{"gene":"KIRREL1","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":2001,"finding":"NEPH1 (KIRREL1) is expressed in glomerular podocytes and its genetic deletion in mice causes effacement of podocyte foot processes and severe proteinuria, establishing an essential role in maintaining the glomerular filtration barrier.","method":"Gene trap knockout mouse, electron microscopy, Northern analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype, replicated across multiple studies","pmids":["11416156"],"is_preprint":false},{"year":2002,"finding":"NEPH1 interacts with the C-terminal domain of podocin via a conserved binding motif; mutation of a centrally located tyrosine residue in NEPH1 dramatically reduces its affinity for podocin. NEPH1 also triggers AP-1 activation requiring Tec family kinases.","method":"Co-immunoprecipitation, site-directed mutagenesis, reporter assays","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP plus mutagenesis with functional reporter assay","pmids":["12424224"],"is_preprint":false},{"year":2003,"finding":"Neph1 localizes to the glomerular slit diaphragm by immunogold electron microscopy and directly interacts with nephrin (via extracellular segments) and ZO-1 (via ZO-1 PDZ domains with Neph1 cytoplasmic tail). Disrupting the Neph1-nephrin interaction in vivo causes proteinuria and loss of ZO-1 protein expression.","method":"Immunogold electron microscopy, native and recombinant protein co-immunoprecipitation, in vivo antibody injection model","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — direct localization, reciprocal Co-IP, and in vivo functional consequence","pmids":["12865409"],"is_preprint":false},{"year":2003,"finding":"Neph1 localizes exclusively to lateral margins of podocyte foot processes at the slit diaphragm insertion. Neph1 and Nephrin form direct cis-heterodimeric interactions involving both their cytoplasmic domains and their extracellular domains; Neph1 does not homodimerize via its extracellular domain.","method":"Immunogold electron microscopy, detergent-resistant membrane fractionation, co-immunoprecipitation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — direct localization experiment with functional context, multiple orthogonal binding assays","pmids":["12646566"],"is_preprint":false},{"year":2003,"finding":"NEPH1 forms homodimers and heterodimers with nephrin through promiscuous Ig-domain interactions; two Ig domains of either protein are sufficient for binding. These interactions are strictly dependent on post-translational glycosylation.","method":"Co-immunoprecipitation, NEPH1-IgG fusion protein pulldown, truncation analysis, overexpression in HEK293T cells","journal":"Journal of the American Society of Nephrology","confidence":"High","confidence_rationale":"Tier 2 — systematic truncation analysis with glycosylation requirement established","pmids":["12660326"],"is_preprint":false},{"year":2006,"finding":"Neph1 is expressed at synaptic sites in the mouse brain (including hippocampus CA1/CA3) and interacts with the PDZ domain of the synaptic scaffold CASK via its cytoplasmic tail, suggesting a role in synaptogenesis.","method":"In situ hybridization, immunohistochemistry, immunogold electron microscopy, co-immunoprecipitation/PDZ domain pulldown","journal":"The Journal of comparative neurology","confidence":"Medium","confidence_rationale":"Tier 3 — direct PDZ-domain interaction assay with localization, single lab","pmids":["16874800"],"is_preprint":false},{"year":2007,"finding":"Neph1 is phosphorylated on specific tyrosine residues by the Src family kinase Fyn, leading to recruitment of the adaptor Grb2. Neph1-Nephrin direct interaction juxtaposes Grb2 and Nck1/2 at the membrane to cooperatively promote actin polymerization at the podocyte intercellular junction.","method":"In vitro kinase assay, site-directed mutagenesis of phosphorylation sites, co-immunoprecipitation, actin polymerization assays at plasma membrane","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro kinase assay plus mutagenesis and functional actin polymerization readout","pmids":["17923684"],"is_preprint":false},{"year":2008,"finding":"Neph1 is phosphorylated in vivo by Src family kinase Fyn on multiple tyrosine residues including Y637 and Y638; phosphorylation-dependent binding of Neph1 to adaptor Grb2 and kinase Csk was demonstrated from rat glomerular lysates. Neph1 attenuates Fyn-elicited ERK activation through its Grb2-binding motif.","method":"In vitro kinase assay, peptide mass fingerprinting, site-directed mutagenesis, pulldown from glomerular lysates, ERK signaling assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro kinase assay with mass fingerprinting and mutagenesis plus endogenous tissue pulldown","pmids":["18258597"],"is_preprint":false},{"year":2008,"finding":"Renal ischemia causes rapid dissociation of the Neph1-ZO-1 interaction; recovery restores interaction dependent on Fyn-mediated tyrosine phosphorylation of Neph1. Tyrosine phosphorylation of Neph1 significantly increases Neph1-ZO-1 binding, establishing phosphorylation as a switch controlling this complex.","method":"In vivo rat ischemia model, cell culture ATP-depletion injury model, co-immunoprecipitation, immunofluorescence","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — in vivo and in vitro models with mechanistic phosphorylation link, two orthogonal systems","pmids":["18922801"],"is_preprint":false},{"year":2009,"finding":"Neph1 interacts with large-conductance Ca2+-activated K+ channels (Slo1/BK) encoded by Slo1, demonstrated by reciprocal co-immunoprecipitation from endogenous podocyte and ciliary ganglion neuron proteins. Neph1 suppresses steady-state surface expression of Slo1 in podocytes and neurons, while siRNA knockdown of Neph1 in neurons increases Slo1 surface expression and BKCa current.","method":"Reciprocal co-immunoprecipitation from endogenous cells, GST pulldown, cell surface biotinylation, siRNA knockdown, whole-cell electrophysiology","journal":"American journal of physiology. Cell physiology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP from multiple endogenous sources plus functional electrophysiology readout","pmids":["19794150"],"is_preprint":false},{"year":2011,"finding":"Motor protein Myo1c directly interacts with Neph1 in an actin-dependent manner and facilitates transport of Neph1 to the podocyte cell membrane; dominant-negative Myo1c or Myo1c knockdown significantly reduces Neph1 membrane localization and impairs tight junction formation and cell migration.","method":"In vivo and in vitro co-immunoprecipitation, dominant-negative overexpression, siRNA knockdown, live-cell imaging, transepithelial electric resistance assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — direct interaction plus loss-of-function with defined membrane trafficking and junction phenotype","pmids":["21402783"],"is_preprint":false},{"year":2011,"finding":"Neph1 and Neph3 independently induce cell adhesion, while nephrin requires trans-interaction with Neph1 or Neph3 to promote cell-cell contact formation. Trans-interaction of nephrin with Neph1 or Neph3 down-regulates tyrosine phosphorylation of nephrin.","method":"L-fibroblast cell adhesion assay, co-immunoprecipitation for heterodimerization, phosphorylation analysis","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 — cell-based adhesion assay with mechanistic phosphorylation link, single lab","pmids":["21306299"],"is_preprint":false},{"year":2012,"finding":"Solution structure of the Neph1 cytoplasmic domain (Neph1-CD) determined by SWAXS; structural modeling of the Neph1-CD·ZO-1-PDZ1 complex identified that residues Lys-761 and Tyr-762 in Neph1 (in addition to C-terminal Thr-His-Val) are critical for ZO-1 binding, validated by alanine-scanning mutagenesis.","method":"Small/wide angle X-ray scattering (SWAXS), circular dichroism, in vivo and in vitro pulldown, site-directed mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — structural determination plus mutagenesis with functional binding validation","pmids":["22262837"],"is_preprint":false},{"year":2014,"finding":"Inhibiting Neph1 signaling by transducing its cytoplasmic domain (Neph1-CD) into podocytes prevents puromycin aminonucleoside (PAN)-induced phosphorylation of Neph1, retains Neph1 in lipid raft fractions and at the membrane, and protects podocytes from cytoskeletal damage and albumin leakage.","method":"Protein transduction domain approach, subcellular fractionation, immunofluorescence, in vivo zebrafish injury model","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with defined cellular phenotype across in vitro and in vivo models, single lab","pmids":["24554715"],"is_preprint":false},{"year":2016,"finding":"Myo1c binds Neph1 at its C-terminal tail domain, as demonstrated by SAXS structural modeling showing an extended S-shaped Myo1c with Neph1 attached. A single point mutation in Neph1 at the identified interaction surface abolishes Myo1c binding in vitro and in live-cell assays. FRAP demonstrates Myo1c-dependent intracellular vesicular movement and membrane turnover of Neph1.","method":"Small angle X-ray scattering, site-directed mutagenesis, in vitro and live-cell binding assays, FRAP live-cell imaging","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — structural determination plus mutagenesis plus live-cell functional imaging","pmids":["27044863"],"is_preprint":false},{"year":2017,"finding":"CD80 interacts with Neph1 via their extracellular domains, demonstrated by pulldown assays in HEK293 cells; CD80 co-localizes with Neph1 in podocytes and its overexpression causes actin derangement.","method":"Co-immunoprecipitation/pulldown in HEK293 cells, immunofluorescence co-localization","journal":"Clinical and experimental nephrology","confidence":"Low","confidence_rationale":"Tier 3 — single pulldown assay, single lab, no mutagenesis","pmids":["29022109"],"is_preprint":false},{"year":2017,"finding":"Stabilizing the Neph1-ZO-1 protein-protein interaction using the small molecule isodesmosine (ISD) enhances Neph1-ZO-1 binding in vitro and in vivo, and protects podocytes from injury-induced loss of transepithelial permeability in cell culture, mouse, and zebrafish models.","method":"Structural pocket screening, small molecule binding assays, biochemical binding analysis, TER assays, in vivo mouse and zebrafish models","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — mechanistic PPI stabilization validated across multiple model systems","pmids":["28935902"],"is_preprint":false},{"year":2019,"finding":"Homozygous mutations in KIRREL1 cause steroid-resistant nephrotic syndrome; mutant KIRREL1 proteins fail to localize to the podocyte cell membrane, indicating defective trafficking and impaired podocyte function.","method":"Human genetic analysis, functional assessment of mutant protein membrane localization in podocytes","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 — human disease mutations with direct cellular trafficking phenotype","pmids":["31472902"],"is_preprint":false},{"year":2021,"finding":"NEPHRIN and NEPH1 are novel receptor proteins for hepatocyte growth factor (HGF); HGF binds their extracellular domains with high affinity (surface plasmon resonance), induces their phosphorylation independently of the MET receptor, and SHP-2 (PTPN11) mediates their dephosphorylation. HGF-induced phosphorylation of NEPHRIN and NEPH1 promotes podocyte repair.","method":"Surface plasmon resonance, baculovirus-expressed recombinant proteins, phosphorylation assays, molecular modeling, in vitro cultured podocytes, ex vivo Drosophila nephrocytes, chemical injury models","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstituted binding with purified proteins (SPR) plus functional cellular validation across multiple models","pmids":["34391780"],"is_preprint":false},{"year":2022,"finding":"KIRREL1 physically interacts with SAV1 and recruits SAV1 to cell-cell contact sites, acting as a positive upstream regulator of the Hippo pathway. Knockout of KIRREL1 increases YAP activity in neighboring cells. During liver regeneration, KIRREL1 ablation enhances hepatic YAP activity and hepatocyte reprogramming.","method":"Co-immunoprecipitation, CRISPR knockout, YAP activity reporter assays, in vivo mouse liver regeneration model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP plus genetic KO with defined pathway phenotype in vitro and in vivo","pmids":["35177623"],"is_preprint":false},{"year":2022,"finding":"KIRREL1 interacts with both SAV1 and LATS1/2, promoting LATS1/2 activation by MST1/2 Hippo kinases, thereby inhibiting YAP/TAZ oncoproteins. YAP/TAZ in turn transcriptionally induce KIRREL1 expression in a TEAD1-4-dependent manner, forming a negative feedback loop. Transgenic KIRREL1 expression blocks tumorigenesis in a mouse intrahepatic cholangiocarcinoma model.","method":"Co-immunoprecipitation, LATS1/2 kinase activity assays, transcriptional reporter assays, in vivo mouse tumor model","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — kinase activation assays, multiple binding partners, in vivo tumor suppressor validation","pmids":["36044856"],"is_preprint":false},{"year":2022,"finding":"In vivo CRISPR screen confirmed KIRREL1 loss promotes tumor growth; KIRREL1 directly binds SAV1 to activate the Hippo tumor suppressor pathway.","method":"In vivo CRISPR screen with custom cell surface protein library, Hippo pathway reporter screen, direct binding assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — unbiased in vivo CRISPR screen plus orthogonal pathway reporter, replicated finding across three independent 2022 studies","pmids":["35704761"],"is_preprint":false},{"year":2024,"finding":"Neph1 is required for neurite branching in developing spinal cord dorsal horn neurons; the homeodomain transcription factor PRRXL1 directly binds Neph1 intronic regions (by ChIP) and prevents premature Neph1 expression in superficial dorsal horn laminae.","method":"Chromatin immunoprecipitation (ChIP), Neph1 loss-of-function analysis, neurite branching morphometric assay, spatiotemporal expression analysis","journal":"Neural development","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP with functional neurite branching phenotype, single lab","pmids":["39049046"],"is_preprint":false},{"year":2025,"finding":"Cryo-electron tomography of human kidney tissue resolves the near-native slit diaphragm architecture as a fishnet-like lattice; an atomic model based on the Nephrin-Neph1 heterodimer reveals ~9 nm spacing in humans, establishing the structural basis for the filtration sieve.","method":"Cryo-electron tomography of native human kidney tissue, atomic modeling based on Nephrin-Neph1 heterodimer","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 — cryo-ET structural determination, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.09.24.678239"],"is_preprint":true}],"current_model":"KIRREL1 (NEPH1) is a transmembrane immunoglobulin superfamily protein essential for glomerular slit diaphragm integrity, where it localizes to podocyte foot process junctions and forms hetero-oligomeric complexes with nephrin (via extracellular Ig domains) and ZO-1 (via PDZ interaction with its cytoplasmic tail), is phosphorylated on specific tyrosines by Fyn kinase to recruit Grb2 and cooperate with nephrin-Nck to drive actin polymerization, is trafficked to the membrane by the motor protein Myo1c, acts as a receptor for HGF to promote podocyte repair, and additionally functions as a cell-surface upstream activator of the Hippo tumor-suppressor pathway by binding SAV1 and LATS1/2 at cell-cell contacts to suppress YAP/TAZ activity in a negative feedback loop."},"narrative":{"teleology":[{"year":2001,"claim":"Establishing that KIRREL1 is essential for podocyte foot process integrity resolved the gene's primary physiological role: its deletion causes slit diaphragm loss and proteinuria, proving it is not redundant with nephrin.","evidence":"Gene-trap knockout mouse with electron microscopy phenotyping","pmids":["11416156"],"confidence":"High","gaps":["Molecular partners at the slit diaphragm were unknown","Whether KIRREL1 functions as an adhesion molecule or solely as a signaling receptor was unclear"]},{"year":2002,"claim":"Identification of the KIRREL1–podocin interaction and its dependence on a central tyrosine residue established the first cytoplasmic signaling link, suggesting KIRREL1 operates within a multi-protein slit diaphragm signaling complex.","evidence":"Reciprocal co-immunoprecipitation with site-directed mutagenesis and AP-1 reporter assays","pmids":["12424224"],"confidence":"High","gaps":["Downstream signaling pathways were not defined","Whether podocin interaction is required in vivo was untested"]},{"year":2003,"claim":"Demonstrating that KIRREL1 forms direct heterodimers with nephrin (via extracellular Ig domains) and binds ZO-1 (via PDZ interaction), and that disrupting these complexes in vivo causes proteinuria, defined the core molecular architecture of the slit diaphragm as a KIRREL1–nephrin–ZO-1 ternary complex.","evidence":"Immunogold EM localization, reciprocal co-IP of native and recombinant proteins, in vivo antibody injection, truncation/glycosylation analysis","pmids":["12865409","12646566","12660326"],"confidence":"High","gaps":["Stoichiometry and geometry of the nephrin–KIRREL1 heterodimer were unresolved","Whether glycosylation-dependent binding reflects a quality-control or a regulatory mechanism was unknown"]},{"year":2007,"claim":"Identifying Fyn-mediated tyrosine phosphorylation of KIRREL1 and its recruitment of Grb2 to cooperate with nephrin–Nck in actin polymerization answered how KIRREL1 transduces extracellular adhesion into cytoskeletal remodeling at podocyte junctions.","evidence":"In vitro kinase assay, phosphosite mutagenesis, actin polymerization assays at the plasma membrane","pmids":["17923684"],"confidence":"High","gaps":["In vivo relevance of individual phosphosites had not been tested genetically","Upstream signals triggering Fyn activation at the slit diaphragm were unknown"]},{"year":2008,"claim":"Mapping specific phosphorylation sites (Y637/Y638) and showing that ischemia disrupts the KIRREL1–ZO-1 interaction while Fyn-dependent re-phosphorylation restores it established tyrosine phosphorylation as a molecular switch controlling slit diaphragm assembly and repair.","evidence":"Peptide mass fingerprinting, site-directed mutagenesis, rat ischemia model and ATP-depletion injury model with co-IP","pmids":["18258597","18922801"],"confidence":"High","gaps":["Which phosphatase reverses the switch was not identified at this time","Whether phosphorylation-dependent ZO-1 binding is required for barrier function in vivo remained untested"]},{"year":2009,"claim":"Discovery that KIRREL1 suppresses surface expression of BK (Slo1) channels in podocytes and neurons revealed an unexpected function as a regulator of ion channel trafficking, extending its role beyond structural adhesion.","evidence":"Reciprocal co-IP from endogenous podocyte and neuronal lysates, siRNA knockdown, whole-cell electrophysiology","pmids":["19794150"],"confidence":"High","gaps":["Mechanism by which KIRREL1 retains Slo1 intracellularly was not determined","Physiological consequence for kidney filtration or neuronal excitability in vivo was not tested"]},{"year":2011,"claim":"Showing that Myo1c directly binds KIRREL1 and transports it to the cell membrane answered how KIRREL1 reaches the slit diaphragm, and that KIRREL1 independently promotes cell adhesion in trans (while nephrin requires KIRREL1 for adhesion) clarified the hierarchy of slit diaphragm assembly.","evidence":"Co-IP, dominant-negative/siRNA Myo1c with FRAP and TER assays; L-fibroblast trans-adhesion assay","pmids":["21402783","21306299"],"confidence":"High","gaps":["Whether Myo1c delivers KIRREL1 via a specific vesicular compartment was uncharacterized","Structural basis of the Myo1c–KIRREL1 interface was not yet resolved"]},{"year":2012,"claim":"Determining the solution structure of the KIRREL1 cytoplasmic domain and identifying critical ZO-1-binding residues (K761, Y762) by SWAXS and mutagenesis provided the first atomic-resolution view of the KIRREL1–ZO-1 interface.","evidence":"SWAXS structural determination, alanine-scanning mutagenesis with in vivo/in vitro pulldown validation","pmids":["22262837"],"confidence":"High","gaps":["Full-length extracellular domain structure remained unresolved","How phosphorylation at nearby sites alters the structural conformation was not addressed"]},{"year":2016,"claim":"SAXS-based structural modeling of the Myo1c–KIRREL1 complex and identification of a single point mutation that abolishes binding defined the molecular interface for KIRREL1 membrane trafficking.","evidence":"SAXS structural modeling, site-directed mutagenesis, FRAP live-cell imaging","pmids":["27044863"],"confidence":"High","gaps":["Whether other motors compensate in the Myo1c-binding mutant in vivo was unknown","Regulation of Myo1c–KIRREL1 binding (e.g., by calcium or phosphorylation) was not explored"]},{"year":2019,"claim":"Identification of homozygous KIRREL1 mutations causing steroid-resistant nephrotic syndrome in humans, with mutant proteins failing to reach the cell surface, translated the mouse knockout phenotype to a defined human Mendelian disease and confirmed trafficking as a disease-relevant mechanism.","evidence":"Human genetic analysis with functional membrane localization assay in podocytes","pmids":["31472902"],"confidence":"Medium","gaps":["Number of independent families was limited","Whether these mutations also affect Hippo pathway signaling in patients was not explored"]},{"year":2021,"claim":"Demonstrating that HGF binds KIRREL1 extracellularly with high affinity and induces its phosphorylation independently of MET identified KIRREL1 as a novel HGF receptor that mediates podocyte repair, with SHP-2 serving as the counteracting phosphatase.","evidence":"Surface plasmon resonance with purified proteins, phosphorylation assays, cultured podocytes and ex vivo Drosophila nephrocytes","pmids":["34391780"],"confidence":"High","gaps":["Whether HGF–KIRREL1 signaling is relevant to Hippo pathway regulation was not tested","In vivo mammalian validation of HGF-dependent podocyte repair via KIRREL1 was lacking"]},{"year":2022,"claim":"Three independent studies converged to show that KIRREL1 directly binds SAV1 and LATS1/2, activating the Hippo kinase cascade to suppress YAP/TAZ, and that YAP/TAZ transcriptionally induces KIRREL1, forming a negative feedback loop — establishing KIRREL1 as a cell-surface tumor suppressor upstream of Hippo signaling.","evidence":"Reciprocal co-IP, CRISPR knockout, YAP reporter assays, in vivo CRISPR screen, LATS kinase activity assays, mouse liver regeneration and cholangiocarcinoma models","pmids":["35177623","36044856","35704761"],"confidence":"High","gaps":["How KIRREL1 simultaneously engages nephrin at the slit diaphragm and SAV1/LATS in Hippo signaling — whether these are tissue-context-dependent or co-occurring — is unresolved","Structural basis of the KIRREL1–SAV1 interaction is unknown","Whether KIRREL1's Hippo function requires its extracellular adhesion or only its cytoplasmic domain was not dissected"]},{"year":2024,"claim":"Demonstrating that KIRREL1 is required for neurite branching in dorsal horn neurons and is transcriptionally regulated by PRRXL1 via intronic binding extended its function beyond kidney and liver to nervous system development.","evidence":"ChIP for PRRXL1 binding to Neph1 intronic regions, loss-of-function neurite morphometry","pmids":["39049046"],"confidence":"Medium","gaps":["Whether the same Fyn/Grb2 signaling axis operates in neurons is untested","In vivo behavioral or circuit-level consequences of neuronal KIRREL1 loss are not characterized"]},{"year":null,"claim":"Key open questions include the high-resolution structure of the full extracellular nephrin–KIRREL1 heterodimer, how KIRREL1 partitions between its slit diaphragm, Hippo, and neuronal functions in different tissues, and whether its HGF receptor and Hippo activator roles intersect.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution crystal or cryo-EM structure of full-length KIRREL1 or the nephrin–KIRREL1 complex exists in the peer-reviewed literature","Mechanism by which tissue context determines KIRREL1's partner selection (nephrin vs. SAV1/LATS) is unknown","Whether the HGF–KIRREL1 axis modulates YAP activity in injured podocytes has not been tested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[0,2,3,11]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[18,19,20]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9,19,20]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[2,3,10,14,17]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[10,14]}],"pathway":[{"term_id":"GO:0001618","term_label":"virus receptor activity","supporting_discovery_ids":[18]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,7,8,18,19,20,21]},{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[2,3,11,19]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[22]}],"complexes":["slit diaphragm complex (nephrin-NEPH1-ZO-1)","Hippo pathway SAV1-LATS complex"],"partners":["NPHS1","TJP1","NPHS2","FYN","GRB2","MYO1C","SAV1","LATS1"],"other_free_text":[]},"mechanistic_narrative":"KIRREL1 (NEPH1) is a transmembrane immunoglobulin superfamily protein that functions as a core structural and signaling component of the glomerular slit diaphragm and as a cell-surface activator of the Hippo tumor-suppressor pathway. At the podocyte slit diaphragm, KIRREL1 forms glycosylation-dependent heterodimers with nephrin via extracellular Ig domains and binds ZO-1 through a C-terminal PDZ-binding motif, assembling an adhesion–scaffolding complex essential for filtration barrier integrity; genetic deletion causes foot process effacement and proteinuria, and homozygous loss-of-function mutations in humans cause steroid-resistant nephrotic syndrome [PMID:11416156, PMID:12865409, PMID:12660326, PMID:31472902]. Fyn kinase phosphorylates KIRREL1 on cytoplasmic tyrosines (including Y637/Y638), creating docking sites for Grb2 and Csk, regulating the KIRREL1–ZO-1 interaction as a phosphorylation-dependent switch, and cooperating with nephrin–Nck signaling to drive actin polymerization at intercellular junctions, while the motor protein Myo1c mediates KIRREL1 vesicular trafficking to the plasma membrane [PMID:17923684, PMID:18258597, PMID:18922801, PMID:21402783]. Independent of its renal role, KIRREL1 directly binds SAV1 and LATS1/2 at cell–cell contacts to promote Hippo pathway kinase activation and YAP/TAZ suppression, forming a TEAD-dependent negative feedback loop; its loss enhances YAP-driven hepatocyte reprogramming and tumor growth in vivo [PMID:35177623, PMID:36044856, PMID:35704761]."},"prefetch_data":{"uniprot":{"accession":"Q96J84","full_name":"Kin of IRRE-like protein 1","aliases":["Kin of irregular chiasm-like protein 1","Nephrin-like protein 1"],"length_aa":757,"mass_kda":83.5,"function":"Required for proper function of the glomerular filtration barrier. It is involved in the maintenance of a stable podocyte architecture with interdigitating foot processes connected by specialized cell-cell junctions, known as the slit diaphragm (PubMed:31472902). It is a signaling protein that needs the presence of TEC kinases to fully trans-activate the transcription factor AP-1 (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q96J84/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/KIRREL1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/KIRREL1","total_profiled":1310},"omim":[{"mim_id":"619201","title":"NEPHROTIC SYNDROME, TYPE 23; NPHS23","url":"https://www.omim.org/entry/619201"},{"mim_id":"607428","title":"KIRRE-LIKE NEPHRIN FAMILY ADHESION MOLECULE 1; KIRREL1","url":"https://www.omim.org/entry/607428"},{"mim_id":"256300","title":"NEPHROTIC SYNDROME, TYPE 1; NPHS1","url":"https://www.omim.org/entry/256300"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/KIRREL1"},"hgnc":{"alias_symbol":["NEPH1"],"prev_symbol":["KIRREL"]},"alphafold":{"accession":"Q96J84","domains":[{"cath_id":"2.60.40.10","chopping":"18-118","consensus_level":"high","plddt":91.5239,"start":18,"end":118},{"cath_id":"2.60.40.10","chopping":"120-302","consensus_level":"medium","plddt":95.0719,"start":120,"end":302},{"cath_id":"2.60.40.10","chopping":"307-391","consensus_level":"high","plddt":94.8241,"start":307,"end":391},{"cath_id":"2.60.40.10","chopping":"395-490","consensus_level":"high","plddt":91.8434,"start":395,"end":490}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96J84","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96J84-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96J84-F1-predicted_aligned_error_v6.png","plddt_mean":75.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=KIRREL1","jax_strain_url":"https://www.jax.org/strain/search?query=KIRREL1"},"sequence":{"accession":"Q96J84","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96J84.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96J84/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96J84"}},"corpus_meta":[{"pmid":"11416156","id":"PMC_11416156","title":"Proteinuria and perinatal lethality in mice lacking NEPH1, a novel protein with homology to NEPHRIN.","date":"2001","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11416156","citation_count":336,"is_preprint":false},{"pmid":"12424224","id":"PMC_12424224","title":"NEPH1 defines a novel family of podocin interacting proteins.","date":"2002","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/12424224","citation_count":178,"is_preprint":false},{"pmid":"12865409","id":"PMC_12865409","title":"Neph1 and nephrin interaction in the slit diaphragm is an important determinant of glomerular permeability.","date":"2003","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/12865409","citation_count":170,"is_preprint":false},{"pmid":"12646566","id":"PMC_12646566","title":"Nephrin and Neph1 co-localize at the podocyte foot process intercellular 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Cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/19794150","citation_count":22,"is_preprint":false},{"pmid":"29022109","id":"PMC_29022109","title":"Interaction of CD80 with Neph1: a potential mechanism of podocyte injury.","date":"2017","source":"Clinical and experimental nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/29022109","citation_count":21,"is_preprint":false},{"pmid":"35704761","id":"PMC_35704761","title":"Integrated screens uncover a cell surface tumor suppressor gene KIRREL involved in Hippo pathway.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/35704761","citation_count":21,"is_preprint":false},{"pmid":"28935902","id":"PMC_28935902","title":"Targeting Neph1 and ZO-1 protein-protein interaction in podocytes prevents podocyte injury and preserves glomerular filtration function.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28935902","citation_count":21,"is_preprint":false},{"pmid":"28815295","id":"PMC_28815295","title":"Loss of Kirrel family members alters glomerular structure and synapse numbers in the accessory olfactory bulb.","date":"2017","source":"Brain structure & function","url":"https://pubmed.ncbi.nlm.nih.gov/28815295","citation_count":14,"is_preprint":false},{"pmid":"34731636","id":"PMC_34731636","title":"Molecular and structural basis of olfactory sensory neuron axon coalescence by Kirrel receptors.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34731636","citation_count":13,"is_preprint":false},{"pmid":"22262837","id":"PMC_22262837","title":"Solution structure analysis of cytoplasmic domain of podocyte protein Neph1 using small/wide angle x-ray scattering (SWAXS).","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22262837","citation_count":13,"is_preprint":false},{"pmid":"25298195","id":"PMC_25298195","title":"Angiotensin II type 1 receptor blockade ameliorates proteinuria in puromycin aminonucleoside nephropathy by inhibiting the reduction of NEPH1 and nephrin.","date":"2014","source":"Journal of nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/25298195","citation_count":11,"is_preprint":false},{"pmid":"34391780","id":"PMC_34391780","title":"Phosphorylation of slit diaphragm proteins NEPHRIN and NEPH1 upon binding of HGF promotes podocyte repair.","date":"2021","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/34391780","citation_count":11,"is_preprint":false},{"pmid":"25404935","id":"PMC_25404935","title":"Neph1 is reduced in primary focal segmental glomerulosclerosis, minimal change nephrotic syndrome, and corresponding experimental animal models of adriamycin-induced nephropathy and puromycin aminonucleoside nephrosis.","date":"2014","source":"Nephron extra","url":"https://pubmed.ncbi.nlm.nih.gov/25404935","citation_count":11,"is_preprint":false},{"pmid":"27044863","id":"PMC_27044863","title":"Structural Analysis of the Myo1c and Neph1 Complex Provides Insight into the Intracellular Movement of Neph1.","date":"2016","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/27044863","citation_count":9,"is_preprint":false},{"pmid":"37909722","id":"PMC_37909722","title":"KIRREL promotes the proliferation of gastric cancer cells and angiogenesis through the PI3K/AKT/mTOR pathway.","date":"2023","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37909722","citation_count":8,"is_preprint":false},{"pmid":"24303129","id":"PMC_24303129","title":"Identification and characterization of novel Kirrel isoform during myogenesis.","date":"2013","source":"Physiological reports","url":"https://pubmed.ncbi.nlm.nih.gov/24303129","citation_count":8,"is_preprint":false},{"pmid":"40815258","id":"PMC_40815258","title":"Anti-nephrin, anti-podocin and anti-Kirrel1 antibodies: biological challenges and clinical implications.","date":"2026","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - 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NEPH1 also triggers AP-1 activation requiring Tec family kinases.\",\n      \"method\": \"Co-immunoprecipitation, site-directed mutagenesis, reporter assays\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus mutagenesis with functional reporter assay\",\n      \"pmids\": [\"12424224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Neph1 localizes to the glomerular slit diaphragm by immunogold electron microscopy and directly interacts with nephrin (via extracellular segments) and ZO-1 (via ZO-1 PDZ domains with Neph1 cytoplasmic tail). Disrupting the Neph1-nephrin interaction in vivo causes proteinuria and loss of ZO-1 protein expression.\",\n      \"method\": \"Immunogold electron microscopy, native and recombinant protein co-immunoprecipitation, in vivo antibody injection model\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization, reciprocal Co-IP, and in vivo functional consequence\",\n      \"pmids\": [\"12865409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Neph1 localizes exclusively to lateral margins of podocyte foot processes at the slit diaphragm insertion. Neph1 and Nephrin form direct cis-heterodimeric interactions involving both their cytoplasmic domains and their extracellular domains; Neph1 does not homodimerize via its extracellular domain.\",\n      \"method\": \"Immunogold electron microscopy, detergent-resistant membrane fractionation, co-immunoprecipitation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment with functional context, multiple orthogonal binding assays\",\n      \"pmids\": [\"12646566\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"NEPH1 forms homodimers and heterodimers with nephrin through promiscuous Ig-domain interactions; two Ig domains of either protein are sufficient for binding. These interactions are strictly dependent on post-translational glycosylation.\",\n      \"method\": \"Co-immunoprecipitation, NEPH1-IgG fusion protein pulldown, truncation analysis, overexpression in HEK293T cells\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic truncation analysis with glycosylation requirement established\",\n      \"pmids\": [\"12660326\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Neph1 is expressed at synaptic sites in the mouse brain (including hippocampus CA1/CA3) and interacts with the PDZ domain of the synaptic scaffold CASK via its cytoplasmic tail, suggesting a role in synaptogenesis.\",\n      \"method\": \"In situ hybridization, immunohistochemistry, immunogold electron microscopy, co-immunoprecipitation/PDZ domain pulldown\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — direct PDZ-domain interaction assay with localization, single lab\",\n      \"pmids\": [\"16874800\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Neph1 is phosphorylated on specific tyrosine residues by the Src family kinase Fyn, leading to recruitment of the adaptor Grb2. Neph1-Nephrin direct interaction juxtaposes Grb2 and Nck1/2 at the membrane to cooperatively promote actin polymerization at the podocyte intercellular junction.\",\n      \"method\": \"In vitro kinase assay, site-directed mutagenesis of phosphorylation sites, co-immunoprecipitation, actin polymerization assays at plasma membrane\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro kinase assay plus mutagenesis and functional actin polymerization readout\",\n      \"pmids\": [\"17923684\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Neph1 is phosphorylated in vivo by Src family kinase Fyn on multiple tyrosine residues including Y637 and Y638; phosphorylation-dependent binding of Neph1 to adaptor Grb2 and kinase Csk was demonstrated from rat glomerular lysates. Neph1 attenuates Fyn-elicited ERK activation through its Grb2-binding motif.\",\n      \"method\": \"In vitro kinase assay, peptide mass fingerprinting, site-directed mutagenesis, pulldown from glomerular lysates, ERK signaling assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro kinase assay with mass fingerprinting and mutagenesis plus endogenous tissue pulldown\",\n      \"pmids\": [\"18258597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Renal ischemia causes rapid dissociation of the Neph1-ZO-1 interaction; recovery restores interaction dependent on Fyn-mediated tyrosine phosphorylation of Neph1. Tyrosine phosphorylation of Neph1 significantly increases Neph1-ZO-1 binding, establishing phosphorylation as a switch controlling this complex.\",\n      \"method\": \"In vivo rat ischemia model, cell culture ATP-depletion injury model, co-immunoprecipitation, immunofluorescence\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo and in vitro models with mechanistic phosphorylation link, two orthogonal systems\",\n      \"pmids\": [\"18922801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Neph1 interacts with large-conductance Ca2+-activated K+ channels (Slo1/BK) encoded by Slo1, demonstrated by reciprocal co-immunoprecipitation from endogenous podocyte and ciliary ganglion neuron proteins. Neph1 suppresses steady-state surface expression of Slo1 in podocytes and neurons, while siRNA knockdown of Neph1 in neurons increases Slo1 surface expression and BKCa current.\",\n      \"method\": \"Reciprocal co-immunoprecipitation from endogenous cells, GST pulldown, cell surface biotinylation, siRNA knockdown, whole-cell electrophysiology\",\n      \"journal\": \"American journal of physiology. Cell physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP from multiple endogenous sources plus functional electrophysiology readout\",\n      \"pmids\": [\"19794150\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Motor protein Myo1c directly interacts with Neph1 in an actin-dependent manner and facilitates transport of Neph1 to the podocyte cell membrane; dominant-negative Myo1c or Myo1c knockdown significantly reduces Neph1 membrane localization and impairs tight junction formation and cell migration.\",\n      \"method\": \"In vivo and in vitro co-immunoprecipitation, dominant-negative overexpression, siRNA knockdown, live-cell imaging, transepithelial electric resistance assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct interaction plus loss-of-function with defined membrane trafficking and junction phenotype\",\n      \"pmids\": [\"21402783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Neph1 and Neph3 independently induce cell adhesion, while nephrin requires trans-interaction with Neph1 or Neph3 to promote cell-cell contact formation. Trans-interaction of nephrin with Neph1 or Neph3 down-regulates tyrosine phosphorylation of nephrin.\",\n      \"method\": \"L-fibroblast cell adhesion assay, co-immunoprecipitation for heterodimerization, phosphorylation analysis\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — cell-based adhesion assay with mechanistic phosphorylation link, single lab\",\n      \"pmids\": [\"21306299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Solution structure of the Neph1 cytoplasmic domain (Neph1-CD) determined by SWAXS; structural modeling of the Neph1-CD·ZO-1-PDZ1 complex identified that residues Lys-761 and Tyr-762 in Neph1 (in addition to C-terminal Thr-His-Val) are critical for ZO-1 binding, validated by alanine-scanning mutagenesis.\",\n      \"method\": \"Small/wide angle X-ray scattering (SWAXS), circular dichroism, in vivo and in vitro pulldown, site-directed mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structural determination plus mutagenesis with functional binding validation\",\n      \"pmids\": [\"22262837\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Inhibiting Neph1 signaling by transducing its cytoplasmic domain (Neph1-CD) into podocytes prevents puromycin aminonucleoside (PAN)-induced phosphorylation of Neph1, retains Neph1 in lipid raft fractions and at the membrane, and protects podocytes from cytoskeletal damage and albumin leakage.\",\n      \"method\": \"Protein transduction domain approach, subcellular fractionation, immunofluorescence, in vivo zebrafish injury model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with defined cellular phenotype across in vitro and in vivo models, single lab\",\n      \"pmids\": [\"24554715\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Myo1c binds Neph1 at its C-terminal tail domain, as demonstrated by SAXS structural modeling showing an extended S-shaped Myo1c with Neph1 attached. A single point mutation in Neph1 at the identified interaction surface abolishes Myo1c binding in vitro and in live-cell assays. FRAP demonstrates Myo1c-dependent intracellular vesicular movement and membrane turnover of Neph1.\",\n      \"method\": \"Small angle X-ray scattering, site-directed mutagenesis, in vitro and live-cell binding assays, FRAP live-cell imaging\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structural determination plus mutagenesis plus live-cell functional imaging\",\n      \"pmids\": [\"27044863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CD80 interacts with Neph1 via their extracellular domains, demonstrated by pulldown assays in HEK293 cells; CD80 co-localizes with Neph1 in podocytes and its overexpression causes actin derangement.\",\n      \"method\": \"Co-immunoprecipitation/pulldown in HEK293 cells, immunofluorescence co-localization\",\n      \"journal\": \"Clinical and experimental nephrology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single pulldown assay, single lab, no mutagenesis\",\n      \"pmids\": [\"29022109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Stabilizing the Neph1-ZO-1 protein-protein interaction using the small molecule isodesmosine (ISD) enhances Neph1-ZO-1 binding in vitro and in vivo, and protects podocytes from injury-induced loss of transepithelial permeability in cell culture, mouse, and zebrafish models.\",\n      \"method\": \"Structural pocket screening, small molecule binding assays, biochemical binding analysis, TER assays, in vivo mouse and zebrafish models\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic PPI stabilization validated across multiple model systems\",\n      \"pmids\": [\"28935902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Homozygous mutations in KIRREL1 cause steroid-resistant nephrotic syndrome; mutant KIRREL1 proteins fail to localize to the podocyte cell membrane, indicating defective trafficking and impaired podocyte function.\",\n      \"method\": \"Human genetic analysis, functional assessment of mutant protein membrane localization in podocytes\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — human disease mutations with direct cellular trafficking phenotype\",\n      \"pmids\": [\"31472902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEPHRIN and NEPH1 are novel receptor proteins for hepatocyte growth factor (HGF); HGF binds their extracellular domains with high affinity (surface plasmon resonance), induces their phosphorylation independently of the MET receptor, and SHP-2 (PTPN11) mediates their dephosphorylation. HGF-induced phosphorylation of NEPHRIN and NEPH1 promotes podocyte repair.\",\n      \"method\": \"Surface plasmon resonance, baculovirus-expressed recombinant proteins, phosphorylation assays, molecular modeling, in vitro cultured podocytes, ex vivo Drosophila nephrocytes, chemical injury models\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted binding with purified proteins (SPR) plus functional cellular validation across multiple models\",\n      \"pmids\": [\"34391780\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"KIRREL1 physically interacts with SAV1 and recruits SAV1 to cell-cell contact sites, acting as a positive upstream regulator of the Hippo pathway. Knockout of KIRREL1 increases YAP activity in neighboring cells. During liver regeneration, KIRREL1 ablation enhances hepatic YAP activity and hepatocyte reprogramming.\",\n      \"method\": \"Co-immunoprecipitation, CRISPR knockout, YAP activity reporter assays, in vivo mouse liver regeneration model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus genetic KO with defined pathway phenotype in vitro and in vivo\",\n      \"pmids\": [\"35177623\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"KIRREL1 interacts with both SAV1 and LATS1/2, promoting LATS1/2 activation by MST1/2 Hippo kinases, thereby inhibiting YAP/TAZ oncoproteins. YAP/TAZ in turn transcriptionally induce KIRREL1 expression in a TEAD1-4-dependent manner, forming a negative feedback loop. Transgenic KIRREL1 expression blocks tumorigenesis in a mouse intrahepatic cholangiocarcinoma model.\",\n      \"method\": \"Co-immunoprecipitation, LATS1/2 kinase activity assays, transcriptional reporter assays, in vivo mouse tumor model\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — kinase activation assays, multiple binding partners, in vivo tumor suppressor validation\",\n      \"pmids\": [\"36044856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In vivo CRISPR screen confirmed KIRREL1 loss promotes tumor growth; KIRREL1 directly binds SAV1 to activate the Hippo tumor suppressor pathway.\",\n      \"method\": \"In vivo CRISPR screen with custom cell surface protein library, Hippo pathway reporter screen, direct binding assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — unbiased in vivo CRISPR screen plus orthogonal pathway reporter, replicated finding across three independent 2022 studies\",\n      \"pmids\": [\"35704761\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Neph1 is required for neurite branching in developing spinal cord dorsal horn neurons; the homeodomain transcription factor PRRXL1 directly binds Neph1 intronic regions (by ChIP) and prevents premature Neph1 expression in superficial dorsal horn laminae.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), Neph1 loss-of-function analysis, neurite branching morphometric assay, spatiotemporal expression analysis\",\n      \"journal\": \"Neural development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP with functional neurite branching phenotype, single lab\",\n      \"pmids\": [\"39049046\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-electron tomography of human kidney tissue resolves the near-native slit diaphragm architecture as a fishnet-like lattice; an atomic model based on the Nephrin-Neph1 heterodimer reveals ~9 nm spacing in humans, establishing the structural basis for the filtration sieve.\",\n      \"method\": \"Cryo-electron tomography of native human kidney tissue, atomic modeling based on Nephrin-Neph1 heterodimer\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — cryo-ET structural determination, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.09.24.678239\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"KIRREL1 (NEPH1) is a transmembrane immunoglobulin superfamily protein essential for glomerular slit diaphragm integrity, where it localizes to podocyte foot process junctions and forms hetero-oligomeric complexes with nephrin (via extracellular Ig domains) and ZO-1 (via PDZ interaction with its cytoplasmic tail), is phosphorylated on specific tyrosines by Fyn kinase to recruit Grb2 and cooperate with nephrin-Nck to drive actin polymerization, is trafficked to the membrane by the motor protein Myo1c, acts as a receptor for HGF to promote podocyte repair, and additionally functions as a cell-surface upstream activator of the Hippo tumor-suppressor pathway by binding SAV1 and LATS1/2 at cell-cell contacts to suppress YAP/TAZ activity in a negative feedback loop.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"KIRREL1 (NEPH1) is a transmembrane immunoglobulin superfamily protein that functions as a core structural and signaling component of the glomerular slit diaphragm and as a cell-surface activator of the Hippo tumor-suppressor pathway. At the podocyte slit diaphragm, KIRREL1 forms glycosylation-dependent heterodimers with nephrin via extracellular Ig domains and binds ZO-1 through a C-terminal PDZ-binding motif, assembling an adhesion–scaffolding complex essential for filtration barrier integrity; genetic deletion causes foot process effacement and proteinuria, and homozygous loss-of-function mutations in humans cause steroid-resistant nephrotic syndrome [PMID:11416156, PMID:12865409, PMID:12660326, PMID:31472902]. Fyn kinase phosphorylates KIRREL1 on cytoplasmic tyrosines (including Y637/Y638), creating docking sites for Grb2 and Csk, regulating the KIRREL1–ZO-1 interaction as a phosphorylation-dependent switch, and cooperating with nephrin–Nck signaling to drive actin polymerization at intercellular junctions, while the motor protein Myo1c mediates KIRREL1 vesicular trafficking to the plasma membrane [PMID:17923684, PMID:18258597, PMID:18922801, PMID:21402783]. Independent of its renal role, KIRREL1 directly binds SAV1 and LATS1/2 at cell–cell contacts to promote Hippo pathway kinase activation and YAP/TAZ suppression, forming a TEAD-dependent negative feedback loop; its loss enhances YAP-driven hepatocyte reprogramming and tumor growth in vivo [PMID:35177623, PMID:36044856, PMID:35704761].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing that KIRREL1 is essential for podocyte foot process integrity resolved the gene's primary physiological role: its deletion causes slit diaphragm loss and proteinuria, proving it is not redundant with nephrin.\",\n      \"evidence\": \"Gene-trap knockout mouse with electron microscopy phenotyping\",\n      \"pmids\": [\"11416156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular partners at the slit diaphragm were unknown\", \"Whether KIRREL1 functions as an adhesion molecule or solely as a signaling receptor was unclear\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Identification of the KIRREL1–podocin interaction and its dependence on a central tyrosine residue established the first cytoplasmic signaling link, suggesting KIRREL1 operates within a multi-protein slit diaphragm signaling complex.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation with site-directed mutagenesis and AP-1 reporter assays\",\n      \"pmids\": [\"12424224\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream signaling pathways were not defined\", \"Whether podocin interaction is required in vivo was untested\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrating that KIRREL1 forms direct heterodimers with nephrin (via extracellular Ig domains) and binds ZO-1 (via PDZ interaction), and that disrupting these complexes in vivo causes proteinuria, defined the core molecular architecture of the slit diaphragm as a KIRREL1–nephrin–ZO-1 ternary complex.\",\n      \"evidence\": \"Immunogold EM localization, reciprocal co-IP of native and recombinant proteins, in vivo antibody injection, truncation/glycosylation analysis\",\n      \"pmids\": [\"12865409\", \"12646566\", \"12660326\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and geometry of the nephrin–KIRREL1 heterodimer were unresolved\", \"Whether glycosylation-dependent binding reflects a quality-control or a regulatory mechanism was unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identifying Fyn-mediated tyrosine phosphorylation of KIRREL1 and its recruitment of Grb2 to cooperate with nephrin–Nck in actin polymerization answered how KIRREL1 transduces extracellular adhesion into cytoskeletal remodeling at podocyte junctions.\",\n      \"evidence\": \"In vitro kinase assay, phosphosite mutagenesis, actin polymerization assays at the plasma membrane\",\n      \"pmids\": [\"17923684\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of individual phosphosites had not been tested genetically\", \"Upstream signals triggering Fyn activation at the slit diaphragm were unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Mapping specific phosphorylation sites (Y637/Y638) and showing that ischemia disrupts the KIRREL1–ZO-1 interaction while Fyn-dependent re-phosphorylation restores it established tyrosine phosphorylation as a molecular switch controlling slit diaphragm assembly and repair.\",\n      \"evidence\": \"Peptide mass fingerprinting, site-directed mutagenesis, rat ischemia model and ATP-depletion injury model with co-IP\",\n      \"pmids\": [\"18258597\", \"18922801\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which phosphatase reverses the switch was not identified at this time\", \"Whether phosphorylation-dependent ZO-1 binding is required for barrier function in vivo remained untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Discovery that KIRREL1 suppresses surface expression of BK (Slo1) channels in podocytes and neurons revealed an unexpected function as a regulator of ion channel trafficking, extending its role beyond structural adhesion.\",\n      \"evidence\": \"Reciprocal co-IP from endogenous podocyte and neuronal lysates, siRNA knockdown, whole-cell electrophysiology\",\n      \"pmids\": [\"19794150\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which KIRREL1 retains Slo1 intracellularly was not determined\", \"Physiological consequence for kidney filtration or neuronal excitability in vivo was not tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showing that Myo1c directly binds KIRREL1 and transports it to the cell membrane answered how KIRREL1 reaches the slit diaphragm, and that KIRREL1 independently promotes cell adhesion in trans (while nephrin requires KIRREL1 for adhesion) clarified the hierarchy of slit diaphragm assembly.\",\n      \"evidence\": \"Co-IP, dominant-negative/siRNA Myo1c with FRAP and TER assays; L-fibroblast trans-adhesion assay\",\n      \"pmids\": [\"21402783\", \"21306299\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Myo1c delivers KIRREL1 via a specific vesicular compartment was uncharacterized\", \"Structural basis of the Myo1c–KIRREL1 interface was not yet resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Determining the solution structure of the KIRREL1 cytoplasmic domain and identifying critical ZO-1-binding residues (K761, Y762) by SWAXS and mutagenesis provided the first atomic-resolution view of the KIRREL1–ZO-1 interface.\",\n      \"evidence\": \"SWAXS structural determination, alanine-scanning mutagenesis with in vivo/in vitro pulldown validation\",\n      \"pmids\": [\"22262837\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length extracellular domain structure remained unresolved\", \"How phosphorylation at nearby sites alters the structural conformation was not addressed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"SAXS-based structural modeling of the Myo1c–KIRREL1 complex and identification of a single point mutation that abolishes binding defined the molecular interface for KIRREL1 membrane trafficking.\",\n      \"evidence\": \"SAXS structural modeling, site-directed mutagenesis, FRAP live-cell imaging\",\n      \"pmids\": [\"27044863\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other motors compensate in the Myo1c-binding mutant in vivo was unknown\", \"Regulation of Myo1c–KIRREL1 binding (e.g., by calcium or phosphorylation) was not explored\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identification of homozygous KIRREL1 mutations causing steroid-resistant nephrotic syndrome in humans, with mutant proteins failing to reach the cell surface, translated the mouse knockout phenotype to a defined human Mendelian disease and confirmed trafficking as a disease-relevant mechanism.\",\n      \"evidence\": \"Human genetic analysis with functional membrane localization assay in podocytes\",\n      \"pmids\": [\"31472902\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Number of independent families was limited\", \"Whether these mutations also affect Hippo pathway signaling in patients was not explored\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrating that HGF binds KIRREL1 extracellularly with high affinity and induces its phosphorylation independently of MET identified KIRREL1 as a novel HGF receptor that mediates podocyte repair, with SHP-2 serving as the counteracting phosphatase.\",\n      \"evidence\": \"Surface plasmon resonance with purified proteins, phosphorylation assays, cultured podocytes and ex vivo Drosophila nephrocytes\",\n      \"pmids\": [\"34391780\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether HGF–KIRREL1 signaling is relevant to Hippo pathway regulation was not tested\", \"In vivo mammalian validation of HGF-dependent podocyte repair via KIRREL1 was lacking\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Three independent studies converged to show that KIRREL1 directly binds SAV1 and LATS1/2, activating the Hippo kinase cascade to suppress YAP/TAZ, and that YAP/TAZ transcriptionally induces KIRREL1, forming a negative feedback loop — establishing KIRREL1 as a cell-surface tumor suppressor upstream of Hippo signaling.\",\n      \"evidence\": \"Reciprocal co-IP, CRISPR knockout, YAP reporter assays, in vivo CRISPR screen, LATS kinase activity assays, mouse liver regeneration and cholangiocarcinoma models\",\n      \"pmids\": [\"35177623\", \"36044856\", \"35704761\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How KIRREL1 simultaneously engages nephrin at the slit diaphragm and SAV1/LATS in Hippo signaling — whether these are tissue-context-dependent or co-occurring — is unresolved\", \"Structural basis of the KIRREL1–SAV1 interaction is unknown\", \"Whether KIRREL1's Hippo function requires its extracellular adhesion or only its cytoplasmic domain was not dissected\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrating that KIRREL1 is required for neurite branching in dorsal horn neurons and is transcriptionally regulated by PRRXL1 via intronic binding extended its function beyond kidney and liver to nervous system development.\",\n      \"evidence\": \"ChIP for PRRXL1 binding to Neph1 intronic regions, loss-of-function neurite morphometry\",\n      \"pmids\": [\"39049046\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the same Fyn/Grb2 signaling axis operates in neurons is untested\", \"In vivo behavioral or circuit-level consequences of neuronal KIRREL1 loss are not characterized\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include the high-resolution structure of the full extracellular nephrin–KIRREL1 heterodimer, how KIRREL1 partitions between its slit diaphragm, Hippo, and neuronal functions in different tissues, and whether its HGF receptor and Hippo activator roles intersect.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution crystal or cryo-EM structure of full-length KIRREL1 or the nephrin–KIRREL1 complex exists in the peer-reviewed literature\", \"Mechanism by which tissue context determines KIRREL1's partner selection (nephrin vs. SAV1/LATS) is unknown\", \"Whether the HGF–KIRREL1 axis modulates YAP activity in injured podocytes has not been tested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [0, 2, 3, 11]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [18, 19, 20]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9, 19, 20]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [2, 3, 10, 14, 17]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [10, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0001618\", \"supporting_discovery_ids\": [18]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 7, 8, 18, 19, 20, 21]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [2, 3, 11, 19]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [22]}\n    ],\n    \"complexes\": [\n      \"slit diaphragm complex (nephrin-NEPH1-ZO-1)\",\n      \"Hippo pathway SAV1-LATS complex\"\n    ],\n    \"partners\": [\n      \"NPHS1\",\n      \"TJP1\",\n      \"NPHS2\",\n      \"FYN\",\n      \"GRB2\",\n      \"MYO1C\",\n      \"SAV1\",\n      \"LATS1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}