---
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onset:
ontologyClass:
id: HP:0011463
label: Childhood onset
term:
id: MONDO:0100308
label: atactic disorder
id: arbitrary.id
interpretations:
- diagnosis:
disease:
id: MONDO:0100340
label: Friedreich ataxia 1
genomicInterpretations:
- gene:
symbol: FXN
valueId: HGNC:3951
interpretationStatus: REJECTED
subjectOrBiosampleId: 16-year-old boy
id: interpretation.1
progressStatus: COMPLETED
summary: Genetic analysis of the frataxin gene confirmed two alleles in the normal
size range and no evidence of an expansion.
- diagnosis:
disease:
id: MONDO:0010188
label: familial isolated deficiency of vitamin E
genomicInterpretations:
- interpretationStatus: CAUSATIVE
subjectOrBiosampleId: 16-year-old boy
variantInterpretation:
acmgPathogenicityClassification: PATHOGENIC
therapeuticActionability: ACTIONABLE
variationDescriptor:
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id: GENO:0000136
label: homozygous
expressions:
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value: NM_000370.3(TTPA):c.706del
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value: NM_000370.3
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valueId: HGNC:12404
id: variant.1
label: NP_000361.1:p.(His236IlefsTer28)
moleculeContext: genomic
variation:
allele:
literalSequenceExpression: {}
sequenceLocation:
sequenceId: refseq:NC_000008.11
sequenceInterval:
endNumber:
value: '63061383'
startNumber:
value: '63061382'
vcfRecord:
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chrom: NC_000008.11
genomeAssembly: GRCh38
pos: '63061382'
ref: TG
id: interpretation.2
progressStatus: SOLVED
measurements:
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id: LOINC:2923-1
label: Retinol [Mass/volume] in Serum or Plasma
timeObserved:
age:
iso8601duration: P16Y
value:
quantity:
referenceRange:
high: 60
low: 20
unit:
id: UCUM:ug.dL-1
label: microgram per deciliter
unit:
id: UCUM:ug.dL-1
label: microgram per deciliter
value: 45
- assay:
id: LOINC:1823-4
label: Alpha tocopherol [Mass/volume] in Serum or Plasma
timeObserved:
age:
iso8601duration: P16Y
value:
quantity:
referenceRange:
high: 10
low: 6
unit:
id: UCUM:mg.dL-1
label: milligram per deciliter
unit:
id: UCUM:mg.dL-1
label: milligram per deciliter
value: 3.9
- assay:
id: LOINC:2157-6
label: Creatine kinase [Enzymatic activity/volume] in Serum or Plasma
timeObserved:
age:
iso8601duration: P16Y
value:
quantity:
referenceRange:
high: 198
low: 22
unit:
id: UCUM:U.L-1
label: enzyme unit per liter
unit:
id: UCUM:U.L-1
label: enzyme unit per liter
value: 80
- assay:
id: LOINC:1823-4
label: Alpha tocopherol [Mass/volume] in Serum or Plasma
timeObserved:
age:
iso8601duration: P16Y6M
value:
quantity:
referenceRange:
high: 10
low: 6
unit:
id: UCUM:mg.dL-1
label: milligram per deciliter
unit:
id: UCUM:mg.dL-1
label: milligram per deciliter
value: 17.34
medicalActions:
- responseToTreatment:
id: NCIT:C123584
label: Favorable Response
treatment:
agent:
id: DrugCentral:257
label: atorvastatin
drugType: UNKNOWN_DRUG_TYPE
routeOfAdministration:
id: NCIT:C38288
label: Oral Route of Administration
metaData:
created: 2022-04-21T10:35:00Z
createdBy: anonymous biocurator
externalReferences:
- description: 'Ataxia due to vitamin E deficiency: A case report and updated
review'
id: doi:10.1002/ccr3.6303
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phenotypicFeatures:
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onset:
age:
iso8601duration: P10Y
type:
id: HP:0001288
label: Gait disturbance
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modifiers:
- id: HP:0012837
label: Generalized
onset:
age:
iso8601duration: P10Y
type:
id: HP:0001324
label: Muscle weakness
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onset:
age:
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type:
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label: Gait ataxia
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onset:
age:
iso8601duration: P16Y
type:
id: HP:0001308
label: Tongue fasciculations
- excluded: !!perl/scalar:JSON::PP::Boolean 0
onset:
age:
iso8601duration: P16Y
type:
id: HP:0002080
label: Intention tremor
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onset:
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iso8601duration: P16Y
type:
id: HP:0002075
label: Dysdiadochokinesis
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onset:
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type:
id: HP:0001251
label: Ataxia
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onset:
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type:
id: HP:0001284
label: Areflexia
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onset:
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iso8601duration: P16Y
type:
id: HP:0011448
label: Ankle clonus
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onset:
age:
iso8601duration: P16Y
type:
id: HP:0003690
label: Limb muscle weakness
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onset:
age:
iso8601duration: P16Y
type:
id: HP:0003474
label: Somatic sensory dysfunction
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onset:
age:
iso8601duration: P16Y
type:
id: HP:0002599
label: Head titubation
- excluded: !!perl/scalar:JSON::PP::Boolean 1
onset:
age:
iso8601duration: P16Y
type:
id: HP:0031910
label: Abnormal cranial nerve physiology
subject:
id: 16-year-old boy
karyotypicSex: UNKNOWN_KARYOTYPE
sex: FEMALE
timeAtLastEncounter:
age:
iso8601duration: P10Y
- id: arbitrary proband id
interpretations:
- diagnosis:
disease:
id: OMIM:158810
label: Bethlem myopathy 1
genomicInterpretations:
- interpretationStatus: CAUSATIVE
subjectOrBiosampleId: arbitrary interpretation id
variantInterpretation:
acmgPathogenicityClassification: PATHOGENIC
therapeuticActionability: UNKNOWN_ACTIONABILITY
variationDescriptor:
allelicState:
id: GENO:0000135
label: heterozygous
expressions:
- syntax: hgvs
value: NM_001848.2:c.877G>A
geneContext:
symbol: COL6A1
valueId: HGNC:2211
id: variant id
moleculeContext: unspecified_molecule_context
vcfRecord:
alt: A
chrom: chr21
genomeAssembly: GRCh38
pos: '45989626'
ref: G
id: arbitrary interpretation id
progressStatus: COMPLETED
metaData:
created: 2021-05-14T10:35:00Z
createdBy: anonymous biocurator
externalReferences:
- description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:
a case report'
id: PMID:30808312
phenopacketSchemaVersion: 2.0.0
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phenotypicFeatures:
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onset:
ontologyClass:
id: HP:0003577
label: Congenital onset
type:
id: HP:0001629
label: Ventricular septal defect
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id: ECO:0000033
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type:
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onset:
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id: HP:0003577
label: Congenital onset
type:
id: HP:0008689
label: Bilateral cryptorchidism
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- evidenceCode:
id: ECO:0000033
label: author statement supported by traceable reference
reference:
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onset:
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label: Fetal onset
type:
id: HP:0001561
label: Polyhydramnios
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onset:
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type:
id: HP:0000054
label: Micropenis
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id: ECO:0000033
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description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:
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id: HP:0003577
label: Congenital onset
type:
id: HP:0001798
label: Anonychia
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id: ECO:0000033
label: author statement supported by traceable reference
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id: PMID:30808312
excluded: !!perl/scalar:JSON::PP::Boolean 0
type:
id: HP:0001320
label: Cerebellar vermis hypoplasia
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id: ECO:0000033
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onset:
ontologyClass:
id: HP:0003593
label: Infantile onset
type:
id: HP:0000518
label: Cataract
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excluded: !!perl/scalar:JSON::PP::Boolean 0
type:
id: HP:0002198
label: Dilated fourth ventricle
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a case report'
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excluded: !!perl/scalar:JSON::PP::Boolean 0
onset:
ontologyClass:
id: HP:0003577
label: Congenital onset
type:
id: HP:0100333
label: Unilateral cleft lip
subject:
id: proband A
karyotypicSex: UNKNOWN_KARYOTYPE
sex: MALE
timeAtLastEncounter:
age:
iso8601duration: P6Y3M
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- excluded: !!perl/scalar:JSON::PP::Boolean 1
term:
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term:
id: MONDO:0004994
label: cardiomyopathy
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onset:
timestamp: 2020-03-17T00:00:00Z
term:
id: MONDO:0100096
label: COVID-19
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measurements:
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id: LOINC:26474-7
label: Lymphocytes [#/volume] in Blood
timeObserved:
interval:
end: 2020-03-01T00:00:00Z
start: 2019-09-01T00:00:00Z
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id: NCIT:C67245
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timestamp: 2020-03-20T00:00:00Z
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quantity:
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label: Thousand Cells
value: 0.7
medicalActions:
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code:
id: NCIT:C80473
label: Left Ventricular Assist Device
performed:
timestamp: 2016-01-01T00:00:00Z
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agent:
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end: 2021-02-02T08:22:42Z
start: 2021-02-01T18:58:43Z
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id: NCIT:C67388
label: Liter per Minute
value: 2
scheduleFrequency:
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label: continuous
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end: 2021-02-02T12:22:42Z
start: 2021-02-02T08:22:42Z
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unit:
id: NCIT:C67388
label: Liter per Minute
value: 50
scheduleFrequency:
id: PATO:0000689
label: continuous
drugType: UNKNOWN_DRUG_TYPE
routeOfAdministration:
id: NCIT:C38284
label: Nasal Route of Administration
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agent:
id: CHEBI:41879
label: dexamethasone
doseIntervals:
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end: 2020-03-30T00:00:00Z
start: 2020-03-20T00:00:00Z
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value: 6
scheduleFrequency:
id: NCIT:C125004
label: Once Daily
drugType: UNKNOWN_DRUG_TYPE
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code:
id: NCIT:C116648
label: Tracheal Intubation
performed:
timestamp: 2020-03-22T00:00:00Z
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id: NCIT:C722
label: Oxygen
doseIntervals:
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end: 2020-03-28T00:00:00Z
start: 2020-03-22T00:00:00Z
quantity:
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id: NCIT:C91060
label: Centimeters of Water
value: 14
scheduleFrequency:
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label: continuous
drugType: UNKNOWN_DRUG_TYPE
routeOfAdministration:
id: NCIT:C50254
label: Positive end Expiratory Pressure Valve Device
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agent:
id: NCIT:C84217
label: Tocilizumab
doseIntervals:
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start: 2020-03-24T00:00:00Z
quantity:
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id: NCIT:C124458
label: Milligram per Kilogram per Dose
value: 4
scheduleFrequency:
id: NCIT:C64529
label: Every Four Weeks
drugType: UNKNOWN_DRUG_TYPE
metaData:
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createdBy: anonymous biocurator
externalReferences:
- description: 'The Imperfect Cytokine Storm: Severe COVID-19 With ARDS in a Patient
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id: DOI:10.1016/j.jaccas.2020.04.001
reference: PMID:32292915
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iso8601duration: P10Y
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karyotypicSex: UNKNOWN_KARYOTYPE
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timeAtLastEncounter:
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iso8601duration: P10Y
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interpretations:
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disease:
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label: Holoprosencephaly 5
genomicInterpretations:
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subjectOrBiosampleId: genomic interpretation id
variantInterpretation:
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therapeuticActionability: UNKNOWN_ACTIONABILITY
variationDescriptor:
allelicState:
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label: heterozygous
expressions:
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geneContext:
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valueId: 'HGNC:12873 '
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vcfRecord:
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genomeAssembly: GRCh38
pos: '99983133'
ref: C
id: arbitrary interpretation id
progressStatus: COMPLETED
metaData:
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