[
  {
    "phenotype_id": "PH4212",
    "phenotype_version_id": 9430,
    "name": "Immunodeficiencies",
    "definition": "Genetic immunologic deficiency diseases and syndromes due to mutations in genes involved in immunity generally characterized by an increased susceptibility to infectious diseases. They are often associated with autoimmune disease manifestations.\n\nUKB baseline self reported fields.\n",
    "implementation": "The earliest record across all sources is obtained.\n",
    "publications": [
      {
        "doi": "https://doi.org/10.1038/s41598-025-05838-9",
        "details": "Torralbo, Ana and Davitte, Jonathan M. and Croteau-Chonka, Damien C. and Ytsma, Cai R. and Tomlinson, Christopher and Fitzpatrick, Natalie and Chung, Sheng-Chia and Fatemifar, Ghazaleh and Cortes, Adrian S. and Richardson, Tom G. and Barclay, Matthew and Carrasco Zanini Sanchez, Julia and Finan, Chris and Hemingway, Harry and Hingorani, Aroon D. and Kuan Po Ai, Valerie and Langenberg, Claudia and Lyratzopoulos, Georgios and Lumbers, Tom and Pietzner, Maik and Shah, Anoop Dinesh and Thygesen, Johan Hilge and Zelenka, Natalie and Whittaker, John C. and Ehm, Margaret G. and Denaxas, Spiros, A Computational Framework for Defining and Validating Reproducible Phenotyping Algorithms of 313 Diseases in the UK Biobank.",
        "primary": true
      }
    ],
    "validation": "Phenotypes underwent a multi\\-layered validation approach that included a) evaluating data source concordance, b) age\\-sex incidence and baseline prevalence patterns, c) an external comparison to a representative and unselected UK EHR dataset, d) modifiable risk factor associations, and e) genetic correlations with external genome\\-wide association studies (GWAS). Results showed consistent disease distributions by age and sex, high ranked correlation with general population prevalence estimates, confirmed risk factor associations, and significant genetic correlations with external GWAS.\n",
    "citation_requirements": null,
    "created": "2026-06-08T20:11:44.342365Z",
    "author": "Torralbo, A; Davitte, J M; Croteau-Chonka, D C; Ytsma, C; Tomlinson, C; Fitzpatrick, N K; Chung, S C; Fatemifar, G; Cortes, A S; Richardson, T G; Barclay, M; Carrasco Zanini, J; Finan, C; Hemingway, H; Hingorani, A; Kuan, V; Langenberg, C; Lyratzopoulos, G; Lumbers, R T; Pietzner, M; Shah, A D; Thygesen, J H; Zelenka, N; Whittaker, J C; Ehm, M G; Denaxas, S",
    "collections": [
      {
        "name": "Phenotype Library",
        "value": 18
      },
      {
        "name": "UK Biobank",
        "value": 32
      }
    ],
    "tags": null,
    "organisation": null,
    "world_access": 1,
    "updated": "2026-06-08T20:11:44.336333Z",
    "sex": [
      {
        "name": "Both",
        "value": "3"
      }
    ],
    "type": [
      {
        "name": "Disease or syndrome",
        "value": "2"
      }
    ],
    "trials": null,
    "ontology": [
      {
        "name": "Primary immune deficiency disorder (disorder)",
        "value": 349031
      }
    ],
    "phenoflowid": null,
    "data_sources": [
      {
        "name": "UK Biobank",
        "value": 13,
        "uid": "6a9f93ad-2434-41d9-93bf-6e9d2eee04e5",
        "url": "https://healthdatagateway.org/en/dataset/700",
        "datasource_id": 700
      },
      {
        "name": "Patient Episode Dataset for Wales (PEDW)",
        "value": 40,
        "uid": "4c33a5d2-164c-41d7-9797-dc2b008cc852",
        "url": "https://healthdatagateway.org/en/dataset/318",
        "datasource_id": 318
      },
      {
        "name": "Scottish Cancer Registry (SMR06)",
        "value": 417,
        "uid": "ad36dc03-1856-44de-99b0-1af6f312d86b",
        "url": "https://healthdatagateway.org/en/dataset/79",
        "datasource_id": 79
      },
      {
        "name": "Cancer Registration Data",
        "value": 788,
        "uid": "6904a2ff-ab44-4dd6-b9ec-25d3cad29e43",
        "url": "https://healthdatagateway.org/en/dataset/880",
        "datasource_id": 880
      }
    ],
    "endorsements": null,
    "project_name": null,
    "coding_system": [
      {
        "name": "ICD10 codes",
        "value": 4
      },
      {
        "name": "Read codes v3",
        "value": 6
      }
    ],
    "corresp_author": "Ana Torralbo",
    "event_date_range": null,
    "concept_information": [
      {
        "concept_id": 10320,
        "concept_version_id": 17805,
        "concept_name": "Diagnoses - main ICD10",
        "coding_system": {
          "id": 4,
          "name": "ICD10 codes",
          "description": "ICD10 Codes"
        },
        "phenotype_id": "PH4212",
        "phenotype_version_id": 9430,
        "phenotype_name": "Immunodeficiencies",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "D80",
            "description": "Immunodeficiency with predominantly antibody defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D81",
            "description": "Combined immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D82",
            "description": "Immunodeficiency associated with other major defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D83",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.0",
            "description": "Lymphocyte function antigen-1 [LFA-1] defect",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.8",
            "description": "Other specified immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.9",
            "description": "Immunodeficiency, unspecified",
            "attributes": {
              "type": "any"
            }
          }
        ]
      },
      {
        "concept_id": 10321,
        "concept_version_id": 17806,
        "concept_name": "Diagnoses - secondary ICD10",
        "coding_system": {
          "id": 4,
          "name": "ICD10 codes",
          "description": "ICD10 Codes"
        },
        "phenotype_id": "PH4212",
        "phenotype_version_id": 9430,
        "phenotype_name": "Immunodeficiencies",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "D80",
            "description": "Immunodeficiency with predominantly antibody defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D81",
            "description": "Combined immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D82",
            "description": "Immunodeficiency associated with other major defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D83",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.0",
            "description": "Lymphocyte function antigen-1 [LFA-1] defect",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.8",
            "description": "Other specified immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.9",
            "description": "Immunodeficiency, unspecified",
            "attributes": {
              "type": "any"
            }
          }
        ]
      },
      {
        "concept_id": 10322,
        "concept_version_id": 17807,
        "concept_name": "Underlying (primary) cause of death: ICD10",
        "coding_system": {
          "id": 4,
          "name": "ICD10 codes",
          "description": "ICD10 Codes"
        },
        "phenotype_id": "PH4212",
        "phenotype_version_id": 9430,
        "phenotype_name": "Immunodeficiencies",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "D80",
            "description": "Immunodeficiency with predominantly antibody defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D81",
            "description": "Combined immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D82",
            "description": "Immunodeficiency associated with other major defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D83",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.0",
            "description": "Lymphocyte function antigen-1 [LFA-1] defect",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.8",
            "description": "Other specified immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.9",
            "description": "Immunodeficiency, unspecified",
            "attributes": {
              "type": "any"
            }
          }
        ]
      },
      {
        "concept_id": 10323,
        "concept_version_id": 17808,
        "concept_name": "Contributory (secondary) causes of death: ICD10",
        "coding_system": {
          "id": 4,
          "name": "ICD10 codes",
          "description": "ICD10 Codes"
        },
        "phenotype_id": "PH4212",
        "phenotype_version_id": 9430,
        "phenotype_name": "Immunodeficiencies",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "D80",
            "description": "Immunodeficiency with predominantly antibody defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D81",
            "description": "Combined immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D82",
            "description": "Immunodeficiency associated with other major defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D83",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.0",
            "description": "Lymphocyte function antigen-1 [LFA-1] defect",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.8",
            "description": "Other specified immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "D84.9",
            "description": "Immunodeficiency, unspecified",
            "attributes": {
              "type": "any"
            }
          }
        ]
      },
      {
        "concept_id": 10324,
        "concept_version_id": 17809,
        "concept_name": "GP clinical event records",
        "coding_system": {
          "id": 6,
          "name": "Read codes v3",
          "description": "Read codes v3"
        },
        "phenotype_id": "PH4212",
        "phenotype_version_id": 9430,
        "phenotype_name": "Immunodeficiencies",
        "code_attribute_header": [
          "type"
        ],
        "codes": [
          {
            "code": "C390.00",
            "description": "Deficiencies of humoral immunity",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390000",
            "description": "Hypogammaglobulinaemia NOS",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390100",
            "description": "Selective IgA immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390.11",
            "description": "Agammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390200",
            "description": "Selective IgM immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390300",
            "description": "Selective IgG immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390400",
            "description": "Other selective immunoglobulin deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390500",
            "description": "Congenital hypogammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390511",
            "description": "Bruton's agammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390512",
            "description": "Congenital X-linked agammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390600",
            "description": "Immunodeficiency with IgM hypergammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C3907",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390700",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390800",
            "description": "Transient infant hypogammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390900",
            "description": "Agammaglobulinaemia NEC",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390A00",
            "description": "Dysimmunoglobulinaemia NEC",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390A11",
            "description": "Dysgammaglobulinaemia NEC",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390B00",
            "description": "Antibod def wth nr-norm imunoglob/or wth hyperimunoglobaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390y00",
            "description": "Other specified deficiency of humoral immunity",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C390z00",
            "description": "Deficiency of humoral immunity NOS",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391.00",
            "description": "Deficiencies of cell-mediated immunity",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391000",
            "description": "Predominantly T-cell immuno-deficiency NOS",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391011",
            "description": "T-lymphocyte deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391012",
            "description": "Cellular immunity syndrome",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391100",
            "description": "Di George syndrome",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391200",
            "description": "Wiskott - Aldrich syndrome",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C391211",
            "description": "Thrombocytopenic eczema with immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392.00",
            "description": "Combined immunity deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392100",
            "description": "Severe combined immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392111",
            "description": "Swiss type agammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392300",
            "description": "Severe combined immunodefiency with reticular dysgenesis",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392400",
            "description": "Severe combined immunodef with low T- and B-cell numbers",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392500",
            "description": "Severe combined immunodef with low or normal B-cell numbers",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392600",
            "description": "Adenosine deaminase deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392700",
            "description": "Purine nucleoside phosphorylase deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392800",
            "description": "Major histocompatibility complex class I deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392900",
            "description": "Major histocompatibility complex class II deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C392z00",
            "description": "Combined immunity deficiency NOS",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C393.00",
            "description": "Unspecified immunity deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C395.00",
            "description": "Immunodeficiency with short-limbed stature",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C396.00",
            "description": "Immunodef follow hereditary defect respon Epstein-Barr vir",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C397.00",
            "description": "Hyperimmunoglobulin E syndrome",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C398.00",
            "description": "Common variable immunodeficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C398000",
            "description": "Com var immunodef with predom abn B-cell numbers and functns",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C398200",
            "description": "Common variable immunodef wth autoantibod to B- or T-cells",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C39X.00",
            "description": "Immunodeficiency associated+major defect, unspecified",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "C39y000",
            "description": "Lymphocyte function antigen-1 defect",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "Cyu0000",
            "description": "[X]Other immunodeficiencies+predominantly antibody defects",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "Cyu0400",
            "description": "[X]Other common variable immunodeficiencies",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "Cyu0500",
            "description": "[X]Other specified immunodeficiency disorders",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "X20Dw",
            "description": "Hyperimmunoglobulin E syndrome",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "X40Ua",
            "description": "Adenosine deaminase deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "X40Uc",
            "description": "Purine nucleoside phosphorylase deficiency",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "XE11u",
            "description": "Deficiencies of humoral immunity",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "XE11v",
            "description": "Congenital hypogammaglobulinaemia",
            "attributes": {
              "type": "any"
            }
          },
          {
            "code": "XE11w",
            "description": "Predominantly T-cell immuno-deficiency NOS",
            "attributes": {
              "type": "any"
            }
          }
        ]
      }
    ],
    "status": 1,
    "doi": "https://doi.org/10.48533/hhz6-xm80",
    "is_deleted": false,
    "publish_status": 2,
    "owner": "ieuan.scanlon",
    "template": {
      "id": 2,
      "name": "BHF Data Science Centre Phenotype",
      "description": "BHF Data Science Centre Phenotype definitions that describe a list of clinical codes, algorithms using clinical codes, or set of clinical trials. Visit the BHF Data Science Centre website to learn more: https://bhfdatasciencecentre.org",
      "version_id": 1
    },
    "versions": [
      {
        "version_id": 9430,
        "version_name": "Immunodeficiencies",
        "version_date": "2026-06-08T20:11:44.352421Z",
        "is_published": true,
        "is_latest": true
      }
    ]
  }
]