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3. Orphanet classification

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Seed-Orphanet edited this page Jan 27, 2026 · 2 revisions

Classification description

The Orphanet nomenclature of RD is classified by medical specialties to reflect the multidimensional nature of rare diseases. Every entity can belong to multiple specialties according to their clinical presentation, and so be included in several classifications. For this purpose, the classification follows a clinical criterion and is mainly organised by anatomical or functional systems, corresponding to the 33 classification medical specialties.

Of these 33 hierarchies, 29 represent a distinct medical domain (e.g. the respiratory system gives rise to the 'Orphanet Classification of Rare Respiratory Diseases', which corresponds to pneumology), and 5 are ad-hoc classifications used for sorting purposes (Orphanet classification of rare genetic disorders, Orphanet classification of rare systemic or rheumatological disorders of childhood included into the Orphanet classification of rare systemic or rheumatologic disordser, Orphanet classification of rare transplant-related disorders, Orphanet classification of teratologic disorders included into the Orphanet classification of rare developmental anomalies during embryogenesis

An additional classification exists: “Orphanet classification of rare disorder without a determined diagnosis”. This hierarchy does not represent a medical domain and is used to class one single disorder ORPHA: 616874 Rare disorder without a determined diagnosis after full investigation allows the identification of undiagnosed rare disorder patients in healthcare information systems.

In the Orphanet nomenclature, each ORPHAcodes is define by a 'classification level' according to its typology :

• Group of disorders: clinical entity defined by a set of common features shared by several disorders and used to group them together.

• Disorders: clinical entity defined by a set of phenotypic abnormalities with a homogeneous evolution and allowing a confirmed clinical diagnosis.

• Subtypes of disorders: subdivision of a disorder, only created when this level of precision is used in clinical practice (not for descriptive purposes) or as confirmed diagnosis. For detailed definitions, see Orphanet nomenclature and classification of rare diseases procedural document. •

How can I browse the Orphanet classifications?

There are several ways to browse the orphanet classifications of RD:

What is the Aggregation level?

To allow data sharing and statistical analysis at EU-level (for more information, consult the Standard procedure and guide for the coding with ORPHAcodes document delivered by the RD-CODE project) ORPHAcodes are also defined in the Orphanet nomenclature Pack by an Aggregation Level.

For a disorder, the aggregation level is itself. For a subtype of disorder, the aggregation level is the parent disorder.

Examples:

  • ORPHA:355 Gaucher disease (Disorder)=> aggregation level ORPHA:355 Gaucher disease (Disorder).
  • ORPHA:77259 Gaucher disease type 1 (Subtype)=> Aggregation level : ORPHA:355 Gaucher disease (Disorder).

Because it is not relevant to use Group of disorders of the Orphanet nomenclature for patient coding and data sharing, these have no aggregation level.

Exceptional cases: Inactive ORPHAcodes

In the case of inactive ORPHAcodes, if there is a replacement ORPHAcode to an active entity (relationship of type "move to" or "referred to"), the Aggregation code is the active ORPHAcode)

Examples:

  • ORPHA:98836 Bilineal acute leukemia (Disorder) deprecated towards ORPHA:530995 Mixed phenotype acute leukemia (Disorder), the aggregation level is: ORPHA:530995 Mixed phenotype acute leukemia (Disorder)
  • ORPHA:157855 HARP syndrome (Subtype) deprecated towards ORPHA:216866 Classic pantothenate kinase-associated neurodegeneration (Subtype), the aggregation level is: ORPHA:157850 Pantothenate kinase-associated neurodegeneration (Disorder)

What does is mean Orphanet classification is multi-hierarchical and polyparental?

The Orphanet classifications have been created to organize the nomenclature in a way that would be relevant to clinical practice for diagnostic and therapeutic use.

Each entity of the nomenclature is classified depending on its clinical presentation and on the relevant medical specialties. There are 33 major classification groups in the Orphanet classification, each corresponding to one specific medical specialty. A single disorder can be classified in as many classification groups as needed according to the medical specialties it is relevant to. This is because many rare diseases are multisystemic (i.e. involve different organ systems). This is why the Orphanet classification system is organised in a multi-hierarchical structure. As a consequence, a disorder or a group of disorders can have different “parents” throughout the classification system. This is why the Orphanet classification system is called "polyparental".

What is the "preferential parent" of an ORPHAcode and how to find it in the Orphanet Nomenclature of RD?

Each entity in the Orphanet nomenclature is assigned one preferred classification group reflecting the specialty or system mostly affected in the disease (or according to a set of explicit rules where no major affected system is recognisable). This is called a "preferential parent". This attribution is done by Orphanet in order to enable the sorting out of all clinical entities by medical domain, and to avoid bias counting of multi-classified entities in statistical analysis when using Orphanet datasets.

This process is called « linearisation », and a descriptive procedure is freely available on the Orphanet website Linearisation rules. e.g. the disorder Atypical HUS (ORPHA:2134) has 'two parents' and is classified under the « Genetic hemolytic uremic syndrome » group (ORPHA:576742) in the hematologic classification and under the « Hemolitic uremic syndrome » group (ORPHA:544458) in the renal classification.

The linearization of ORPHAcodes is available in a dedicated file of the Orphanet Nomenclature pack Save xml file

Open Excel and open xml file in xls

Select Open xml ‘As a read-only workbook'

Then you can just save the file as an xls document

When you open the xls document, you will find the ORPHAcode in the 'AD' column and the preferential parent in the 'X' column.

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