---
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ontologyClass:
id: HP:0011463
label: Childhood onset
diseaseCode:
id: MONDO:0100308
label: atactic disorder
excluded: 0
id: 16-year-old boy
info:
phenopacket:
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:
allelicState:
id: GENO:0000136
label: homozygous
expressions:
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value: NM_000370.3(TTPA):c.706del
- syntax: transcript_reference
value: NM_000370.3
geneContext:
symbol: TTPA
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:
alt: T
chrom: NC_000008.11
genomeAssembly: GRCh38
pos: 63061382
ref: TG
id: interpretation.2
progressStatus: SOLVED
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
phenopacketSchemaVersion: 2.0.0
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version: 2022-03-05
- id: drugcentral
iriPrefix: https://drugcentral.org/drugcard/
name: Drug Central
namespacePrefix: DrugCentral
url: https://drugcentral.org/
version: 2022-08-22
karyotypicSex: UNKNOWN_KARYOTYPE
measures:
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id: LOINC:2923-1
label: Retinol [Mass/volume] in Serum or Plasma
measurementValue:
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
observationMoment: &1
age:
iso8601duration: P16Y
timeObserved: *1
- assayCode:
id: LOINC:1823-4
label: Alpha tocopherol [Mass/volume] in Serum or Plasma
measurementValue:
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
observationMoment: &2
age:
iso8601duration: P16Y
timeObserved: *2
- assayCode:
id: LOINC:2157-6
label: Creatine kinase [Enzymatic activity/volume] in Serum or Plasma
measurementValue:
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
observationMoment: &3
age:
iso8601duration: P16Y
timeObserved: *3
- assayCode:
id: LOINC:1823-4
label: Alpha tocopherol [Mass/volume] in Serum or Plasma
measurementValue:
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
observationMoment: &4
age:
iso8601duration: P16Y6M
timeObserved: *4
phenotypicFeatures:
- excluded: 0
featureType:
id: HP:0001288
label: Gait disturbance
onset:
age:
iso8601duration: P10Y
- excluded: 0
featureType:
id: HP:0001324
label: Muscle weakness
modifiers:
- id: HP:0012837
label: Generalized
onset:
age:
iso8601duration: P10Y
- excluded: 0
featureType:
id: HP:0002066
label: Gait ataxia
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0001308
label: Tongue fasciculations
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0002080
label: Intention tremor
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0002075
label: Dysdiadochokinesis
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0001251
label: Ataxia
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0001284
label: Areflexia
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0011448
label: Ankle clonus
onset:
age:
iso8601duration: P16Y
- excluded: 0
featureType:
id: HP:0003690
label: Limb muscle weakness
onset:
age:
iso8601duration: P16Y
- excluded: 1
featureType:
id: HP:0003474
label: Somatic sensory dysfunction
onset:
age:
iso8601duration: P16Y
- excluded: 1
featureType:
id: HP:0002599
label: Head titubation
onset:
age:
iso8601duration: P16Y
- excluded: 1
featureType:
id: HP:0031910
label: Abnormal cranial nerve physiology
onset:
age:
iso8601duration: P16Y
sex:
id: NCIT:C16576
label: Female
treatments:
- drugType: UNKNOWN_DRUG_TYPE
routeOfAdministration:
id: NCIT:C38288
label: Oral Route of Administration
treatmentCode:
id: DrugCentral:257
label: atorvastatin
- id: proband A
info:
phenopacket:
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
resources:
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karyotypicSex: UNKNOWN_KARYOTYPE
phenotypicFeatures:
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featureType:
id: HP:0001629
label: Ventricular septal defect
onset:
ontologyClass:
id: HP:0003577
label: Congenital onset
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featureType:
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label: Coarse facial features
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featureType:
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label: Bilateral cryptorchidism
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excluded: 0
featureType:
id: HP:0001561
label: Polyhydramnios
onset:
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id: HP:0011461
label: Fetal onset
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featureType:
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label: Micropenis
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excluded: 0
featureType:
id: HP:0001798
label: Anonychia
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label: Congenital onset
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id: ECO:0000033
label: author statement supported by traceable reference
reference:
description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:
a case report'
id: PMID:30808312
excluded: 0
featureType:
id: HP:0001320
label: Cerebellar vermis hypoplasia
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id: ECO:0000033
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reference:
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a case report'
id: PMID:30808312
excluded: 0
featureType:
id: HP:0000518
label: Cataract
onset:
ontologyClass:
id: HP:0003593
label: Infantile onset
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id: ECO:0000033
label: author statement supported by traceable reference
reference:
description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:
a case report'
id: PMID:30808312
excluded: 0
featureType:
id: HP:0002198
label: Dilated fourth ventricle
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- evidenceCode:
id: ECO:0000033
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reference:
description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:
a case report'
id: PMID:30808312
excluded: 0
featureType:
id: HP:0100333
label: Unilateral cleft lip
onset:
ontologyClass:
id: HP:0003577
label: Congenital onset
sex:
id: NCIT:C20197
label: Male
- diseases:
- diseaseCode:
id: MONDO:0005015
label: diabetes mellitus
excluded: 1
- diseaseCode:
id: MONDO:0004994
label: cardiomyopathy
excluded: 0
- ageOfOnset:
timestamp: 2020-03-17T00:00:00Z
diseaseCode:
id: MONDO:0100096
label: COVID-19
excluded: 0
id: P123542
info:
phenopacket:
metaData:
created: 2021-08-17T00:00:00Z
createdBy: anonymous biocurator
externalReferences:
- description: 'The Imperfect Cytokine Storm: Severe COVID-19 With ARDS in
a Patient on Durable LVAD Support'
id: DOI:10.1016/j.jaccas.2020.04.001
reference: PMID:32292915
phenopacketSchemaVersion: 2.0.0
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interventionsOrProcedures:
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timestamp: 2016-01-01T00:00:00Z
procedureCode:
id: NCIT:C80473
label: Left Ventricular Assist Device
- ageOfProcedure:
timestamp: 2020-03-22T00:00:00Z
procedureCode:
id: NCIT:C116648
label: Tracheal Intubation
karyotypicSex: UNKNOWN_KARYOTYPE
measures:
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label: Lymphocytes [#/volume] in Blood
measurementValue:
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id: NCIT:C67245
label: Thousand Cells
value: 1.4
observationMoment: &5
interval:
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label: Lymphocytes [#/volume] in Blood
measurementValue:
quantity:
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id: NCIT:C67245
label: Thousand Cells
value: 0.7
observationMoment: &6
timestamp: 2020-03-20T00:00:00Z
timeObserved: *6
phenotypicFeatures:
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featureType:
id: HP:0001945
label: 'Fever '
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timestamp: 2021-02-01T05:00:00Z
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featureType:
id: HP:0030157
label: Flank pain
onset:
timestamp: 2021-02-01T05:00:00Z
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featureType:
id: HP:0000790
label: Hematuria
onset:
timestamp: 2021-02-01T05:00:00Z
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featureType:
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timestamp: 2021-02-01T05:00:00Z
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label: Myalgia
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label: Diarrhea
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id: HP:0002094
label: Dyspnea
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featureType:
id: HP:0033677
label: Acute respiratory distress syndrome
onset:
timestamp: 2020-03-20T00:00:00Z
sex: &7
id: NCIT:C20197
label: Male
treatments:
- doseIntervals:
- interval:
end: 2021-02-02T08:22:42Z
start: 2021-02-01T18:58:43Z
quantity:
unit:
id: NCIT:C67388
label: Liter per Minute
value: 2
scheduleFrequency:
id: PATO:0000689
label: continuous
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end: 2021-02-02T12:22:42Z
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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
treatmentCode:
id: NCIT:C722
label: Oxygen
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end: 2020-03-30T00:00:00Z
start: 2020-03-20T00:00:00Z
quantity:
unit:
id: UCUM:mg
label: milligram
value: 6
scheduleFrequency:
id: NCIT:C125004
label: Once Daily
drugType: UNKNOWN_DRUG_TYPE
treatmentCode:
id: CHEBI:41879
label: dexamethasone
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end: 2020-03-28T00:00:00Z
start: 2020-03-22T00:00:00Z
quantity:
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id: NCIT:C91060
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value: 14
scheduleFrequency:
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label: continuous
drugType: UNKNOWN_DRUG_TYPE
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label: Positive end Expiratory Pressure Valve Device
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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
treatmentCode:
id: NCIT:C84217
label: Tocilizumab
- id: 10-year old boy
info:
phenopacket:
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- diagnosis:
disease:
id: MONDO:0010679
label: Duchenne muscular dystrophy
genomicInterpretations:
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subjectOrBiosampleId: 10-year old boy
variantInterpretation:
acmgPathogenicityClassification: PATHOGENIC
therapeuticActionability: UNKNOWN_ACTIONABILITY
variationDescriptor:
allelicState:
id: GENO:0000134
label: hemizygous
expressions:
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value: NM_004006.3:c.7310-11543_7359del
- syntax: transcript_reference
value: NM_004006.3
geneContext:
symbol: DMD
valueId: HGNC:2928
id: variant-id
moleculeContext: genomic
variation:
copyNumber:
derivedSequenceExpression:
location:
sequenceId: refseq:NC_000023.11
sequenceInterval:
endNumber:
value: 31785736
startNumber:
value: 31774144
reverseComplement: 0
number:
value: 1
id: interpretation.id
progressStatus: SOLVED
metaData:
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createdBy: anonymous biocurator
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featureType:
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featureType:
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label: Elevated circulating creatine kinase concentration
onset:
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iso8601duration: P10Y
sex: *7
- id: nine-month old infant
info:
phenopacket:
interpretations:
- diagnosis:
disease:
id: OMIM:609637
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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value: NM_007129.3:c.1069C>G
geneContext:
symbol: ZIC2
valueId: 'HGNC:12873 '
id: variant id
moleculeContext: unspecified_molecule_context
vcfRecord:
alt: G
chrom: NC_000013.11
genomeAssembly: GRCh38
pos: 99983133
ref: C
id: arbitrary interpretation id
progressStatus: COMPLETED
metaData:
created: 2021-05-14T10:35:00Z
createdBy: anonymous biocurator
externalReferences:
- description: Xiong J, et al., 2019
id: PMID:30855487
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karyotypicSex: UNKNOWN_KARYOTYPE
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reference:
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