{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.il1rn","code":"thing-q14914156","url":"https://ver.cy/models/thing/q14914156/","name":"IL1RN","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"IL1RN is the human gene encoding interleukin-1 receptor antagonist, a protein that inhibits interleukin-1 signalling by competing with IL-1α and IL-1β for binding to the type I interleukin-1 receptor.","purpose":"Enable an agent to identify IL1RN, interpret observations of its sequence and expression, and judge which functional conclusions or follow-up analyses the evidence supports.","scope":{"in":["Species-qualified IL1RN gene identity and reference-sequence mapping","Alleles, sequence variants and their transcript-specific consequences","Transcript and encoded protein-isoform relationships","Expression observations qualified by tissue, cell type and experimental condition","Evidence connecting IL1RN alterations to antagonist activity and phenotypes"],"out":["Standalone physical and biochemical characterization of isolated IL-1 receptor antagonist protein","IL1R1 receptor identity and receptor-specific signaling machinery","Independent models of IL1A, IL1B and other interleukin-family genes","Nonhuman orthologs as interchangeable instances of the human gene","Recombinant medicines, their manufacturing specifications and dosing","Patient diagnosis and treatment decisions"],"boundaries":[]},"distinguishingFeatures":["Resolve the symbol with species and stable identifier: the human IL1RN record is NCBI Gene 3557. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/3557/)","Distinguish an IL1RN DNA locus from its RNA transcripts and encoded IL-1 receptor antagonist protein; these require different identifiers and assays.","Distinguish the antagonist-encoding gene from receptor genes: a record describing the IL-1 receptor itself does not identify IL1RN.","Check whether a sequence maps specifically to IL1RN rather than another interleukin-family locus.","Require product and preparation metadata when a reagent catalog uses IL1RN as a protein label; the label alone does not identify a genomic entity."],"structure":{"bundles":[{"id":"il1rn-identity","name":"IL1RN identity and entity boundary","description":"Resolve what biological entity the registry name denotes.","layers":[{"id":"gene-and-species","name":"Gene and species","description":"Anchor the entry to an organism and stable gene record.","findings":[{"id":"species-qualified-anchor","name":"Species-qualified anchor","description":"Record the evidence supporting the provisional human-gene interpretation.","questions":[{"text":"Does the registry's originating identifier resolve to human IL1RN or to a different species or entity?","id":"species-qualified-anchor-q01","kind":"provenance"},{"text":"Which stable gene identifier and approved symbol establish the intended identity?","id":"species-qualified-anchor-q02","kind":"definition"}]}]},{"id":"gene-product-separation","name":"Gene and product separation","description":"Keep locus, transcript, protein and reagent references distinguishable.","findings":[{"id":"label-resolution","name":"Ambiguous IL1RN labels","description":"Require molecular-entity evidence before attaching a reported observation to the gene.","questions":[{"text":"Does this IL1RN record describe genomic DNA, RNA, endogenous protein or a recombinant preparation?","id":"label-resolution-q01","kind":"boundary"},{"text":"Which accession or preparation identifier resolves the label, and which neighboring model should own product-specific properties?","id":"label-resolution-q02","kind":"action"}]}]}]},{"id":"locus-and-alleles","name":"Reference locus and allelic state","description":"Represent sequence observations against explicit IL1RN references.","layers":[{"id":"reference-mapping","name":"Reference mapping","description":"Make genomic and transcript coordinates reproducible.","findings":[{"id":"coordinate-anchoring","name":"Coordinate anchoring","description":"Retain the reference and mapping assumptions behind each IL1RN sequence assertion.","questions":[{"text":"Which assembly, accession version, strand and coordinate convention locate the reported IL1RN interval?","id":"coordinate-anchoring-q01","kind":"provenance"},{"text":"Does the reported sequence map uniquely to IL1RN, and what alignment evidence excludes related loci?","id":"coordinate-anchoring-q02","kind":"measurement"}]}]},{"id":"variant-configuration","name":"Variant configuration","description":"Separate individual variants from the genotype carried by a sample.","findings":[{"id":"alleles-and-consequences","name":"Alleles and transcript consequences","description":"Capture sequence changes, copy-number findings and unresolved phase without presuming functional loss.","questions":[{"text":"What IL1RN variants, copy-number changes, zygosity and phase were measured, and which regions were inadequately covered?","id":"alleles-and-consequences-q01","kind":"measurement"},{"text":"Which transcript-specific effects are predicted, and which have direct experimental support?","id":"alleles-and-consequences-q02","kind":"provenance"}]}]}]},{"id":"transcripts-and-expression","name":"Transcripts, products and expression","description":"Connect gene-level observations to identifiable molecular products and biological contexts.","layers":[{"id":"transcript-product-resolution","name":"Transcript and product resolution","description":"Track isoforms without assuming that numbering is consistent across resources.","findings":[{"id":"isoform-compartment-link","name":"Isoform and compartment linkage","description":"Establish which transcript encodes the observed product and how its compartment was determined.","questions":[{"text":"Which versioned IL1RN transcript and protein accessions correspond to the isoform named in this source?","id":"isoform-compartment-link-q01","kind":"definition"},{"text":"What evidence assigns the product to a secreted or intracellular form in the observed system?","id":"isoform-compartment-link-q02","kind":"provenance"}]}]},{"id":"expression-context","name":"Expression context","description":"Qualify abundance by sample composition, condition and time.","findings":[{"id":"contextual-abundance","name":"Contextual abundance","description":"Keep total IL1RN expression, transcript-specific expression and product abundance as distinct observations.","questions":[{"text":"In which tissue, cell population, stimulation condition and time point was IL1RN expression measured?","id":"contextual-abundance-q01","kind":"measurement"},{"text":"Does the assay measure total IL1RN RNA, a specific transcript or protein, and what normalization supports comparison?","id":"contextual-abundance-q02","kind":"measurement"}]}]}]},{"id":"antagonist-function","name":"Product-mediated IL-1 antagonism","description":"Connect IL1RN observations to tested antagonist function through identified products.","layers":[{"id":"functional-readout","name":"Functional readout","description":"Specify the receptor system, agonist and endpoint used to assess antagonism.","findings":[{"id":"antagonism-assay","name":"Antagonism assay interpretation","description":"Separate receptor binding from demonstrated suppression of an IL-1 response.","questions":[{"text":"Which IL1RN product, IL-1 agonist, receptor context and concentration range were tested?","id":"antagonism-assay-q01","kind":"measurement"},{"text":"Does the endpoint establish binding, inhibition of signaling or a downstream response, and what controls distinguish these?","id":"antagonism-assay-q02","kind":"boundary"}]}]},{"id":"gene-to-function","name":"Gene-to-function attribution","description":"Evaluate whether a gene alteration explains the observed functional change.","findings":[{"id":"causal-functional-link","name":"Causal functional link","description":"Track the steps between IL1RN sequence or expression changes and product activity.","questions":[{"text":"Were altered transcription, splicing, product abundance, localization or antagonist activity directly measured?","id":"causal-functional-link-q01","kind":"provenance"},{"text":"Would a matched control, rescue experiment or orthogonal assay resolve the remaining attribution uncertainty?","id":"causal-functional-link-q02","kind":"action"}]}]}]},{"id":"phenotype-evidence","name":"Phenotype evidence and interpretation limits","description":"Evaluate claims linking IL1RN variation to biological or disease phenotypes.","layers":[{"id":"variant-phenotype-links","name":"Variant-to-phenotype links","description":"Keep causal assertions separate from statistical associations.","findings":[{"id":"assertion-strength","name":"Assertion strength","description":"Require allele-specific evidence and an explicit phenotype definition.","questions":[{"text":"Which exact IL1RN allele or genotype is linked to which phenotype, and is the claim causal, associative or unresolved?","id":"assertion-strength-q01","kind":"definition"},{"text":"What segregation, functional, population or replication evidence supports that claim?","id":"assertion-strength-q02","kind":"provenance"}]}]},{"id":"interpretation-and-next-actions","name":"Interpretation and next actions","description":"Translate evidence gaps into bounded analytical follow-up.","findings":[{"id":"evidence-limited-action","name":"Evidence-limited action","description":"Preserve uncertainty when applying published IL1RN findings to a new sample.","questions":[{"text":"Do conflicting assertions, unresolved phase or assay limitations prevent a supported interpretation of this IL1RN observation?","id":"evidence-limited-action-q01","kind":"boundary"},{"text":"Which additional reference check, sequence confirmation or functional measurement would most directly resolve the uncertainty?","id":"evidence-limited-action-q02","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of IL1RN this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of IL1RN this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of IL1RN this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of IL1RN this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of IL1RN this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe IL1RN and the interleukin-1 receptor antagonist it encodes, citing sources.","Explain in general terms that rare inherited loss of this gene causes severe inflammation needing specialist care."],"mustNot":["Diagnose an autoinflammatory disease in a person from a variant or symptoms.","Share genetic data without consent.","Recommend biological medicines that block interleukin-1 to a person.","Classify a variant of uncertain significance as harmful without evidence."],"requiresHuman":["Returning genetic results to a family.","Any treatment decision for a person."]},"ethics":{"considerations":["Severe inherited inflammatory disease often affects newborns, so results reach worried families.","Genetic data about children needs particular care."],"affectedParties":["Children and families","Patients","Clinicians"]},"owners":{"steward":"The person whose genome carries it; laboratories and clinical variant databases hold records.","roles":[],"masterSystems":["Clinical variant databases","Gene and variant databases"]},"relations":[{"target":"Q20747295","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.il1rn","Wikidata: Q14914156 (https://www.wikidata.org/wiki/Q14914156)"]},"properties":{"applicability":"required","items":["Species-qualified gene identity: Taxonomy identifier plus stable gene identifier","Reference locus: Genome assembly, chromosome or contig accession, interval in bp, strand and coordinate convention","Transcript-product mapping: Versioned transcript accession linked to versioned protein accession","Allelic configuration: Reference-qualified variants, zygosity, copy number and phase; unknown where unresolved","IL1RN RNA abundance: TPM, normalized counts or relative qPCR expression with method and normalization","Product compartment: Secreted, intracellular, mixed or unresolved, qualified by isoform and evidence","Product-mediated antagonism: Assay-specific inhibition percentage or concentration-response parameter with units and conditions","Variant interpretation: Unassessed, uncertain or evidence-supported interpretation, with assertion source and date"]},"recognition":{"applicability":"required","items":["Not visible; known from sequence data and protein assays.","Identified by its approved gene symbol."]},"capabilities":{"applicability":"required","items":["Resolve an IL1RN label to a species-qualified gene and reference sequence.","Map a reported variant to affected IL1RN transcripts and candidate product consequences.","Assess whether an assay distinguishes IL1RN from related loci and individual transcripts from total expression.","Compare expression observations with compatible sample context and normalization.","Trace a functional or phenotype claim to the specific allele, product and experiment supporting it.","Recommend additional sequence, expression or functional analysis when competing interpretations remain unresolved."]},"hazards":{"applicability":"required","items":["Misclassification of variants.","Delayed diagnosis of severe neonatal inflammation."]},"interfaces":{"applicability":"required","items":["Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol."]},"context":{"applicability":"required","items":["IL1RN is encountered in human genomic sequencing, gene expression studies and research on inflammatory regulation.","Its sequence and expression are examined to assess evidence about interleukin-1 antagonism, while distinguishing the gene from its protein products.","Interpretation depends on the sampled tissue, transcript and experimental conditions."]}},"sources":[{"title":"Wikidata item Q14914156: IL1RN","url":"https://www.wikidata.org/wiki/Q14914156","note":"identity and sense of the item"},{"title":"Wikipedia: Interleukin-1 receptor antagonist","url":"https://en.wikipedia.org/wiki/Interleukin-1_receptor_antagonist","note":"general description of the item"}],"openQuestions":["Does the registry's originating record identify the human IL1RN gene, its protein product or a species-unspecified concept?","Which reference assembly and transcript set should govern the initial model, and how should subsequent annotation changes be reconciled?","Which IL1RN transcripts and intracellular or secreted products have direct evidence in the biological contexts the catalogue must support?","Which allele-specific functional and phenotype assertions are sufficiently supported, and where do sources disagree?","Does an existing Vercy publication already own this gene concept or its protein product, requiring a link rather than another model?"],"resources":{"spec":"/models/things/publications/thing-q14914156/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q14914156/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T10:25:16Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:26+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}