FHIR Extensions Pack
5.2.0-ballot - 5.2.0 Ballot - September 2024) International flag

FHIR Extensions Pack, published by HL7 International / FHIR Infrastructure. This guide is not an authorized publication; it is the continuous build for version 5.2.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-extensions/ and changes regularly. See the Directory of published versions

Extension: Amino Acid Change

Official URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange Version: 5.2.0-ballot
Standards status: Deprecated Maturity Level: 1 Responsible: HL7 International / Orders and Observations Computable Name: AminoAcidChange

AminoAcidChange information.

Context of Use

This extension is deprecated and should no longer be used

This extension has been replaced by the profiles and extensions defined in the Genomics Reporting Guide

This extension may be used on the following element(s)

Usage info

Usages:

  • This Extension is not used by any profiles in this Implementation Guide

Changes since version 1.0.0:

  • New Content

    • Formal Views of Extension Content

    Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

    This structure is derived from Extension

    Summary

    Complex Extension: AminoAcidChange information.

    • Name: CodeableConcept: Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be annotated. An amino acid is a sequence feature that corresponds to a single amino acid residue in a polypeptide (SO:0001237). LOINC Code: (48005-3).
    • Type: CodeableConcept: Codified type for associated Amino Acid Change. LOINC Code: (48006-1).

    Maturity: 1

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension HGVS nomenclature for observed Amino Acid Change
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description: (example): NCBI central repository of potentially clinically relevant variants.
    .... extension:Type 0..1 Extension Amino Acid Change Type
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
    ... value[x] 0..0

    doco Documentation for this format
    NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... id 0..1 id Unique id for inter-element referencing
    ... Slices for extension 0..* Extension Additional content defined by implementations
    Slice: Unordered, Open by value:url
    .... extension:Name 0..1 Extension HGVS nomenclature for observed Amino Acid Change
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description: (example): NCBI central repository of potentially clinically relevant variants.
    .... extension:Type 0..1 Extension Amino Acid Change Type
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"

    doco Documentation for this format

    This structure is derived from Extension

    Summary

    Complex Extension: AminoAcidChange information.

    • Name: CodeableConcept: Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be annotated. An amino acid is a sequence feature that corresponds to a single amino acid residue in a polypeptide (SO:0001237). LOINC Code: (48005-3).
    • Type: CodeableConcept: Codified type for associated Amino Acid Change. LOINC Code: (48006-1).

    Maturity: 1

    Differential View

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension HGVS nomenclature for observed Amino Acid Change
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description: (example): NCBI central repository of potentially clinically relevant variants.
    .... extension:Type 0..1 Extension Amino Acid Change Type
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
    ... value[x] 0..0

    doco Documentation for this format

    Snapshot View

    NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... id 0..1 id Unique id for inter-element referencing
    ... Slices for extension 0..* Extension Additional content defined by implementations
    Slice: Unordered, Open by value:url
    .... extension:Name 0..1 Extension HGVS nomenclature for observed Amino Acid Change
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description: (example): NCBI central repository of potentially clinically relevant variants.
    .... extension:Type 0..1 Extension Amino Acid Change Type
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"

    doco Documentation for this format

     

    Other representations of profile: CSV, Excel, Schematron

    Terminology Bindings

    PathConformanceValueSetURI
    Extension.extension:Name.value[x]example

    Constraints

    IdGradePath(s)DetailsRequirements
    ele-1error**ALL** elementsAll FHIR elements must have a @value or children
    : hasValue() or (children().count() > id.count())
    ext-1error**ALL** extensionsMust have either extensions or value[x], not both
    : extension.exists() != value.exists()

    R4B

    The extension is unchanged in R4B

    R4

    The extension is unchanged in R4

    R3

    The extension is unchanged in R3

    Search Parameters for this Extension

    (none found)