{"gene":"KIFBP","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":2005,"finding":"KIAA1279 encodes a protein with two tetratricopeptide repeat (TPR) domains, and homozygous nonsense mutations in KIAA1279 cause Goldberg-Shprintzen syndrome (GOSHS), establishing that KBP is essential for both enteric and central nervous system development.","method":"Homozygosity mapping and identification of truncating mutations in patients with GOSHS (microcephaly, polymicrogyria, Hirschsprung disease)","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human genetics with loss-of-function mutations establishing disease gene identity; single study but definitive gene-disease link with functional domain annotation","pmids":["15883926"],"is_preprint":false},{"year":2005,"finding":"KBP (KIF1 binding protein) interacts with KIF1Bα (a kinesin-3 family mitochondria-distributing motor) and co-immunoprecipitates with it from untransfected HEK293 cells. KBP localizes predominantly to mitochondria, and overexpression of a KBP deletion mutant or reduction of KBP via antisense causes mitochondrial aggregation, phenocopying reduced KIF1Bα motility activity.","method":"Yeast two-hybrid screen (using N-terminal KIF1C fragment homologous to KIF1B as bait), co-immunoprecipitation from endogenous and overexpressed conditions, immunofluorescence, motility assays","journal":"BMC cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP from endogenous cells plus functional motility assay, single lab, multiple methods","pmids":["16225668"],"is_preprint":false},{"year":2008,"finding":"In zebrafish, kbp is required for axonal outgrowth and maintenance. Live in vivo time-lapse imaging shows reduced speed of early axonal outgrowth in both peripheral and central nervous systems. Ultrastructural studies reveal disruption of axonal microtubules during outgrowth, and later-stage axons show mislocalized mitochondria and axonal degeneration in PNS, CNS, and ENS.","method":"Zebrafish kbp mutant characterization, in vivo time-lapse imaging of axonal outgrowth, electron microscopy ultrastructural analysis","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic loss-of-function with multiple orthogonal methods (live imaging, EM) revealing mechanistic basis (microtubule disruption, mitochondria mislocalization)","pmids":["18192286"],"is_preprint":false},{"year":2010,"finding":"KBP interacts with SCG10 (a microtubule destabilizing protein) as identified by yeast two-hybrid screen and validated by co-immunoprecipitation. KBP-depleted PC12 cells are defective in NGF-induced differentiation and neurite outgrowth. Zebrafish studies reveal an epistatic interaction between KBP and SCG10 in vivo. No direct KBP–microtubule binding was detected in co-localization and in vitro binding assays.","method":"Yeast two-hybrid screen, co-immunoprecipitation validation, siRNA knockdown in PC12 cells with NGF-induced differentiation assay, zebrafish epistasis analysis, in vitro microtubule binding assay (negative result for direct KBP-MT interaction)","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — yeast two-hybrid discovery confirmed by Co-IP, functional KD phenotype, and in vivo epistasis; multiple orthogonal methods across cell and animal models","pmids":["20621975"],"is_preprint":false},{"year":2013,"finding":"KBP does not co-localize with mitochondria in human control fibroblasts; instead it interacts with both actin filaments and tubulin cytoskeleton. Loss of KBP function (via nonsense mutations causing NMD) does not affect mitochondrial respiratory chain complex activity. KBP expression directly affects neurite growth in SH-SY5Y neuroblastoma cells, supporting a cytoskeletal (actin-MT cross-linking) mechanism for GOSHS neuronal developmental defects.","method":"Patient fibroblast analysis (respiratory chain enzyme assay), immunofluorescence co-localization in human fibroblasts, KBP overexpression/depletion in SH-SY5Y cells with neurite length assay, actin/tubulin interaction assays","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in a single study (localization, enzymatic assay, cell-based functional assay), negative result for mitochondrial co-localization is itself mechanistically informative","pmids":["23427148"],"is_preprint":false},{"year":2013,"finding":"Homozygous truncating mutation in the KBP gene (encoding a KIF1B-binding protein) causes fetal polymicrogyria, extending the GOSHS-associated phenotypic spectrum of KIAA1279 mutations.","method":"Genetic sequencing of fetal polymicrogyria cases identifying homozygous truncating KIAA1279 mutation","journal":"Neurogenetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — human genetics identifying gene-disease link but no direct mechanistic experiment beyond mutation identification","pmids":["24072599"],"is_preprint":false},{"year":2016,"finding":"KBP is required for anterograde transport of SCG10 (Stathmin-2) to axon growth cones by the Kif1B motor. In kbp zebrafish mutants, SCG10 levels in growth cones are reduced, leading to altered microtubule stability and axon truncation. Overexpression of SCG10 suppresses axon truncation in kbp mutants, confirming the direct mechanistic link. Notably, loss of Kif1B or KBP does not inhibit mitochondrial transport (negative result).","method":"Zebrafish genetic mutants, in vivo live imaging of SCG10 transport, genetic epistasis (SCG10 overexpression rescuing kbp mutant axon phenotype), microtubule stability assays","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic rescue epistasis plus live imaging and microtubule assays in a single rigorous study; directly defines mechanistic pathway (Kif1B→KBP→SCG10 transport→MT dynamics→axon extension)","pmids":["27358458"],"is_preprint":false},{"year":2017,"finding":"In mouse embryonic stem cells (mESCs), KBP (encoded by Kif1bp) is acetylated on Lys501 by the combined action of TDH (which produces mitochondrial acetyl-CoA) and the acetyltransferase GCN5L1. This acetylation marks KBP for recognition and degradation by Fbxo15, an F-box protein transcriptionally controlled by pluripotency core factors. KBP degradation limits mitochondrial biogenesis in self-renewing mESCs; defects in KBP degradation cause unscheduled mitochondrial biogenesis, enhanced respiration, ROS production, and inhibited cell proliferation. Silencing of Kif1Bα reverts the aberrant mitochondrial increase caused by KBP stabilization.","method":"Mass spectrometry identification of KBP-Fbxo15 interaction, acetylation site mapping (Lys501), acetyltransferase assay (GCN5L1), genetic knockouts and knockdowns in mESCs, mitochondrial biogenesis assays, respiration/ROS measurements, embryoid body formation","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods including MS, mutagenesis of acetylation site, enzymatic assay, and genetic rescue; rigorous single-study with comprehensive mechanistic dissection","pmids":["28319092"],"is_preprint":false},{"year":2017,"finding":"KBP acts as a novel mitotic interaction partner of Kif15 (a kinesin involved in spindle bipolarity). KBP promotes localization of Kif15 to the spindle equator close to chromosomes. Both Kif15 and KBP are required for alignment of all chromosomes to the metaphase plate and assembly of stable kinetochore fibers of correct length.","method":"Co-immunoprecipitation identifying KBP-Kif15 interaction in mitosis, siRNA knockdown of KBP and Kif15 with chromosome alignment and kinetochore fiber assembly phenotypic readouts, immunofluorescence","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional KD with specific mitotic phenotype readouts, single lab, two methods","pmids":["28445502"],"is_preprint":false},{"year":2017,"finding":"Kif1bp knockout mice die shortly after birth and show smaller brains, olfactory bulbs and anterior commissures, and defects in vagal and sympathetic innervation of the gut. KIF1BP interacts with Ret to regulate vagal innervation of the stomach. Colonization of the gut by neural crest-derived cells is delayed in Kif1bp-/- mice, demonstrating an essential in vivo role for KIF1BP in axon extension.","method":"Kif1bp knockout mouse generation and characterization, co-immunoprecipitation (KIF1BP–Ret interaction), histology, immunofluorescence of enteric nervous system colonization","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO in mice with specific CNS/ENS phenotypes plus biochemical Co-IP validation of Ret interaction; multiple methods, replicates and extends zebrafish work","pmids":["29192291"],"is_preprint":false}],"current_model":"KBP (KIFBP/KIF1BP/KIAA1279) is a tetratricopeptide repeat-containing protein that interacts with multiple kinesin motors (KIF1Bα, KIF1B, Kif15) and the microtubule-destabilizing protein SCG10, primarily functioning as a regulator of axonal microtubule dynamics and anterograde cargo transport: in neurons, the Kif1B–KBP complex transports SCG10 to growth cones where it modulates microtubule stability required for axon extension, while KBP degradation in embryonic stem cells (via TDH/GCN5L1-mediated Lys501 acetylation and subsequent Fbxo15-mediated proteasomal degradation) limits mitochondrial biogenesis during pluripotency; loss-of-function mutations in humans and mice cause Goldberg-Shprintzen syndrome featuring polymicrogyria, Hirschsprung disease, and axonal degeneration."},"narrative":{"mechanistic_narrative":"KIFBP (KBP/KIF1BP/KIAA1279) is a tetratricopeptide repeat-containing adaptor that regulates kinesin motor function to control axonal microtubule dynamics and cargo transport during nervous system development [PMID:15883926, PMID:18192286]. Its best-defined role is in neurons, where KBP couples the Kif1B motor to anterograde transport of the microtubule-destabilizing protein SCG10 (Stathmin-2): in zebrafish kbp mutants, SCG10 fails to reach growth cones, microtubule stability is altered, and axons truncate, a defect rescued by SCG10 overexpression and confirmed by an epistatic interaction between KBP and SCG10 [PMID:20621975, PMID:27358458]. Consistent with a cytoskeletal mechanism, KBP loss disrupts axonal microtubules and slows axon outgrowth in vivo, while KBP itself does not bind microtubules directly but associates with the actin and tubulin cytoskeleton [PMID:18192286, PMID:23427148]. KBP additionally functions in mitosis as an interaction partner of the kinesin Kif15, promoting its localization to the spindle equator and supporting chromosome alignment and stable kinetochore fiber assembly [PMID:28445502], and in mouse embryonic stem cells KBP is acetylated on Lys501 by GCN5L1 (using TDH-derived acetyl-CoA), marking it for Fbxo15-mediated proteasomal degradation that limits Kif1Bα-dependent mitochondrial biogenesis during pluripotency [PMID:28319092]. In vivo, KIFBP is essential for enteric and central nervous system development, interacting with Ret to control vagal gut innervation [PMID:29192291], and homozygous loss-of-function mutations in humans cause Goldberg-Shprintzen syndrome with microcephaly, polymicrogyria, and Hirschsprung disease [PMID:15883926, PMID:24072599].","teleology":[{"year":2005,"claim":"Establishing that KIAA1279 is a disease gene defined KBP's biological importance and revealed its TPR-domain architecture as a likely protein-interaction scaffold.","evidence":"homozygosity mapping and truncating mutation identification in Goldberg-Shprintzen syndrome patients","pmids":["15883926"],"confidence":"Medium","gaps":["No molecular mechanism linking TPR domains to a specific motor or pathway","Causality from mutation to neuronal phenotype not experimentally dissected"]},{"year":2005,"claim":"Identifying KIF1Bα as a binding partner gave KBP its first molecular activity, framing it as a kinesin-3 motor regulator.","evidence":"yeast two-hybrid screen, reciprocal co-immunoprecipitation from HEK293 cells, immunofluorescence, and motility assays","pmids":["16225668"],"confidence":"Medium","gaps":["Mitochondrial localization later contradicted by fibroblast studies","Whether KBP directly regulates motor processivity not resolved at biochemical level"]},{"year":2008,"claim":"In vivo loss-of-function moved KBP from an interactor to a developmental regulator, showing it is required for axon outgrowth via maintenance of axonal microtubules.","evidence":"zebrafish kbp mutant analysis with in vivo time-lapse imaging and electron microscopy","pmids":["18192286"],"confidence":"High","gaps":["Did not identify the molecular cargo or mechanism linking KBP to microtubule integrity","Mitochondrial mislocalization vs primary microtubule defect not disentangled"]},{"year":2010,"claim":"Discovery of the SCG10 interaction supplied a microtubule-destabilizing effector, explaining how KBP influences microtubule dynamics without binding microtubules itself.","evidence":"yeast two-hybrid, co-immunoprecipitation, PC12 NGF-differentiation knockdown, zebrafish epistasis, and negative in vitro microtubule-binding assay","pmids":["20621975"],"confidence":"High","gaps":["Did not show how KBP delivers SCG10 to its site of action","Relationship between SCG10 and the Kif1B motor not yet established"]},{"year":2013,"claim":"Reassessment in patient fibroblasts shifted KBP away from a mitochondrial role toward a cytoskeletal cross-linking function relevant to neuronal development.","evidence":"patient fibroblast respiratory chain assays, immunofluorescence co-localization with actin/tubulin, and SH-SY5Y neurite assays","pmids":["23427148"],"confidence":"Medium","gaps":["Contradicts earlier mitochondrial localization without fully reconciling cell-type differences","Molecular nature of actin-MT cross-linking not defined"]},{"year":2016,"claim":"Defining the Kif1B→KBP→SCG10 transport axis unified prior interactions into a single pathway controlling growth-cone microtubule stability and axon extension.","evidence":"zebrafish genetic mutants with in vivo SCG10 transport imaging, SCG10-overexpression rescue, and microtubule stability assays","pmids":["27358458"],"confidence":"High","gaps":["Did not establish whether the same axis operates outside developing axons","Excludes mitochondrial transport as the relevant cargo without explaining earlier mitochondrial phenotypes"]},{"year":2017,"claim":"A pluripotency-specific degradation circuit revealed post-translational control of KBP that links it to mitochondrial biogenesis via Kif1Bα.","evidence":"mass spectrometry, Lys501 acetylation mapping, GCN5L1 acetyltransferase assay, and genetic knockouts/rescue in mouse embryonic stem cells","pmids":["28319092"],"confidence":"High","gaps":["Whether this acetylation-degradation axis operates in neurons is not addressed","Mechanism by which KBP stabilization expands mitochondria beyond Kif1Bα dependence not detailed"]},{"year":2017,"claim":"Identification of a Kif15 interaction extended KBP's adaptor role from interphase axons to the mitotic spindle.","evidence":"mitotic co-immunoprecipitation and siRNA knockdown with chromosome alignment and kinetochore fiber readouts","pmids":["28445502"],"confidence":"Medium","gaps":["Single lab with Co-IP and knockdown only; no reconstitution of KBP-Kif15 regulation","How KBP targets Kif15 to the spindle equator mechanistically unknown"]},{"year":2017,"claim":"A knockout mouse confirmed the in vivo requirement for KBP in CNS and enteric innervation and added Ret as a partner relevant to gut neural crest colonization.","evidence":"Kif1bp knockout mouse phenotyping, histology, ENS colonization imaging, and KIF1BP–Ret co-immunoprecipitation","pmids":["29192291"],"confidence":"High","gaps":["Mechanistic link between the Ret interaction and axon extension not defined","Whether Ret regulation involves the Kif1B/SCG10 axis unresolved"]},{"year":null,"claim":"It remains unresolved how KBP's distinct activities — Kif1B/SCG10 axonal transport, Kif15 spindle regulation, Ret signaling, and acetylation-dependent mitochondrial control — are coordinated or selected in different cell types.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of how TPR domains engage distinct kinesin partners","Cell-type-specific cytoskeletal vs mitochondrial role not reconciled","Direct biochemical mechanism of motor regulation not reconstituted"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3,6,8]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,8]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[4]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2,6,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8]}],"complexes":[],"partners":["KIF1B","SCG10","KIF15","RET","FBXO15","GCN5L1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96EK5","full_name":"KIF-binding protein","aliases":["KIF1-binding protein","Kinesin family binding protein"],"length_aa":621,"mass_kda":71.8,"function":"Activator of KIF1B plus-end-directed microtubule motor activity (PubMed:16225668). Required for organization of axonal microtubules, and axonal outgrowth and maintenance during peripheral and central nervous system development","subcellular_location":"Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/Q96EK5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/KIFBP","classification":"Not Classified","n_dependent_lines":153,"n_total_lines":1208,"dependency_fraction":0.12665562913907286},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000198954","cell_line_id":"CID001416","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"big_aggregates","grade":2},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"PTGES3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001416","total_profiled":1310},"omim":[{"mim_id":"609460","title":"GOLDBERG-SHPRINTZEN SYNDROME; GOSHS","url":"https://www.omim.org/entry/609460"},{"mim_id":"609367","title":"KINESIN FAMILY BINDING PROTEIN; KIFBP","url":"https://www.omim.org/entry/609367"},{"mim_id":"600621","title":"STATHMIN-LIKE 2; STMN2","url":"https://www.omim.org/entry/600621"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/KIFBP"},"hgnc":{"alias_symbol":["DKFZP586B0923","TTC20","KBP"],"prev_symbol":["KIAA1279","KIF1BP"]},"alphafold":{"accession":"Q96EK5","domains":[{"cath_id":"1.25.40.10","chopping":"80-243","consensus_level":"medium","plddt":94.5635,"start":80,"end":243},{"cath_id":"-","chopping":"246-284_302-330_360-438","consensus_level":"medium","plddt":94.941,"start":246,"end":438},{"cath_id":"1.20.58","chopping":"532-621","consensus_level":"medium","plddt":94.2182,"start":532,"end":621}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96EK5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96EK5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96EK5-F1-predicted_aligned_error_v6.png","plddt_mean":90.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=KIFBP","jax_strain_url":"https://www.jax.org/strain/search?query=KIFBP"},"sequence":{"accession":"Q96EK5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96EK5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96EK5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96EK5"}},"corpus_meta":[{"pmid":"88264","id":"PMC_88264","title":"In 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hypertension.","date":"2021","source":"Expert opinion on investigational drugs","url":"https://pubmed.ncbi.nlm.nih.gov/34595995","citation_count":12,"is_preprint":false},{"pmid":"16195888","id":"PMC_16195888","title":"Nick-forming sequences may be involved in the organization of eukaryotic chromatin into approximately 50 kbp loops.","date":"2005","source":"Histochemistry and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/16195888","citation_count":12,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47103,"output_tokens":3053,"usd":0.093552,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10491,"output_tokens":3291,"usd":0.067365,"stage2_stop_reason":"end_turn"},"total_usd":0.160917,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"KIAA1279 encodes a protein with two tetratricopeptide repeat (TPR) domains, and homozygous nonsense mutations in KIAA1279 cause Goldberg-Shprintzen syndrome (GOSHS), establishing that KBP is essential for both enteric and central nervous system development.\",\n      \"method\": \"Homozygosity mapping and identification of truncating mutations in patients with GOSHS (microcephaly, polymicrogyria, Hirschsprung disease)\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human genetics with loss-of-function mutations establishing disease gene identity; single study but definitive gene-disease link with functional domain annotation\",\n      \"pmids\": [\"15883926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"KBP (KIF1 binding protein) interacts with KIF1Bα (a kinesin-3 family mitochondria-distributing motor) and co-immunoprecipitates with it from untransfected HEK293 cells. KBP localizes predominantly to mitochondria, and overexpression of a KBP deletion mutant or reduction of KBP via antisense causes mitochondrial aggregation, phenocopying reduced KIF1Bα motility activity.\",\n      \"method\": \"Yeast two-hybrid screen (using N-terminal KIF1C fragment homologous to KIF1B as bait), co-immunoprecipitation from endogenous and overexpressed conditions, immunofluorescence, motility assays\",\n      \"journal\": \"BMC cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP from endogenous cells plus functional motility assay, single lab, multiple methods\",\n      \"pmids\": [\"16225668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In zebrafish, kbp is required for axonal outgrowth and maintenance. Live in vivo time-lapse imaging shows reduced speed of early axonal outgrowth in both peripheral and central nervous systems. Ultrastructural studies reveal disruption of axonal microtubules during outgrowth, and later-stage axons show mislocalized mitochondria and axonal degeneration in PNS, CNS, and ENS.\",\n      \"method\": \"Zebrafish kbp mutant characterization, in vivo time-lapse imaging of axonal outgrowth, electron microscopy ultrastructural analysis\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic loss-of-function with multiple orthogonal methods (live imaging, EM) revealing mechanistic basis (microtubule disruption, mitochondria mislocalization)\",\n      \"pmids\": [\"18192286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"KBP interacts with SCG10 (a microtubule destabilizing protein) as identified by yeast two-hybrid screen and validated by co-immunoprecipitation. KBP-depleted PC12 cells are defective in NGF-induced differentiation and neurite outgrowth. Zebrafish studies reveal an epistatic interaction between KBP and SCG10 in vivo. No direct KBP–microtubule binding was detected in co-localization and in vitro binding assays.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation validation, siRNA knockdown in PC12 cells with NGF-induced differentiation assay, zebrafish epistasis analysis, in vitro microtubule binding assay (negative result for direct KBP-MT interaction)\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — yeast two-hybrid discovery confirmed by Co-IP, functional KD phenotype, and in vivo epistasis; multiple orthogonal methods across cell and animal models\",\n      \"pmids\": [\"20621975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"KBP does not co-localize with mitochondria in human control fibroblasts; instead it interacts with both actin filaments and tubulin cytoskeleton. Loss of KBP function (via nonsense mutations causing NMD) does not affect mitochondrial respiratory chain complex activity. KBP expression directly affects neurite growth in SH-SY5Y neuroblastoma cells, supporting a cytoskeletal (actin-MT cross-linking) mechanism for GOSHS neuronal developmental defects.\",\n      \"method\": \"Patient fibroblast analysis (respiratory chain enzyme assay), immunofluorescence co-localization in human fibroblasts, KBP overexpression/depletion in SH-SY5Y cells with neurite length assay, actin/tubulin interaction assays\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in a single study (localization, enzymatic assay, cell-based functional assay), negative result for mitochondrial co-localization is itself mechanistically informative\",\n      \"pmids\": [\"23427148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Homozygous truncating mutation in the KBP gene (encoding a KIF1B-binding protein) causes fetal polymicrogyria, extending the GOSHS-associated phenotypic spectrum of KIAA1279 mutations.\",\n      \"method\": \"Genetic sequencing of fetal polymicrogyria cases identifying homozygous truncating KIAA1279 mutation\",\n      \"journal\": \"Neurogenetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — human genetics identifying gene-disease link but no direct mechanistic experiment beyond mutation identification\",\n      \"pmids\": [\"24072599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"KBP is required for anterograde transport of SCG10 (Stathmin-2) to axon growth cones by the Kif1B motor. In kbp zebrafish mutants, SCG10 levels in growth cones are reduced, leading to altered microtubule stability and axon truncation. Overexpression of SCG10 suppresses axon truncation in kbp mutants, confirming the direct mechanistic link. Notably, loss of Kif1B or KBP does not inhibit mitochondrial transport (negative result).\",\n      \"method\": \"Zebrafish genetic mutants, in vivo live imaging of SCG10 transport, genetic epistasis (SCG10 overexpression rescuing kbp mutant axon phenotype), microtubule stability assays\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic rescue epistasis plus live imaging and microtubule assays in a single rigorous study; directly defines mechanistic pathway (Kif1B→KBP→SCG10 transport→MT dynamics→axon extension)\",\n      \"pmids\": [\"27358458\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In mouse embryonic stem cells (mESCs), KBP (encoded by Kif1bp) is acetylated on Lys501 by the combined action of TDH (which produces mitochondrial acetyl-CoA) and the acetyltransferase GCN5L1. This acetylation marks KBP for recognition and degradation by Fbxo15, an F-box protein transcriptionally controlled by pluripotency core factors. KBP degradation limits mitochondrial biogenesis in self-renewing mESCs; defects in KBP degradation cause unscheduled mitochondrial biogenesis, enhanced respiration, ROS production, and inhibited cell proliferation. Silencing of Kif1Bα reverts the aberrant mitochondrial increase caused by KBP stabilization.\",\n      \"method\": \"Mass spectrometry identification of KBP-Fbxo15 interaction, acetylation site mapping (Lys501), acetyltransferase assay (GCN5L1), genetic knockouts and knockdowns in mESCs, mitochondrial biogenesis assays, respiration/ROS measurements, embryoid body formation\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods including MS, mutagenesis of acetylation site, enzymatic assay, and genetic rescue; rigorous single-study with comprehensive mechanistic dissection\",\n      \"pmids\": [\"28319092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"KBP acts as a novel mitotic interaction partner of Kif15 (a kinesin involved in spindle bipolarity). KBP promotes localization of Kif15 to the spindle equator close to chromosomes. Both Kif15 and KBP are required for alignment of all chromosomes to the metaphase plate and assembly of stable kinetochore fibers of correct length.\",\n      \"method\": \"Co-immunoprecipitation identifying KBP-Kif15 interaction in mitosis, siRNA knockdown of KBP and Kif15 with chromosome alignment and kinetochore fiber assembly phenotypic readouts, immunofluorescence\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional KD with specific mitotic phenotype readouts, single lab, two methods\",\n      \"pmids\": [\"28445502\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Kif1bp knockout mice die shortly after birth and show smaller brains, olfactory bulbs and anterior commissures, and defects in vagal and sympathetic innervation of the gut. KIF1BP interacts with Ret to regulate vagal innervation of the stomach. Colonization of the gut by neural crest-derived cells is delayed in Kif1bp-/- mice, demonstrating an essential in vivo role for KIF1BP in axon extension.\",\n      \"method\": \"Kif1bp knockout mouse generation and characterization, co-immunoprecipitation (KIF1BP–Ret interaction), histology, immunofluorescence of enteric nervous system colonization\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO in mice with specific CNS/ENS phenotypes plus biochemical Co-IP validation of Ret interaction; multiple methods, replicates and extends zebrafish work\",\n      \"pmids\": [\"29192291\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"KBP (KIFBP/KIF1BP/KIAA1279) is a tetratricopeptide repeat-containing protein that interacts with multiple kinesin motors (KIF1Bα, KIF1B, Kif15) and the microtubule-destabilizing protein SCG10, primarily functioning as a regulator of axonal microtubule dynamics and anterograde cargo transport: in neurons, the Kif1B–KBP complex transports SCG10 to growth cones where it modulates microtubule stability required for axon extension, while KBP degradation in embryonic stem cells (via TDH/GCN5L1-mediated Lys501 acetylation and subsequent Fbxo15-mediated proteasomal degradation) limits mitochondrial biogenesis during pluripotency; loss-of-function mutations in humans and mice cause Goldberg-Shprintzen syndrome featuring polymicrogyria, Hirschsprung disease, and axonal degeneration.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"KIFBP (KBP/KIF1BP/KIAA1279) is a tetratricopeptide repeat-containing adaptor that regulates kinesin motor function to control axonal microtubule dynamics and cargo transport during nervous system development [#0, #2]. Its best-defined role is in neurons, where KBP couples the Kif1B motor to anterograde transport of the microtubule-destabilizing protein SCG10 (Stathmin-2): in zebrafish kbp mutants, SCG10 fails to reach growth cones, microtubule stability is altered, and axons truncate, a defect rescued by SCG10 overexpression and confirmed by an epistatic interaction between KBP and SCG10 [#3, #6]. Consistent with a cytoskeletal mechanism, KBP loss disrupts axonal microtubules and slows axon outgrowth in vivo, while KBP itself does not bind microtubules directly but associates with the actin and tubulin cytoskeleton [#2, #4]. KBP additionally functions in mitosis as an interaction partner of the kinesin Kif15, promoting its localization to the spindle equator and supporting chromosome alignment and stable kinetochore fiber assembly [#8], and in mouse embryonic stem cells KBP is acetylated on Lys501 by GCN5L1 (using TDH-derived acetyl-CoA), marking it for Fbxo15-mediated proteasomal degradation that limits Kif1Bα-dependent mitochondrial biogenesis during pluripotency [#7]. In vivo, KIFBP is essential for enteric and central nervous system development, interacting with Ret to control vagal gut innervation [#9], and homozygous loss-of-function mutations in humans cause Goldberg-Shprintzen syndrome with microcephaly, polymicrogyria, and Hirschsprung disease [#0, #5].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing that KIAA1279 is a disease gene defined KBP's biological importance and revealed its TPR-domain architecture as a likely protein-interaction scaffold.\",\n      \"evidence\": \"homozygosity mapping and truncating mutation identification in Goldberg-Shprintzen syndrome patients\",\n      \"pmids\": [\"15883926\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular mechanism linking TPR domains to a specific motor or pathway\", \"Causality from mutation to neuronal phenotype not experimentally dissected\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identifying KIF1Bα as a binding partner gave KBP its first molecular activity, framing it as a kinesin-3 motor regulator.\",\n      \"evidence\": \"yeast two-hybrid screen, reciprocal co-immunoprecipitation from HEK293 cells, immunofluorescence, and motility assays\",\n      \"pmids\": [\"16225668\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mitochondrial localization later contradicted by fibroblast studies\", \"Whether KBP directly regulates motor processivity not resolved at biochemical level\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"In vivo loss-of-function moved KBP from an interactor to a developmental regulator, showing it is required for axon outgrowth via maintenance of axonal microtubules.\",\n      \"evidence\": \"zebrafish kbp mutant analysis with in vivo time-lapse imaging and electron microscopy\",\n      \"pmids\": [\"18192286\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the molecular cargo or mechanism linking KBP to microtubule integrity\", \"Mitochondrial mislocalization vs primary microtubule defect not disentangled\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovery of the SCG10 interaction supplied a microtubule-destabilizing effector, explaining how KBP influences microtubule dynamics without binding microtubules itself.\",\n      \"evidence\": \"yeast two-hybrid, co-immunoprecipitation, PC12 NGF-differentiation knockdown, zebrafish epistasis, and negative in vitro microtubule-binding assay\",\n      \"pmids\": [\"20621975\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not show how KBP delivers SCG10 to its site of action\", \"Relationship between SCG10 and the Kif1B motor not yet established\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Reassessment in patient fibroblasts shifted KBP away from a mitochondrial role toward a cytoskeletal cross-linking function relevant to neuronal development.\",\n      \"evidence\": \"patient fibroblast respiratory chain assays, immunofluorescence co-localization with actin/tubulin, and SH-SY5Y neurite assays\",\n      \"pmids\": [\"23427148\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Contradicts earlier mitochondrial localization without fully reconciling cell-type differences\", \"Molecular nature of actin-MT cross-linking not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defining the Kif1B\\u2192KBP\\u2192SCG10 transport axis unified prior interactions into a single pathway controlling growth-cone microtubule stability and axon extension.\",\n      \"evidence\": \"zebrafish genetic mutants with in vivo SCG10 transport imaging, SCG10-overexpression rescue, and microtubule stability assays\",\n      \"pmids\": [\"27358458\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish whether the same axis operates outside developing axons\", \"Excludes mitochondrial transport as the relevant cargo without explaining earlier mitochondrial phenotypes\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A pluripotency-specific degradation circuit revealed post-translational control of KBP that links it to mitochondrial biogenesis via Kif1Bα.\",\n      \"evidence\": \"mass spectrometry, Lys501 acetylation mapping, GCN5L1 acetyltransferase assay, and genetic knockouts/rescue in mouse embryonic stem cells\",\n      \"pmids\": [\"28319092\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this acetylation-degradation axis operates in neurons is not addressed\", \"Mechanism by which KBP stabilization expands mitochondria beyond Kif1Bα dependence not detailed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identification of a Kif15 interaction extended KBP's adaptor role from interphase axons to the mitotic spindle.\",\n      \"evidence\": \"mitotic co-immunoprecipitation and siRNA knockdown with chromosome alignment and kinetochore fiber readouts\",\n      \"pmids\": [\"28445502\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab with Co-IP and knockdown only; no reconstitution of KBP-Kif15 regulation\", \"How KBP targets Kif15 to the spindle equator mechanistically unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A knockout mouse confirmed the in vivo requirement for KBP in CNS and enteric innervation and added Ret as a partner relevant to gut neural crest colonization.\",\n      \"evidence\": \"Kif1bp knockout mouse phenotyping, histology, ENS colonization imaging, and KIF1BP\\u2013Ret co-immunoprecipitation\",\n      \"pmids\": [\"29192291\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between the Ret interaction and axon extension not defined\", \"Whether Ret regulation involves the Kif1B/SCG10 axis unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how KBP's distinct activities — Kif1B/SCG10 axonal transport, Kif15 spindle regulation, Ret signaling, and acetylation-dependent mitochondrial control — are coordinated or selected in different cell types.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of how TPR domains engage distinct kinesin partners\", \"Cell-type-specific cytoskeletal vs mitochondrial role not reconciled\", \"Direct biochemical mechanism of motor regulation not reconstituted\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3, 6, 8]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2, 6, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"KIF1B\", \"SCG10\", \"KIF15\", \"RET\", \"FBXO15\", \"GCN5L1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}