ARCHETYPE Allele details (openEHR-EHR-CLUSTER.allele_details.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.allele_details.v0
ConceptAllele details
DescriptionDetails of a genetic sequence on one allele.
UseTo be used as part of genetic_variant.
MisuseNot to be used to describe chromosomes or chromosomal abnormalities.
PurposeTo describe the genetic sequence and mutations of one allele.
ReferencesGinsbury G & Huntington FW: Essentials of genomic and personalized medicine. Academic press 2010 ISBN 978-0-12-374934-5
Copyright© Nasjonal IKT HF
AuthorsForfatternavn: Hallvard Lærum
Organisasjon: Oslo Universitetssykehus HF
E-post: hallar@ous-hf.no
Opprinnelig skrevet dato: 2016-02-09
Other Details LanguageForfatternavn: Hallvard Lærum
Organisasjon: Oslo Universitetssykehus HF
E-post: hallar@ous-hf.no
Opprinnelig skrevet dato: 2016-02-09
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/., custodian_organisation=Nasjonal IKT, references=Ginsbury G & Huntington FW: Essentials of genomic and personalized medicine. Academic press 2010 ISBN 978-0-12-374934-5, current_contact=Hallvard Lærum, Oslo Universitetssykehus HF, original_namespace=no.nasjonalikt, original_publisher=Nasjonal IKT, custodian_namespace=no.nasjonalikt, MD5-CAM-1.0.1=EDF71C92BFC0842D453AF62AC70080B4, build_uid=e32ce912-5b10-49ae-b36f-8e7f7e0c6660, revision=0.0.1-alpha}
Keywordsallele, DNA, mRNA, mutation, inheritance, genetic variant
Lifecyclein_development
UID9098ab7b-2d35-4e66-ab1e-5e4b00120e27
Language useden
Citeable Identifier1078.36.1322
Revision Number0.0.1-alpha
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Hallvard Lærum, Oslo Universitetssykehus HF, Norway (Nasjonal IKT redaktør)
Lars Retterstøl MD PhD, Department of medical genetics, Oslo University Hospital HF, Norway, originalLanguage=en, translators=, subjectOfData=ubegrenset, archetypeTranslationTree=null, topLevelToAshis={context=[], state=[], capabilities=[], contacts=[], details=[], identities=[], description=[], events=[], source=[], protocol=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0045], code=at0045, itemType=ELEMENT, level=1, text=NM notation name, description=Name of the variant as defined by standard mutation., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Valgfritt, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=Star notation variant, description=The star notation description of the variant, e.g. *1, *2 or *3., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Valgfritt, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0052], code=at0052, itemType=ELEMENT, level=1, text=RefSeq number, description=Number of the variant as defined by NCBI Reference sequence database., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Valgfritt, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Molecular effect, description=A description of the direct molecular effects of the mutation, eg. disruption of active site of enzyme, configuration change of protein., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Valgfritt, gjentagende, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0030], code=at0030, itemType=CLUSTER, level=1, text=Small-scale mutations, description=Details on mutations involving one single or a few nucleotids., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Valgfritt, gjentagende, cardinalityFormal=1..*, cardinalityText=, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0030]/items[at0032], code=at0032, itemType=ELEMENT, level=2, text=Structural type, description=The principal type of small-scale mutation of structure., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Valgfritt, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • Point mutation [One single nucleotid has been changed.]
  • Deletion [One or more nucleotids have been removed from the sequence.]
  • Insertion [One or more nucleotids have been inserted into the sequence.]
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  • Silent mutation [The mutation codes for the same or sufficiently similar amino acid.]
  • Missense mutation [The mutation codes for a differenct amino acid.]
  • Nonsense mutation [The mutation codes for a stop codon and can truncate the protein.]
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  • None or non significant [The mutation does not change the overall structure of the mRNA.]
  • Frameshift mutation [The mutation produces a frameshift, i.e. a shift in triplet reading frame for amino acid translation.]
  • Splice site mutation [The mutation changes how the mRNA strand is spliced after transcription.]
  • Unknown [The effect of the mutation on transcripted mRNA is not known or undecided.]
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  • Duplication [Multiple copies of chromosomal regions, increasing the dosage of the genes located within them.]
  • Deletion [Deletion of large chromosomal regions, leading to loss of the genes within those regions.]
  • Other [Other large-scale mutations.]
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  • Autosomal dominant [Autosomal dominant mode of inheritance.]
  • Autosomal recessive [Autosomal recessive mode of inheritance.]
  • X-linked dominant [X-linked dominant mode of inheritance.]
  • X-linked recessive [X-linked recessive mode of inheritance.]
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  • Point mutation [One single nucleotid has been changed.]
  • Deletion [One or more nucleotids have been removed from the sequence.]
  • Insertion [One or more nucleotids have been inserted into the sequence.]
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  • Silent mutation [The mutation codes for the same or sufficiently similar amino acid.]
  • Missense mutation [The mutation codes for a differenct amino acid.]
  • Nonsense mutation [The mutation codes for a stop codon and can truncate the protein.]
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  • None or non significant [The mutation does not change the overall structure of the mRNA.]
  • Frameshift mutation [The mutation produces a frameshift, i.e. a shift in triplet reading frame for amino acid translation.]
  • Splice site mutation [The mutation changes how the mRNA strand is spliced after transcription.]
  • Unknown [The effect of the mutation on transcripted mRNA is not known or undecided.]
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  • Duplication [Multiple copies of chromosomal regions, increasing the dosage of the genes located within them.]
  • Deletion [Deletion of large chromosomal regions, leading to loss of the genes within those regions.]
  • Other [Other large-scale mutations.]
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  • Autosomal dominant [Autosomal dominant mode of inheritance.]
  • Autosomal recessive [Autosomal recessive mode of inheritance.]
  • X-linked dominant [X-linked dominant mode of inheritance.]
  • X-linked recessive [X-linked recessive mode of inheritance.]
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