{"gene":"NECAP1","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2004,"finding":"NECAP1 contains a WXX(F/W)X(D/E) interaction motif that binds the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage, a site distinct from the platform subdomain that binds DP(F/W) or FXDXF motifs. Both alpha appendage binding sites can be engaged simultaneously, allowing temporal ordering of endocytic accessory proteins during clathrin-mediated endocytosis.","method":"Biochemical binding assays identifying interaction motifs and sites on the AP-2 alpha appendage (dual-site engagement experiments)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — direct binding assays with mutagenesis of interaction motifs and defined structural sites on AP-2 alpha appendage, rigorous mechanistic characterization in a focused study","pmids":["15292237"],"is_preprint":false},{"year":2004,"finding":"NECAP1 and NECAP2 were identified as novel components of clathrin-coated vesicles (CCVs) isolated from adult brain, and characterization of these proteins led to identification of a new consensus motif mediating protein interactions with clathrin adaptor protein 2 (AP-2).","method":"Subcellular fractionation of brain CCVs combined with mass spectrometry proteomics; biochemical characterization of AP-2 interaction motif","journal":"Biochemical Society transactions","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — subcellular proteomics plus biochemical motif characterization in a single study; consistent with the more detailed study (PMID:15292237)","pmids":["15494011"],"is_preprint":false},{"year":2019,"finding":"In rodents, Necap1 protein is enriched in neuronal clathrin-coated vesicles and modulates synaptic vesicle recycling, as established by prior experimental work cited in this clinical report. Loss of the WXXF motif (through truncating mutations) is proposed as a common pathomechanism for disease.","method":"cDNA analysis confirming abnormal splicing leading to truncated mRNA; reference to prior rodent experimental localization data","journal":"Journal of human genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — functional localization data cited from prior rodent work, not directly demonstrated in this paper; cDNA splicing confirmation is supportive but indirect","pmids":["30626896"],"is_preprint":false}],"current_model":"NECAP1 is a clathrin-coated vesicle accessory protein that interacts with the AP-2 adaptor complex via a WXX(F/W)X(D/E) motif binding the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage (distinct from the platform subdomain used by other endocytic motifs), enabling dual-site engagement that temporally orders endocytic accessory proteins during clathrin-mediated endocytosis; in neurons, NECAP1 is enriched in clathrin-coated vesicles and is required for synaptic vesicle recycling, with loss-of-function causing early infantile epileptic encephalopathy."},"narrative":{"mechanistic_narrative":"NECAP1 is a clathrin-coated vesicle accessory protein that organizes the recruitment of endocytic factors during clathrin-mediated endocytosis [PMID:15292237, PMID:15494011]. It carries a WXX(F/W)X(D/E) interaction motif that binds the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage, a site distinct from the platform subdomain that engages DP(F/W) or FXDXF motifs; because both appendage sites can be occupied at once, NECAP1 binding supports dual-site engagement that imposes a temporal order on endocytic accessory proteins [PMID:15292237]. NECAP1 was identified as a component of clathrin-coated vesicles isolated from brain, and its characterization defined the consensus motif used for this mode of AP-2 binding [PMID:15494011]. In neurons, NECAP1 is enriched in clathrin-coated vesicles and contributes to synaptic vesicle recycling, with loss of the WXXF motif through truncating mutations linked to disease [PMID:30626896]. Beyond these AP-2-centered interactions, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2004,"claim":"Defined how NECAP1 engages the AP-2 adaptor, answering whether it uses a known or novel binding mode and how that could coordinate accessory-protein assembly.","evidence":"Biochemical binding and mutagenesis assays mapping the NECAP1 motif to the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage and showing simultaneous dual-site engagement","pmids":["15292237"],"confidence":"High","gaps":["Functional consequence of temporal ordering for endocytosis not tested in cells","No structural model of the NECAP1-appendage complex reported here","Substrate/cargo selectivity of NECAP1-dependent assembly unaddressed"]},{"year":2004,"claim":"Established NECAP1 (and NECAP2) as bona fide constituents of clathrin-coated vesicles and identified the new consensus AP-2 interaction motif, placing the protein in the endocytic machinery.","evidence":"Subcellular fractionation of brain clathrin-coated vesicles with mass spectrometry plus biochemical motif characterization","pmids":["15494011"],"confidence":"Medium","gaps":["Quantitative role within the CCV proteome not defined","Functional requirement for vesicle formation not tested"]},{"year":2019,"claim":"Connected NECAP1 loss-of-function to human disease and proposed disruption of the WXXF motif as the shared pathomechanism, linking the AP-2 binding mode to physiology.","evidence":"cDNA analysis confirming abnormal splicing producing truncated mRNA, with neuronal CCV localization and synaptic vesicle recycling roles cited from prior rodent work","pmids":["30626896"],"confidence":"Low","gaps":["Synaptic vesicle recycling role cited from prior rodent work, not directly demonstrated here","Direct demonstration that motif loss abolishes AP-2 binding in patient cells absent","Mechanistic link between truncation and neuronal phenotype not established experimentally"]},{"year":null,"claim":"How NECAP1-mediated temporal ordering of accessory proteins shapes synaptic vesicle recycling and how its disruption causes neuronal dysfunction remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No in-cell mechanistic test of the dual-site ordering model","No structural data on the NECAP1-AP-2 interface","Phenotypic mechanism of disease mutations not directly established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":["AP2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NC96","full_name":"Adaptin ear-binding coat-associated protein 1","aliases":["NECAP endocytosis-associated protein 1","NECAP-1"],"length_aa":275,"mass_kda":29.7,"function":"Involved in endocytosis","subcellular_location":"Cytoplasmic vesicle, clathrin-coated vesicle membrane; Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q8NC96/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NECAP1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000089818","cell_line_id":"CID000538","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"membrane","grade":3},{"compartment":"nucleoplasm","grade":3}],"interactors":[{"gene":"HIST1H1D","stoichiometry":4.0},{"gene":"H1FX","stoichiometry":4.0},{"gene":"HIST3H2BB","stoichiometry":4.0},{"gene":"H2AFY","stoichiometry":0.2},{"gene":"SMARCA5","stoichiometry":0.2},{"gene":"WHSC1","stoichiometry":0.2},{"gene":"AP2A2","stoichiometry":0.2},{"gene":"AP2A1","stoichiometry":0.2},{"gene":"SUZ12","stoichiometry":0.2},{"gene":"TOP2A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000538","total_profiled":1310},"omim":[{"mim_id":"615833","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 21; DEE21","url":"https://www.omim.org/entry/615833"},{"mim_id":"611624","title":"NECAP ENDOCYTOSIS-ASSOCIATED PROTEIN 2; NECAP2","url":"https://www.omim.org/entry/611624"},{"mim_id":"611623","title":"NECAP ENDOCYTOSIS-ASSOCIATED PROTEIN 1; NECAP1","url":"https://www.omim.org/entry/611623"},{"mim_id":"308350","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 1; DEE1","url":"https://www.omim.org/entry/308350"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"brain","ntpm":64.7}],"url":"https://www.proteinatlas.org/search/NECAP1"},"hgnc":{"alias_symbol":["DKFZP566B183"],"prev_symbol":[]},"alphafold":{"accession":"Q8NC96","domains":[{"cath_id":"2.30.29.30","chopping":"9-130","consensus_level":"high","plddt":90.5833,"start":9,"end":130}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NC96","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NC96-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NC96-F1-predicted_aligned_error_v6.png","plddt_mean":69.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NECAP1","jax_strain_url":"https://www.jax.org/strain/search?query=NECAP1"},"sequence":{"accession":"Q8NC96","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NC96.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NC96/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NC96"}},"corpus_meta":[{"pmid":"15292237","id":"PMC_15292237","title":"Dual engagement regulation of protein interactions with the AP-2 adaptor alpha appendage.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15292237","citation_count":69,"is_preprint":false},{"pmid":"24399846","id":"PMC_24399846","title":"NECAP1 loss of function leads to a severe infantile epileptic encephalopathy.","date":"2014","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24399846","citation_count":24,"is_preprint":false},{"pmid":"15494011","id":"PMC_15494011","title":"Molecular mechanisms in clathrin-mediated membrane budding revealed through subcellular proteomics.","date":"2004","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/15494011","citation_count":19,"is_preprint":false},{"pmid":"32092130","id":"PMC_32092130","title":"Phosphoinositide-binding proteins mark, shape and functionally modulate highly-diverged endocytic compartments in the parasitic protist Giardia lamblia.","date":"2020","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/32092130","citation_count":15,"is_preprint":false},{"pmid":"31117272","id":"PMC_31117272","title":"Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration.","date":"2019","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/31117272","citation_count":10,"is_preprint":false},{"pmid":"35638367","id":"PMC_35638367","title":"Early infantile epileptic encephalopathy related to NECAP1: Clinical delineation of the disease and review.","date":"2022","source":"European journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/35638367","citation_count":7,"is_preprint":false},{"pmid":"35051475","id":"PMC_35051475","title":"ChIP-seq assay revealed histone modification H3K9ac involved in heat shock response of the sea cucumber Apostichopus japonicus.","date":"2022","source":"The Science of the total environment","url":"https://pubmed.ncbi.nlm.nih.gov/35051475","citation_count":7,"is_preprint":false},{"pmid":"26890086","id":"PMC_26890086","title":"Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p.","date":"2016","source":"Epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/26890086","citation_count":6,"is_preprint":false},{"pmid":"30525121","id":"PMC_30525121","title":"Confirming the pathogenicity of NECAP1 in early onset epileptic encephalopathy.","date":"2018","source":"Epilepsia open","url":"https://pubmed.ncbi.nlm.nih.gov/30525121","citation_count":5,"is_preprint":false},{"pmid":"30626896","id":"PMC_30626896","title":"A novel homozygous truncating variant of NECAP1 in early infantile epileptic encephalopathy: the second case report of EIEE21.","date":"2019","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30626896","citation_count":5,"is_preprint":false},{"pmid":"38187229","id":"PMC_38187229","title":"Identification of the transcriptome signatures and immune-inflammatory responses in postmenopausal osteoporosis.","date":"2023","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/38187229","citation_count":5,"is_preprint":false},{"pmid":"37820178","id":"PMC_37820178","title":"Importance of targeted next-generation sequencing in pediatric patients with developmental epileptic encephalopathy.","date":"2023","source":"Revista da Associacao Medica Brasileira (1992)","url":"https://pubmed.ncbi.nlm.nih.gov/37820178","citation_count":5,"is_preprint":false},{"pmid":"32754889","id":"PMC_32754889","title":"Association of Maternal DNA Methylation and Offspring Birthweight.","date":"2020","source":"Reproductive sciences (Thousand Oaks, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/32754889","citation_count":3,"is_preprint":false},{"pmid":"36777869","id":"PMC_36777869","title":"Identification of methylation-driven genes, circulating miRNAs and their potential regulatory mechanisms in gestational diabetes mellitus.","date":"2023","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/36777869","citation_count":3,"is_preprint":false},{"pmid":"40765230","id":"PMC_40765230","title":"PCR-based detection of hereditary mutations in SLC2A9, BTBD17, and NECAP1 among native Korean dog breeds.","date":"2025","source":"Journal of veterinary science","url":"https://pubmed.ncbi.nlm.nih.gov/40765230","citation_count":1,"is_preprint":false},{"pmid":"40729072","id":"PMC_40729072","title":"Decoding Molecular Interactions: Unraveling the Crosstalk between the Wnt Pathway and Key Signaling Networks by miRNA in Colorectal Cancer Progression.","date":"2025","source":"Asian Pacific journal of cancer prevention : APJCP","url":"https://pubmed.ncbi.nlm.nih.gov/40729072","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9761,"output_tokens":890,"usd":0.021316,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7355,"output_tokens":1563,"usd":0.037925,"stage2_stop_reason":"end_turn"},"total_usd":0.059241,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"NECAP1 contains a WXX(F/W)X(D/E) interaction motif that binds the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage, a site distinct from the platform subdomain that binds DP(F/W) or FXDXF motifs. Both alpha appendage binding sites can be engaged simultaneously, allowing temporal ordering of endocytic accessory proteins during clathrin-mediated endocytosis.\",\n      \"method\": \"Biochemical binding assays identifying interaction motifs and sites on the AP-2 alpha appendage (dual-site engagement experiments)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — direct binding assays with mutagenesis of interaction motifs and defined structural sites on AP-2 alpha appendage, rigorous mechanistic characterization in a focused study\",\n      \"pmids\": [\"15292237\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NECAP1 and NECAP2 were identified as novel components of clathrin-coated vesicles (CCVs) isolated from adult brain, and characterization of these proteins led to identification of a new consensus motif mediating protein interactions with clathrin adaptor protein 2 (AP-2).\",\n      \"method\": \"Subcellular fractionation of brain CCVs combined with mass spectrometry proteomics; biochemical characterization of AP-2 interaction motif\",\n      \"journal\": \"Biochemical Society transactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — subcellular proteomics plus biochemical motif characterization in a single study; consistent with the more detailed study (PMID:15292237)\",\n      \"pmids\": [\"15494011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In rodents, Necap1 protein is enriched in neuronal clathrin-coated vesicles and modulates synaptic vesicle recycling, as established by prior experimental work cited in this clinical report. Loss of the WXXF motif (through truncating mutations) is proposed as a common pathomechanism for disease.\",\n      \"method\": \"cDNA analysis confirming abnormal splicing leading to truncated mRNA; reference to prior rodent experimental localization data\",\n      \"journal\": \"Journal of human genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — functional localization data cited from prior rodent work, not directly demonstrated in this paper; cDNA splicing confirmation is supportive but indirect\",\n      \"pmids\": [\"30626896\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NECAP1 is a clathrin-coated vesicle accessory protein that interacts with the AP-2 adaptor complex via a WXX(F/W)X(D/E) motif binding the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage (distinct from the platform subdomain used by other endocytic motifs), enabling dual-site engagement that temporally orders endocytic accessory proteins during clathrin-mediated endocytosis; in neurons, NECAP1 is enriched in clathrin-coated vesicles and is required for synaptic vesicle recycling, with loss-of-function causing early infantile epileptic encephalopathy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NECAP1 is a clathrin-coated vesicle accessory protein that organizes the recruitment of endocytic factors during clathrin-mediated endocytosis [#0, #1]. It carries a WXX(F/W)X(D/E) interaction motif that binds the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage, a site distinct from the platform subdomain that engages DP(F/W) or FXDXF motifs; because both appendage sites can be occupied at once, NECAP1 binding supports dual-site engagement that imposes a temporal order on endocytic accessory proteins [#0]. NECAP1 was identified as a component of clathrin-coated vesicles isolated from brain, and its characterization defined the consensus motif used for this mode of AP-2 binding [#1]. In neurons, NECAP1 is enriched in clathrin-coated vesicles and contributes to synaptic vesicle recycling, with loss of the WXXF motif through truncating mutations linked to disease [#2]. Beyond these AP-2-centered interactions, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined how NECAP1 engages the AP-2 adaptor, answering whether it uses a known or novel binding mode and how that could coordinate accessory-protein assembly.\",\n      \"evidence\": \"Biochemical binding and mutagenesis assays mapping the NECAP1 motif to the N-terminal beta-sandwich subdomain of the AP-2 alpha appendage and showing simultaneous dual-site engagement\",\n      \"pmids\": [\"15292237\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of temporal ordering for endocytosis not tested in cells\", \"No structural model of the NECAP1-appendage complex reported here\", \"Substrate/cargo selectivity of NECAP1-dependent assembly unaddressed\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Established NECAP1 (and NECAP2) as bona fide constituents of clathrin-coated vesicles and identified the new consensus AP-2 interaction motif, placing the protein in the endocytic machinery.\",\n      \"evidence\": \"Subcellular fractionation of brain clathrin-coated vesicles with mass spectrometry plus biochemical motif characterization\",\n      \"pmids\": [\"15494011\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Quantitative role within the CCV proteome not defined\", \"Functional requirement for vesicle formation not tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected NECAP1 loss-of-function to human disease and proposed disruption of the WXXF motif as the shared pathomechanism, linking the AP-2 binding mode to physiology.\",\n      \"evidence\": \"cDNA analysis confirming abnormal splicing producing truncated mRNA, with neuronal CCV localization and synaptic vesicle recycling roles cited from prior rodent work\",\n      \"pmids\": [\"30626896\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Synaptic vesicle recycling role cited from prior rodent work, not directly demonstrated here\", \"Direct demonstration that motif loss abolishes AP-2 binding in patient cells absent\", \"Mechanistic link between truncation and neuronal phenotype not established experimentally\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NECAP1-mediated temporal ordering of accessory proteins shapes synaptic vesicle recycling and how its disruption causes neuronal dysfunction remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No in-cell mechanistic test of the dual-site ordering model\", \"No structural data on the NECAP1-AP-2 interface\", \"Phenotypic mechanism of disease mutations not directly established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"AP2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":4,"faith_total":4,"faith_pct":100.0}}