Class: GeneticFindings

Table containing genetic_findings information

classDiagram class GeneticFindings click GeneticFindings href "../GeneticFindings" GeneticFindings : additional_family_members_with_variant GeneticFindings : allele_balance_or_heteroplasmy_percentage GeneticFindings : alt GeneticFindings : chrom GeneticFindings --> "1" ChromEnum : chrom click ChromEnum href "../ChromEnum" GeneticFindings : chrom_end GeneticFindings --> "0..1" ChromEndEnum : chrom_end click ChromEndEnum href "../ChromEndEnum" GeneticFindings : ClinGen_allele_ID GeneticFindings : condition_id GeneticFindings : condition_inheritance GeneticFindings --> "1..*" ConditionInheritanceEnum : condition_inheritance click ConditionInheritanceEnum href "../ConditionInheritanceEnum" GeneticFindings : copy_number GeneticFindings : experiment_id GeneticFindings : gene_disease_validity GeneticFindings --> "0..1" GeneDiseaseValidityEnum : gene_disease_validity click GeneDiseaseValidityEnum href "../GeneDiseaseValidityEnum" GeneticFindings : gene_known_for_phenotype GeneticFindings --> "1" GeneKnownForPhenotypeEnum : gene_known_for_phenotype click GeneKnownForPhenotypeEnum href "../GeneKnownForPhenotypeEnum" GeneticFindings : gene_of_interest GeneticFindings : genetic_findings_id GeneticFindings : GREGoR_ClinVar_SCV GeneticFindings : GREGoR_variant_classification GeneticFindings --> "0..1" GregorVariantClassificationEnum : GREGoR_variant_classification click GregorVariantClassificationEnum href "../GregorVariantClassificationEnum" GeneticFindings : hgvs GeneticFindings : hgvsc GeneticFindings : hgvsp GeneticFindings : known_condition_name GeneticFindings : linked_variant GeneticFindings : linked_variant_phase GeneticFindings --> "0..1" LinkedVariantPhaseEnum : linked_variant_phase click LinkedVariantPhaseEnum href "../LinkedVariantPhaseEnum" GeneticFindings : method_of_discovery GeneticFindings --> "*" MethodOfDiscoveryEnum : method_of_discovery click MethodOfDiscoveryEnum href "../MethodOfDiscoveryEnum" GeneticFindings : notes GeneticFindings : partial_contribution_explained GeneticFindings : participant_id GeneticFindings : phenotype_contribution GeneticFindings --> "0..1" PhenotypeContributionEnum : phenotype_contribution click PhenotypeContributionEnum href "../PhenotypeContributionEnum" GeneticFindings : pos GeneticFindings : pos_end GeneticFindings : public_database_ID_other GeneticFindings : public_database_other GeneticFindings : ref GeneticFindings : sv_type GeneticFindings --> "0..1" SvTypeEnum : sv_type click SvTypeEnum href "../SvTypeEnum" GeneticFindings : transcript GeneticFindings : variant_inheritance GeneticFindings --> "0..1" VariantInheritanceEnum : variant_inheritance click VariantInheritanceEnum href "../VariantInheritanceEnum" GeneticFindings : variant_reference_assembly GeneticFindings --> "1" VariantReferenceAssemblyEnum : variant_reference_assembly click VariantReferenceAssemblyEnum href "../VariantReferenceAssemblyEnum" GeneticFindings : variant_type GeneticFindings --> "1" VariantTypeEnum : variant_type click VariantTypeEnum href "../VariantTypeEnum" GeneticFindings : zygosity GeneticFindings --> "1" ZygosityEnum : zygosity click ZygosityEnum href "../ZygosityEnum"

Slots

Name	Cardinality and Range	Description	Inheritance
genetic_findings_id	1 String	Unique ID of this variant in this participant (primary key)	direct
participant_id	1 String		direct
experiment_id	1 String	table_name	direct
variant_type	1 VariantTypeEnum		direct
sv_type	0..1 SvTypeEnum		direct
variant_reference_assembly	1 VariantReferenceAssemblyEnum	The genome build for identifying the variant position	direct
chrom	1 ChromEnum	Chromosome of the variant	direct
chrom_end	0..1 ChromEndEnum	End position chromosome of SV	direct
pos	1 Integer	Start position of the variant	direct
pos_end	0..1 Integer	End position of SV	direct
ref	1 String	Reference allele of the variant	direct
alt	1 String	Alternate position of the variant	direct
copy_number	0..1 Integer	CNV copy number	direct
ClinGen_allele_ID	0..1 String	ClinGen Allele ID for cross table refrence	direct
gene_of_interest	1..* String	HGNC approved symbol of the known or candidate gene(s) that are relevant for ...	direct
transcript	0..1 String	Text description of transcript overlapping the variant	direct
hgvsc	0..1 String	HGVS c	direct
hgvsp	0..1 String	HGVS p	direct
hgvs	0..1 String	genomic HGVS description of the variant	direct
zygosity	1 ZygosityEnum	Zygosity of variant	direct
allele_balance_or_heteroplasmy_percentage	0..1 Float	Reported allele balance (mosaic) or heteroplasmy percentage (mitochondrial)	direct
variant_inheritance	0..1 VariantInheritanceEnum	Detection of variant in parents	direct
linked_variant	0..1 String	Second variant in recessive cases	direct
linked_variant_phase	0..1 LinkedVariantPhaseEnum		direct
gene_known_for_phenotype	1 GeneKnownForPhenotypeEnum	Indicate if the gene listed is a candidate or known disease gene	direct
known_condition_name	1 String	Free text of condition name	direct
condition_id	1 String	MONDO/OMIM number for condition used for variant interpretation	direct
condition_inheritance	1..* ConditionInheritanceEnum	Description of the expected inheritance of condition used for variant interpr...	direct
GREGoR_variant_classification	0..1 GregorVariantClassificationEnum	Clinical significance of variant described to condition listed as determined ...	direct
GREGoR_ClinVar_SCV	0..1 String	ClinVar accession number for the variant curation submitted by your center	direct
gene_disease_validity	0..1 GeneDiseaseValidityEnum	Validity assessment of the gene-disease relationship	direct
public_database_other	* String	Public databases that this variant in this participant has been submitted by ...	direct
public_database_ID_other	* String	Public database variant/case ID	direct
phenotype_contribution	0..1 PhenotypeContributionEnum	Contribution of variant-linked condition to participant's phenotype	direct
partial_contribution_explained	1..* String	List of specific phenotypes (HPO IDs) explained by the condition associated w...	direct
additional_family_members_with_variant	* String	List of related participant IDs carrying the same variant	direct
method_of_discovery	* MethodOfDiscoveryEnum	The method/assay(s) used to identify the candidate	direct
notes	0..1 String	Free text field to explain edge cases or discovery updates or list parallel e...	direct

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/madanucd/gregor_linkml

Mappings

Mapping Type	Mapped Value
self	gregor_linkml:GeneticFindings
native	gregor_linkml:GeneticFindings

LinkML Source

Direct

name: Genetic_findings
description: Table containing genetic_findings information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- genetic_findings_id
- participant_id
- experiment_id
- variant_type
- sv_type
- variant_reference_assembly
- chrom
- chrom_end
- pos
- pos_end
- ref
- alt
- copy_number
- ClinGen_allele_ID
- gene_of_interest
- transcript
- hgvsc
- hgvsp
- hgvs
- zygosity
- allele_balance_or_heteroplasmy_percentage
- variant_inheritance
- linked_variant
- linked_variant_phase
- gene_known_for_phenotype
- known_condition_name
- condition_id
- condition_inheritance
- GREGoR_variant_classification
- GREGoR_ClinVar_SCV
- gene_disease_validity
- public_database_other
- public_database_ID_other
- phenotype_contribution
- partial_contribution_explained
- additional_family_members_with_variant
- method_of_discovery
- notes

Induced

name: Genetic_findings
description: Table containing genetic_findings information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  genetic_findings_id:
    name: genetic_findings_id
    description: Unique ID of this variant in this participant (primary key)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: genetic_findings_id
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  participant_id:
    name: participant_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: participant_id
    owner: Genetic_findings
    domain_of:
    - Participant
    - Phenotype
    - Genetic_findings
    - Analyte
    - Experiment
    - Aligned
    range: string
    required: true
  experiment_id:
    name: experiment_id
    description: table_name.experiment_id_in_table
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: experiment_id
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    - Experiment
    range: string
    required: true
  variant_type:
    name: variant_type
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: variant_type
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Variant_typeEnum
    required: true
  sv_type:
    name: sv_type
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sv_type
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Sv_typeEnum
  variant_reference_assembly:
    name: variant_reference_assembly
    description: The genome build for identifying the variant position
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: variant_reference_assembly
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Variant_reference_assemblyEnum
    required: true
  chrom:
    name: chrom
    description: Chromosome of the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: chrom
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: ChromEnum
    required: true
  chrom_end:
    name: chrom_end
    description: End position chromosome of SV
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: chrom_end
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Chrom_endEnum
  pos:
    name: pos
    description: Start position of the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: pos
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: integer
    required: true
  pos_end:
    name: pos_end
    description: End position of SV
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: pos_end
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: integer
  ref:
    name: ref
    description: Reference allele of the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: ref
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  alt:
    name: alt
    description: Alternate position of the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: alt
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  copy_number:
    name: copy_number
    description: CNV copy number
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: copy_number
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: integer
  ClinGen_allele_ID:
    name: ClinGen_allele_ID
    description: ClinGen Allele ID for cross table refrence
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: ClinGen_allele_ID
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  gene_of_interest:
    name: gene_of_interest
    description: HGNC approved symbol of the known or candidate gene(s) that are relevant
      for the observed phenotype.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: gene_of_interest
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  transcript:
    name: transcript
    description: Text description of transcript overlapping the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: transcript
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  hgvsc:
    name: hgvsc
    description: HGVS c. description of the variant (m. for mitochondrial)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: hgvsc
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  hgvsp:
    name: hgvsp
    description: HGVS p. description of the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: hgvsp
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  hgvs:
    name: hgvs
    description: genomic HGVS description of the variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: hgvs
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  zygosity:
    name: zygosity
    description: Zygosity of variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: zygosity
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: ZygosityEnum
    required: true
  allele_balance_or_heteroplasmy_percentage:
    name: allele_balance_or_heteroplasmy_percentage
    description: Reported allele balance (mosaic) or heteroplasmy percentage (mitochondrial)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: allele_balance_or_heteroplasmy_percentage
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: float
  variant_inheritance:
    name: variant_inheritance
    description: Detection of variant in parents
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: variant_inheritance
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Variant_inheritanceEnum
  linked_variant:
    name: linked_variant
    description: Second variant in recessive cases
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: linked_variant
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  linked_variant_phase:
    name: linked_variant_phase
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: linked_variant_phase
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Linked_variant_phaseEnum
  gene_known_for_phenotype:
    name: gene_known_for_phenotype
    description: Indicate if the gene listed is a candidate or known disease gene.
      Known disease genes can be identified using OMIM or MONDO or MitoMap. Variant/phenotype
      in proband should be consistent with the described MOD/phenotype to be considered
      a known gene for condition.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: gene_known_for_phenotype
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Gene_known_for_phenotypeEnum
    required: true
  known_condition_name:
    name: known_condition_name
    description: Free text of condition name. Variant/phenotype/inheritance in proband
      should be consistent with the condition.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: known_condition_name
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  condition_id:
    name: condition_id
    description: MONDO/OMIM number for condition used for variant interpretation.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: condition_id
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  condition_inheritance:
    name: condition_inheritance
    description: Description of the expected inheritance of condition used for variant
      interpretation
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: condition_inheritance
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Condition_inheritanceEnum
    required: true
  GREGoR_variant_classification:
    name: GREGoR_variant_classification
    description: Clinical significance of variant described to condition listed as
      determined by the RC's variant curation.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: GREGoR_variant_classification
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Gregor_variant_classificationEnum
  GREGoR_ClinVar_SCV:
    name: GREGoR_ClinVar_SCV
    description: ClinVar accession number for the variant curation submitted by your
      center
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: GREGoR_ClinVar_SCV
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  gene_disease_validity:
    name: gene_disease_validity
    description: Validity assessment of the gene-disease relationship
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: gene_disease_validity
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Gene_disease_validityEnum
  public_database_other:
    name: public_database_other
    description: Public databases that this variant in this participant has been submitted
      by the RC.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: public_database_other
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  public_database_ID_other:
    name: public_database_ID_other
    description: Public database variant/case ID
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: public_database_ID_other
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  phenotype_contribution:
    name: phenotype_contribution
    description: Contribution of variant-linked condition to participant's phenotype.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: phenotype_contribution
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Phenotype_contributionEnum
  partial_contribution_explained:
    name: partial_contribution_explained
    description: List of specific phenotypes (HPO IDs) explained by the condition
      associated with this variant/gene in cases of partial contribution
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: partial_contribution_explained
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
    required: true
  additional_family_members_with_variant:
    name: additional_family_members_with_variant
    description: List of related participant IDs carrying the same variant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: additional_family_members_with_variant
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string
  method_of_discovery:
    name: method_of_discovery
    description: The method/assay(s) used to identify the candidate
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: method_of_discovery
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: Method_of_discoveryEnum
  notes:
    name: notes
    description: Free text field to explain edge cases or discovery updates or list
      parallel experiment IDs or list parental allele balance when mosaic... etc.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: notes
    owner: Genetic_findings
    domain_of:
    - Genetic_findings
    range: string