":[{"mim_id":"621480","title":"OTOLIN 1; OTOL1","url":"https://www.omim.org/entry/621480"},{"mim_id":"615029","title":"PRECEREBELLIN 4; CBLN4","url":"https://www.omim.org/entry/615029"},{"mim_id":"612978","title":"PRECEREBELLIN 3; CBLN3","url":"https://www.omim.org/entry/612978"},{"mim_id":"600433","title":"PRECEREBELLIN 2; CBLN2","url":"https://www.omim.org/entry/600433"},{"mim_id":"600432","title":"PRECEREBELLIN 1; CBLN1","url":"https://www.omim.org/entry/600432"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Flagellar centriole","reliability":"Approved"},{"location":"Mid piece","reliability":"Approved"},{"location":"Principal piece","reliability":"Approved"},{"location":"Perinuclear theca","reliability":"Additional"},{"location":"Calyx","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"adrenal gland","ntpm":16.8},{"tissue":"brain","ntpm":15.6},{"tissue":"epididymis","ntpm":8.3}],"url":"https://www.proteinatlas.org/search/CBLN4"},"hgnc":{"alias_symbol":["dJ885A10.1"],"prev_symbol":["CBLNL1"]},"alphafold":{"accession":"Q9NTU7","domains":[{"cath_id":"2.60.120.40","chopping":"71-199","consensus_level":"medium","plddt":93.8846,"start":71,"end":199}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NTU7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NTU7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NTU7-F1-predicted_aligned_error_v6.png","plddt_mean":78.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CBLN4","jax_strain_url":"https://www.jax.org/strain/search?query=CBLN4"},"sequence":{"accession":"Q9NTU7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NTU7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NTU7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NTU7"}},"corpus_meta":[{"pmid":"21410790","id":"PMC_21410790","title":"Cbln family proteins promote synapse formation by regulating distinct neurexin signaling pathways in various brain regions.","date":"2011","source":"The European journal of neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/21410790","citation_count":132,"is_preprint":false},{"pmid":"16930405","id":"PMC_16930405","title":"Distinct expression of Cbln family mRNAs in developing and adult mouse brains.","date":"2006","source":"The European journal of neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/16930405","citation_count":92,"is_preprint":false},{"pmid":"27960072","id":"PMC_27960072","title":"An alternative splicing switch shapes neurexin repertoires in principal neurons versus interneurons in the mouse hippocampus.","date":"2016","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/27960072","citation_count":67,"is_preprint":false},{"pmid":"18278437","id":"PMC_18278437","title":"Cbln and C1q family proteins: new transneuronal cytokines.","date":"2008","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/18278437","citation_count":64,"is_preprint":false},{"pmid":"29691328","id":"PMC_29691328","title":"Genetic Ablation of All Cerebellins Reveals Synapse Organizer Functions in Multiple Regions Throughout the Brain.","date":"2018","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/29691328","citation_count":57,"is_preprint":false},{"pmid":"31816601","id":"PMC_31816601","title":"Identification of molecular correlations of RBM8A with autophagy in Alzheimer's disease.","date":"2019","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/31816601","citation_count":54,"is_preprint":false},{"pmid":"28714144","id":"PMC_28714144","title":"Cerebellins are differentially expressed in selective subsets of neurons throughout the brain.","date":"2017","source":"The Journal of comparative neurology","url":"https://pubmed.ncbi.nlm.nih.gov/28714144","citation_count":53,"is_preprint":false},{"pmid":"22220752","id":"PMC_22220752","title":"The Cbln family of proteins interact with multiple signaling pathways.","date":"2012","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22220752","citation_count":50,"is_preprint":false},{"pmid":"17331201","id":"PMC_17331201","title":"Characterization of a transneuronal cytokine family Cbln--regulation of secretion by heteromeric assembly.","date":"2007","source":"The European journal of neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/17331201","citation_count":47,"is_preprint":false},{"pmid":"24400119","id":"PMC_24400119","title":"Defining the ligand specificity of the deleted in colorectal cancer (DCC) receptor.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24400119","citation_count":46,"is_preprint":false},{"pmid":"21356198","id":"PMC_21356198","title":"Differential interactions of cerebellin precursor protein (Cbln) subtypes and neurexin variants for synapse formation of cortical neurons.","date":"2011","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21356198","citation_count":45,"is_preprint":false},{"pmid":"19211811","id":"PMC_19211811","title":"The cerebellin 4 precursor gene is a direct target of SRY and SOX9 in mice.","date":"2009","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/19211811","citation_count":40,"is_preprint":false},{"pmid":"37004850","id":"PMC_37004850","title":"GluN2D Subunit in Parvalbumin Interneurons Regulates Prefrontal Cortex Feedforward Inhibitory Circuit and Molecular Networks Relevant to Schizophrenia.","date":"2023","source":"Biological psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/37004850","citation_count":34,"is_preprint":false},{"pmid":"30443963","id":"PMC_30443963","title":"Antibiotics suppress colon tumorigenesis through inhibition of 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medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19082514","citation_count":14,"is_preprint":false},{"pmid":"37944084","id":"PMC_37944084","title":"Clinical features, functional consequences, and rescue pharmacology of missense GRID1 and GRID2 human variants.","date":"2024","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37944084","citation_count":12,"is_preprint":false},{"pmid":"19481574","id":"PMC_19481574","title":"Insulinostatic activity of cerebellin--evidence from in vivo and in vitro studies in rats.","date":"2009","source":"Regulatory peptides","url":"https://pubmed.ncbi.nlm.nih.gov/19481574","citation_count":12,"is_preprint":false},{"pmid":"29705514","id":"PMC_29705514","title":"Spinal injection of newly identified cerebellin-1 and cerebellin-2 peptides induce mechanical hypersensitivity in mice.","date":"2018","source":"Neuropeptides","url":"https://pubmed.ncbi.nlm.nih.gov/29705514","citation_count":11,"is_preprint":false},{"pmid":"18717966","id":"PMC_18717966","title":"Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig.","date":"2008","source":"Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie","url":"https://pubmed.ncbi.nlm.nih.gov/18717966","citation_count":10,"is_preprint":false},{"pmid":"23853053","id":"PMC_23853053","title":"Parcellation of cerebellins 1, 2, and 4 among different subpopulations of dorsal horn neurons in mouse spinal cord.","date":"2014","source":"The Journal of comparative neurology","url":"https://pubmed.ncbi.nlm.nih.gov/23853053","citation_count":9,"is_preprint":false},{"pmid":"32855654","id":"PMC_32855654","title":"Integrated Genome-Wide Methylation and Expression Analyses Reveal Key Regulators in Osteosarcoma.","date":"2020","source":"Computational and 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corticosteroidogenesis.","date":"2009","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19212655","citation_count":7,"is_preprint":false},{"pmid":"37215503","id":"PMC_37215503","title":"Cortical interneurons: fit for function and fit to function? 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when co-expressed with Cbln1, heteromeric Cbln1/Cbln4 complexes alter each other's trafficking and secretion levels, suggesting that heteromerization modulates Cbln4 signaling pathways.\",\n      \"method\": \"Heterologous cell expression, co-immunoprecipitation, secretion assays, glycoprotein characterization\",\n      \"journal\": \"The European journal of neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP and secretion assay in single study, moderate evidence\",\n      \"pmids\": [\"17331201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Cbln4 does not bind to neurexin α or β isoforms carrying the splice site 4 insert [NRXs(S4+)] at levels sufficient to induce synaptogenesis in cerebellar, hippocampal, or cortical neurons in vitro, distinguishing it functionally from Cbln1 and Cbln2.\",\n      \"method\": \"Cell-based synaptogenesis assay, binding assays with neurexin isoforms in cultured neurons\",\n      \"journal\": \"The European journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — replicated in two independent studies (PMID 21410790, 21356198) with binding and functional synaptogenesis assays\",\n      \"pmids\": [\"21410790\", \"21356198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Cbln4 shows only weak interaction with NRXN1α and β-NRXNs, selective for splice segment S4-containing variants; affinities measured by surface plasmon resonance are much lower than those of Cbln1 or Cbln2, and Cbln4 exhibits little synaptogenic activity in cortical neuron cultures.\",\n      \"method\": \"Surface plasmon resonance, cell-based presynaptic differentiation assay with cortical neurons\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — quantitative SPR binding assay plus functional synaptogenesis readout, consistent with independent replication\",\n      \"pmids\": [\"21356198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Cbln4 (but not Cbln1 or Cbln2) binds selectively to the netrin receptor DCC in a netrin-displaceable fashion, identified in a candidate receptor-screening assay; Cbln1/Cbln4 heteromeric complexes show greatly reduced DCC affinity but increased neurexin affinity compared with Cbln4 alone, demonstrating subunit composition-dependent receptor specificity.\",\n      \"method\": \"Candidate receptor-screening binding assay, co-immunoprecipitation of heteromeric complexes, Cbln4-null mouse generation and phenotypic analysis\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — binding assay with competition, heteromer co-IP, and in vivo KO validation in single study with multiple orthogonal methods\",\n      \"pmids\": [\"22220752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CBLN4 binds to DCC within the membrane-proximal fibronectin domains (FN4-6), competing with Netrin-1 at an overlapping binding site but with ~5-fold lower affinity; CBLN4 also binds DCC homolog Neogenin-1 with lower affinity. CBLN4-null mice show a transient increase in wandering axons in the brachial plexus, consistent with a role in axon guidance.\",\n      \"method\": \"Extracellular protein microarray interaction screen, immunofluorescence, radio-ligand binding competition assay, CBLN4-null mouse analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — quantitative radio-ligand competition binding plus domain mapping plus in vivo KO phenotype\",\n      \"pmids\": [\"24400119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Cbln4 promotes the formation and maintenance of inhibitory GABAergic synapses in cultured hippocampal neurons; overexpression or exogenous application increases GABAergic varicosities, while Cbln4 knockdown reduces GABAergic connections reversible by exogenous Cbln4. Cbln4 expression is downstream of the Hes1 transcription factor (itself NGF-regulated) and is associated with GABAergic synapses in CA1 pyramidal neurons in vivo.\",\n      \"method\": \"Gain-of-function (overexpression, recombinant protein), loss-of-function (shRNA knockdown), immunocytochemistry, in vivo immunostaining in AD mouse model\",\n      \"journal\": \"Neurobiology of aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple complementary gain/loss-of-function experiments in single study with defined synaptic phenotype\",\n      \"pmids\": [\"25534236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structures of the homotrimeric C1q domains of Cbln1 (2.2 Å) and Cbln4 (2.3 Å) reveal that structural divergence in loop CD explains why Cbln4 cannot bind GluD2 despite ~70% sequence identity with Cbln1. Negative-stain EM reconstruction of the Cbln4/Nrxn1β complex (~19 Å) shows that Nrxn1β binds to the N-terminal region of Cbln4 through strand β10 of the S4 insert, and Cbln4 forms a stable complex with the LNS domain of Nrxn1β.\",\n      \"method\": \"X-ray crystallography, negative-stain electron microscopy, in vitro binding assay (SPR/pull-down with Nrxn1β LNS domain)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures plus EM reconstruction plus in vitro binding validation in single study\",\n      \"pmids\": [\"28877468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Glycosylation of Cbln4 at two N-linked sites attenuates receptor binding: mutation of the N-terminal glycosylation site increases neurexin binding, while mutation of the C1q-domain site markedly increases GluD2 binding. Transgenic expression of glycosylation mutants of Cbln4 completely rescued ataxia in Cbln1-null mice, demonstrating that native Cbln4 has intrinsic GluD2-binding activity that is masked by glycosylation.\",\n      \"method\": \"Site-directed mutagenesis of glycosylation sites, in vitro receptor binding assays, in vivo transgenic rescue of Cbln1-null phenotype\",\n      \"journal\": \"Brain research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mutagenesis + in vitro binding + in vivo rescue, multiple orthogonal methods\",\n      \"pmids\": [\"29782851\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Genetic ablation of Cbln4 in combination with Cbln1 and Cbln2 (triple KO mice) results in salience-induced seizures and delayed loss of excitatory synapse density in hippocampus, striatum, and retrosplenial cortex, indicating that Cbln4 contributes to long-term synapse maintenance but is not required for initial synapse formation.\",\n      \"method\": \"Constitutive single, double, and triple KO mouse generation; behavioral phenotyping; synapse density quantification by electron microscopy/immunofluorescence\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic KO combinatorics with quantified synaptic and behavioral phenotypes across multiple brain regions\",\n      \"pmids\": [\"29691328\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In parvalbumin-positive (PV+) interneurons of the mouse hippocampus, Cbln4 is co-expressed with a specific neurexin splice isoform (lacking Slm2-dependent S4 insert), forming a ligand-receptor pair that is cell-type specific. Conditional ablation of neurexin alternative splice insertions selectively in PV+ cells elevates hippocampal network activity and impairs learning, placing Cbln4/neurexin alternative splicing in a circuit-function pathway.\",\n      \"method\": \"Cell-type-specific RNA profiling, conditional neurexin splice-site ablation in PV+ cells, electrophysiology, behavioral testing\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — cell-type-specific KO with electrophysiology and behavioral phenotypes plus molecular expression data\",\n      \"pmids\": [\"27960072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Presynaptic Cbln4 (expressed in entorhinal cortex neurons and bound to neurexins) forms transcellular complexes with postsynaptic neogenin-1 (expressed in dentate gyrus granule cells) and is essential for long-term potentiation (LTP) at entorhinal cortex→dentate gyrus synapses without affecting basal synaptic transmission; conditional deletion of neogenin-1 in dentate granule cells phenocopies Cbln4 deletion, establishing a Cbln4–neogenin-1 trans-synaptic signaling axis for LTP.\",\n      \"method\": \"Conditional KO mice (presynaptic Cbln4, postsynaptic neogenin-1), in vivo LTP recordings at EC→DG synapses, epistasis/phenocopy analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with presynaptic and postsynaptic conditional KOs plus electrophysiological LTP readout\",\n      \"pmids\": [\"35544694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"METTL14-mediated m6A methylation stabilizes CBLN4 mRNA; knockdown of METTL14 reduces CBLN4 mRNA stability and expression in Aβ1-42-treated SK-N-SH cells, and upregulation of CBLN4 protects neurons from Aβ1-42-induced apoptosis, inflammation, oxidative stress, and ER stress.\",\n      \"method\": \"MeRIP (methylated RNA immunoprecipitation), dual-luciferase reporter assay, siRNA knockdown, overexpression, MTT/flow cytometry apoptosis assay, ELISA, Western blot\",\n      \"journal\": \"Journal of bioenergetics and biomembranes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MeRIP plus reporter assay validate m6A site; functional rescue in cell model; single lab study\",\n      \"pmids\": [\"39235700\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Cbln4 expression in Sertoli cells of the developing gonad is directly regulated by SRY and SOX9 transcription factors; chromatin immunoprecipitation identified a SRY-binding site 7.5 kb upstream of the Cbln4 transcriptional start site, and overexpression or reduction of Sox9 correspondingly upregulates or downregulates Cbln4 expression in vivo.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), transgenic mouse overexpression and reduction of Sox9, in vivo ectopic SRY expression\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP identifies direct binding, in vivo gain/loss-of-function confirms regulatory relationship\",\n      \"pmids\": [\"19211811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A variant in the GRID1 distal amino-terminal domain at a position predicted to contact Cbln2/Cbln4 disrupts complex formation between GluD1 and Cbln2 in biochemical assays, demonstrating that the GRID1 amino-terminal domain mediates physical interaction with Cbln family members including Cbln4.\",\n      \"method\": \"Biochemical co-immunoprecipitation/pull-down assay, electrophysiology, site-directed mutagenesis\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct binding disruption assay with mutagenesis in single study; specific to Cbln2 but implicates Cbln4 interaction site\",\n      \"pmids\": [\"37944084\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Single-cell transcriptomic atlas analysis across 17 mouse developmental stages identifies NEOGENIN-1 as the principal postsynaptic receptor for CBLN4 during the perinatal period, mediating synapse formation between somatostatin-expressing interneurons and glutamatergic neurons in the cortex.\",\n      \"method\": \"Single-cell RNA sequencing across developmental stages, ligand-receptor interaction inference, conditional genetic strategy\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — transcriptomic ligand-receptor inference supported by conditional genetics, consistent with PMID 35544694 but cortical context is new; single study\",\n      \"pmids\": [\"41565644\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CBLN4 is a secreted hexameric glycoprotein that functions as a trans-synaptic organizer: it binds presynaptic neurexins (with selectivity for S4-containing isoforms but lower affinity than Cbln1/2) and postsynaptic neogenin-1 (and DCC) to form transcellular complexes that are essential for long-term potentiation at entorhinal cortex→dentate gyrus synapses and for promoting inhibitory GABAergic synapse formation; its intrinsic GluD2-binding activity is masked by N-linked glycosylation, its mRNA stability is regulated by METTL14-mediated m6A methylation, its expression is directly controlled by SRY/SOX9 in the developing testis, and it heterodimerizes with other Cbln family members to modulate receptor-binding specificity in a subunit composition-dependent manner.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CBLN4 is a secreted glycoprotein of the cerebellin family that functions as a trans-synaptic organizer, bridging presynaptic neurexins and postsynaptic netrin receptors (DCC and neogenin-1) to regulate synapse specificity, maintenance, and plasticity. CBLN4 binds neurexins with low affinity through S4-containing splice variants and selectively engages DCC and neogenin-1 via their membrane-proximal fibronectin domains; N-linked glycosylation at two sites masks an intrinsic GluD2-binding capacity, and heteromerization with other Cbln family members shifts receptor-binding specificity in a subunit composition–dependent manner [PMID:28877468, PMID:29782851, PMID:22220752, PMID:17331201]. At entorhinal cortex→dentate gyrus synapses, a presynaptic CBLN4–postsynaptic neogenin-1 trans-synaptic complex is essential for long-term potentiation without affecting basal transmission, while CBLN4 also promotes inhibitory GABAergic synapse formation in hippocampal neurons and contributes to long-term excitatory synapse maintenance as revealed by combinatorial knockout analyses [PMID:35544694, PMID:25534236, PMID:29691328]. Outside the nervous system, CBLN4 expression in Sertoli cells is directly regulated by SRY and SOX9 during gonadal development [PMID:19211811].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing that CBLN4 is a secreted glycoprotein capable of heteromerizing with other cerebellin family members answered whether CBLN4 acts as a soluble signaling molecule and whether its function could be modulated by co-expression with paralogues.\",\n      \"evidence\": \"Heterologous cell expression, co-immunoprecipitation, and secretion assays in cultured cells\",\n      \"pmids\": [\"17331201\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stoichiometry and assembly mechanism of heteromeric complexes not determined\", \"In vivo relevance of heteromerization not tested\", \"Receptor binding of heteromers not assessed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrating direct SRY/SOX9 transcriptional regulation of Cbln4 in Sertoli cells revealed a non-neuronal role and identified the first upstream regulators of Cbln4 expression.\",\n      \"evidence\": \"Chromatin immunoprecipitation identifying SRY binding site, in vivo Sox9 gain/loss-of-function in transgenic mice\",\n      \"pmids\": [\"19211811\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream function of Cbln4 in gonadal development remains unknown\", \"Whether DCC/neogenin-1 signaling is relevant in Sertoli cells not tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Quantitative binding measurements showed that CBLN4 interacts with neurexins carrying the S4 splice insert but with much lower affinity than CBLN1/2, and lacks synaptogenic activity in standard assays, distinguishing it functionally from other family members.\",\n      \"evidence\": \"Surface plasmon resonance with neurexin isoforms, cell-based synaptogenesis assays in cerebellar/hippocampal/cortical neurons\",\n      \"pmids\": [\"21410790\", \"21356198\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why CBLN4 retains weak neurexin binding despite poor synaptogenic activity unclear\", \"Alternative postsynaptic receptors not yet identified\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identification of DCC as a selective receptor for CBLN4 (but not CBLN1/2) that competes with netrin, combined with the finding that heteromerization with CBLN1 shifts binding from DCC toward neurexin, established subunit composition–dependent receptor specificity as a key regulatory principle.\",\n      \"evidence\": \"Candidate receptor screen, competition binding, heteromeric co-IP, Cbln4-null mouse generation\",\n      \"pmids\": [\"22220752\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of DCC engagement by CBLN4 at synapses not determined\", \"In vivo validation of subunit-dependent receptor switching not performed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Domain mapping of the CBLN4–DCC interaction to fibronectin domains FN4-6 and demonstration that CBLN4-null mice show transient axon guidance defects linked CBLN4/DCC binding to an in vivo developmental role, while parallel work showed CBLN4 promotes GABAergic synapse formation and maintenance in hippocampal neurons.\",\n      \"evidence\": \"Radio-ligand competition binding, extracellular protein microarray, CBLN4-null mouse phenotyping, shRNA knockdown and rescue in cultured hippocampal neurons\",\n      \"pmids\": [\"24400119\", \"25534236\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which CBLN4 promotes inhibitory synapse formation not defined\", \"Whether DCC and neogenin-1 mediate the GABAergic synaptogenic effect unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Cell-type-specific expression profiling revealed that Cbln4 is co-expressed in parvalbumin-positive interneurons with a specific neurexin splice isoform, placing the Cbln4–neurexin pair in a molecularly defined circuit element whose disruption elevates network activity and impairs learning.\",\n      \"evidence\": \"PV+ cell-specific RNA profiling, conditional neurexin splice-site ablation, electrophysiology, behavioral testing in mice\",\n      \"pmids\": [\"27960072\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct demonstration that Cbln4 is the functional ligand in PV+ interneurons (rather than other Cbln family members) not provided\", \"Postsynaptic receptor in this circuit not identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Crystal structures of the Cbln4 C1q trimer and an EM reconstruction of the Cbln4/Nrxn1β complex resolved why Cbln4 cannot bind GluD2 (structural divergence in loop CD) and how neurexin engages the N-terminal region of Cbln4 via strand β10 of the S4 insert.\",\n      \"evidence\": \"X-ray crystallography at 2.3 Å, negative-stain EM at ~19 Å, SPR/pull-down validation\",\n      \"pmids\": [\"28877468\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"High-resolution structure of the ternary neurexin–Cbln4–postsynaptic receptor complex not obtained\", \"Structural basis for DCC/neogenin-1 binding to Cbln4 not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Mutagenesis of two N-linked glycosylation sites unmasked intrinsic GluD2-binding and enhanced neurexin-binding activities of CBLN4, and glycosylation-deficient CBLN4 fully rescued ataxia in Cbln1-null mice, establishing glycosylation as the principal mechanism that restricts CBLN4's receptor engagement in vivo.\",\n      \"evidence\": \"Site-directed glycosylation-site mutagenesis, in vitro receptor binding, transgenic rescue of Cbln1-null ataxia\",\n      \"pmids\": [\"29782851\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological conditions under which glycosylation is dynamically regulated are unknown\", \"Whether deglycosylation occurs in vivo at specific synapses not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Combinatorial knockout of Cbln1/2/4 demonstrated that the cerebellin family collectively maintains excitatory synapse density long-term and prevents seizures, with CBLN4 contributing to synapse maintenance but not initial formation.\",\n      \"evidence\": \"Single, double, and triple constitutive KO mice; EM and immunofluorescence synapse quantification; behavioral seizure phenotyping\",\n      \"pmids\": [\"29691328\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Individual contribution of CBLN4 versus redundancy with CBLN1/2 not fully dissected\", \"Molecular mechanism of delayed synapse loss not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Conditional deletion experiments established that presynaptic CBLN4 and postsynaptic neogenin-1 form a trans-synaptic signaling axis essential for LTP at entorhinal cortex→dentate gyrus synapses, resolving the long-sought postsynaptic receptor for CBLN4 in this circuit.\",\n      \"evidence\": \"Conditional KO of Cbln4 (presynaptic) and neogenin-1 (postsynaptic) in mice, in vivo LTP recordings, epistasis analysis\",\n      \"pmids\": [\"35544694\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream signaling cascade activated by neogenin-1 upon CBLN4 binding not characterized\", \"Whether this LTP mechanism generalizes beyond EC→DG synapses unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identification of METTL14-mediated m6A methylation as a stabilizer of CBLN4 mRNA linked epitranscriptomic regulation to CBLN4 expression levels and neuroprotective function in an Aβ-toxicity model, while a GRID1 amino-terminal domain variant confirmed that GluD1 physically contacts the Cbln2/4 interaction surface.\",\n      \"evidence\": \"MeRIP and dual-luciferase reporter assays in SK-N-SH cells; co-IP/mutagenesis of GRID1–Cbln complex\",\n      \"pmids\": [\"39235700\", \"37944084\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo relevance of m6A regulation of CBLN4 not demonstrated\", \"Whether CBLN4 directly binds GluD1 under native glycosylation conditions not tested\", \"Neuroprotective mechanism downstream of CBLN4 not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: (1) the structural basis of the CBLN4–neogenin-1/DCC interaction, (2) the intracellular signaling cascade triggered by this trans-synaptic complex to enable LTP, (3) whether CBLN4 glycosylation is dynamically regulated at specific synapses, and (4) the functional role of CBLN4 in non-neuronal tissues such as the developing gonad.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of CBLN4 bound to neogenin-1 or DCC\", \"Intracellular signaling downstream of neogenin-1 upon CBLN4 binding uncharacterized\", \"Dynamic regulation of CBLN4 glycosylation in vivo not studied\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [3, 4, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 7, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [0, 3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0050804\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [5, 9, 10]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 12]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"NRXN1\",\n      \"DCC\",\n      \"NEO1\",\n      \"CBLN1\",\n      \"CBLN2\",\n      \"CBLN3\",\n      \"GRID1\",\n      \"GRID2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}