1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    No data
    Coding System
    ICD9 codesICD10 codesRead codes v2
    Data Sources
    CPRD GOLD
    CPRD Aurum
    Welsh Longitudinal General Practice Dataset (WLGP) - Welsh Primary Care
    Admitted Patient Care Dataset
    Collections
    No data
    Tags
    No data
    Ontology
    epilepsy

  2. Definition

    Phenotyping epilepsy cases

    In order to use coded data effectively to study epilepsy, it is vital that we are able to phenotype epilepsy according to aetiology. Here we have brought together the codes to identify the epilepsy aetiologies, including epilepsy syndromes and epilepsy which is due to genetic, structural, metabolic, inflammatory/immune mediated, central nervous system infections and unknown aetiology.

    In the data we define epilepsy of unknown aetiology as one which does not have any of the other aetiologies identified in the preceeding medical records.

    Note that many aetiologies will span multiple categories - here each is aetiology is only represented once. e.g. Tuberous sclerosis is included on the gentic associated epilepsy list, but not on the structural. We do have more comprehensive mapping files that take this into account and we would be happy to share these resources with other researchers in this field.

    These code lists should be used to phenotype epilepsy cases. Note that this code list was not developed to be used alone to identify epilepsy cases and we would reccomend that our algorithm for identifying incident epilepsy is used for this.

    Data sources

    Epilepsy syndromes

    Using the International league against epilepsy (ILAE) 2021-2022 guidelines, we have created a list of all epilepy syndromes and corresponding code lists. These syndrome code lists are based on information from the following papers:

    Wirrell EC, Nabbout R, Scheffer IE, Alsaadi T, Bogacz A, French JA, et al. Methodology for classification and definition of epilepsy syndromes with list of syndromes: Report of the ILAE Task Force on Nosology and Definitions. Epilepsia. 2022; 63: 1333–1348. https://doi.org/10.1111/epi.17237

    Zuberi SM, Wirrell E, Yozawitz E, Wilmshurst JM, Specchio N, Riney K, et al. ILAE classification and definition of epilepsy syndromes with onset in neonates and infants: Position statement by the ILAE Task Force on Nosology and Definitions. Epilepsia. 2022; 63: 1349–1397. https://doi.org/10.1111/epi.17239

    Specchio N, Wirrell EC, Scheffer IE, Nabbout R, Riney K, Samia P, et al. International League Against Epilepsy classification and definition of epilepsy syndromes with onset in childhood: Position paper by the ILAE Task Force on Nosology and Definitions. Epilepsia. 2022; 63: 1398–1442. https://doi.org/10.1111/epi.17241

    Riney K, Bogacz A, Somerville E, Hirsch E, Nabbout R, Scheffer IE, et al. International League Against Epilepsy classification and definition of epilepsy syndromes with onset at a variable age: position statement by the ILAE Task Force on Nosology and Definitions. Epilepsia. 2022; 63: 1443–1474. https://doi.org/10.1111/epi.17240

    Hirsch E, French J, Scheffer IE, Bogacz A, Alsaadi T, Sperling MR, et al. ILAE definition of the Idiopathic Generalized Epilepsy Syndromes: Position statement by the ILAE Task Force on Nosology and Definitions. Epilepsia. 2022; 63: 1475–1499. https://doi.org/10.1111/epi.17236

    Epilepy aetiologies

    These lists were generated by clinicians and all codes have been reviewed by a minimum of 2 clinical specialists (Neurologists).

    The code lists are based on clinical practice, clinical reserach and information which can be found summarised here:

    https://epilepsydiagnosis.org/aetiology/epilepsies-etiology-groupoverview.html

    **References for code lists **

    Many of the code lists here are built upon previously published code lists compiled for other disorders. All have been modified - with additional codes added and codes excluded on a clinical basis. We acknowledge the significant amount of work that goes into code list development and validation and thank the authors for sharing their code freely with others.

    Where no code list is referenced here the code list has been independently developed by KJB and reviewed by at least 2 other clinicians working in neurology.

    Central nervous system infections:

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH229 / 458 - Other nervous system infections. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH229/version/458/detail/. [Accessed 19 November 2025]

    Encephalitis:

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH160 / 320 - Encephalitis. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH160/version/320/detail/. [Accessed 19 November 2025]

    Dementia:

    UK Biobank Algorithmically-defined outcomes. Version 2.0. January 2022. UKbiobank

    Stroke:

    UK Biobank Algorithmically-defined outcomes. Version 2.0. Januaru 2022. UKbiobank

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH85 / 170 - Stroke NOS. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH85/version/170/detail/. [Accessed 19 November 2025]

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH56 / 112 - Ischaemic stroke. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH56/version/112/detail/. [Accessed 19 November 2025]

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH86 / 172 - Subarachnoid haemorrhage. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH86/version/172/detail/. [Accessed 19 November 2025]

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH316 / 632 - Subdural haematoma - nontraumatic. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH316/version/632/detail/. [Accessed 19 November 2025]

    Tumours:

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH251 / 502 - Primary Malignancy_Brain, Other CNS and Intracranial. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH251/version/502/detail/. [Accessed 19 November 2025]

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH293 / 586 - Secondary Malignancy_Brain, Other CNS and Intracranial. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH293/version/586/detail/. [Accessed 19 November 2025]

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH120 / 240 - Benign neoplasm of brain and other parts of central nervous system. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH120/version/240/detail/. [Accessed 19 November 2025]

    Alcohol and drug use: Rees, S., Watkins, A., Keauffling, J., \\\\\\\\\\\\\\\\\\\\\\\& John, A. (2022). Incidence, mortality and survival in young people with co-occurring mental disorders and substance use: a retrospective linked routine data study in Wales. Clinical Epidemiology, 21-38.

    Michael Doyle, David While, Pearl L H Mok, Kirsten Windfuhr, Darren M Aschroft, Evangelos Kontopantelis, Carolyn A Chew-Graham, Louis Appleby, Jenny Shaw, Roger T Webb. PH444 / 888 - Clinically Significant Alcohol Misuse. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH444/version/888/detail/. [Accessed 19 November 2025]

    Hayley C Gorton, Roger T Webb, Mathew J Carr, Marcos Delpozo-Banos, Ann John, Darren M Ashcroft. PH472 / 944 - Substance Misuse. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH472/version/944/detail/. [Accessed 19 November 2025]

    Inflammatory disorders Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH63 / 126 - Multiple sclerosis. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH63/version/126/detail/. [Accessed 19 November 2025]

    Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH284 / 568 - Sarcoidosis. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH284/version/568/detail/. [Accessed 19 November 2025]

    Cerebral palsy Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A. PH132 / 264 - Cerebral Palsy. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH132/version/264/detail/. [Accessed 19 November 2025]

  3. Implementation

    Implementation

    Once an epilepsy case has been identified, these code lists may be used to identify whether or not the case also has any of the potential epilepsy aetiologies identified here.

    For all categories apart from Genetic and Epilepsy syndromes, we would suggest that an aetiology should preceed the epilepsy diagnosis in time, or occur within + 1 year of the epilepsy diagnosis. This one year window takes into account the fact that epilepsy may be the presenting feature of an (unknown) underlying brain disorder or aetiology.

    We allow Genetic and Epilepsy syndrome cases to occur at any point in the medical record, including post epilepsy diagnosis. This reflects the fact that some genetic diagnoses may not be reached until late in the disease course, but will have preceeded the epilepsy in time.

    Where multiple formatted versions of the same Read code exist all versions have been provided. Note that there are now a large number of local system generated codes being used, due to the ongoing use of Read coding, despite the retirements of updates.

    Note that this code list should be used in conjunction with our other published code lists for identifying incident epilepsy cases, and for phenotyping epilepsy syndromes.

  4. Clinical Codelist

  5. Publication

    Related publications

    No known publications

    Citation Example

    Kathryn J. Bush, Beata Fonferko-Shadrach, Huw A. Strafford, Rajish Sanjit, Gemma Maxwell, Tim Wilkinson, Alexander Grundman, Arron S. Lacey, Andrew Kingston, Rhys H. Thomas, Sheena E. Ramsay, William O Pickrell. PH1927 / 9241 - Epilepsy aetiologies and epilepsy phenotyping (Genetic, structural, inflammatory, metabolic, infective and epilepsy syndromes). Phenotype Library [Online]. 03 March 2026. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH1927/version/9241/detail/. [Accessed 19 August 2026]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1927/version/9241/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of Phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH1927',
     version_id=9241
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get details of Phenotype

    phenotype_detail = client.phenotypes.get_detail(
     'PH1927',
     version_id=9241
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH1927/version/9241/export/codes/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of Phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH1927',
     version_id=9241
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of Phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH1927',
     version_id=9241
    )

  7. Version History