Propositions

A proposition defines what a statement asserts — the relationship between a variant and a condition. Each proposition follows the subject-predicate-object pattern from the GA4GH VA-Spec specification:

• Subject (subjectVariant) — a reference to a ClinVar variation via #/variation/clinvar:{id}
• Predicate — the relationship type (e.g., isCausalFor, isOncogenicFor)
• Object (objectCondition) — a condition, disease, or phenotype

The ClinvarProposition union type encompasses all 12 proposition types valid in ClinVar-GKS.

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Proposition Types

ClinVar-GKS uses 12 proposition types: 3 from the GA4GH VA-Spec standard and 9 defined specifically for ClinVar submission categories.

GA4GH Standard Types

These types are defined in the VA-Spec and used directly:

Code	Type	Predicate	Description
PATH	VariantPathogenicityProposition	isCausalFor	Germline pathogenicity/benignity
ONCO	VariantOncogenicityProposition	isOncogenicFor	Oncogenicity classification
SCI	VariantClinicalSignificanceProposition	isClinicallySignificantFor	Somatic clinical impact

ClinVar-Specific Types

These types handle ClinVar submission categories not covered by the GA4GH specifications. Several are no longer accepted as new submissions by ClinVar, but historical submissions remain in the dataset.

Code	Type	Predicate	Description
RF	ClinvarRiskFactorProposition	isRiskFactorFor	Risk factor
PROT	ClinvarProtectiveProposition	isProtectiveFor	Protective
DR	ClinvarDrugResponseProposition	hasDrugResponseFor	Drug response
AFF	ClinvarAffectsProposition	hasAffectFor	Affects
ASSOC	ClinvarAssociationProposition	isAssociatedWith	Association
CS	ClinvarConfersSensitivityProposition	confersSensitivityFor	Confers sensitivity
OTH	ClinvarOtherProposition	isClinvarOtherAssociationFor	Other
NP	ClinvarNotProvidedProposition	hasNoProvidedClassificationFor	Not provided
CONF	ClinvarConflictingDataFromSubmitterProposition	isConflictingDataFromSubmittersFor	Conflicting data (germline only)

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Somatic Evidence Line Propositions

Somatic clinical impact (SCI) statements carry evidence lines with their own target propositions. These 3 types appear only on ClinvarSomaticEvidenceLine objects, not as top-level statement propositions:

Code	Type	Predicates
TR	VariantTherapeuticResponseProposition	predictsSensitivityTo, predictsResistanceTo
DIAG	VariantDiagnosticProposition	isDiagnosticInclusionCriterionFor, isDiagnosticExclusionCriterionFor
PROG	VariantPrognosticProposition	associatedWithBetterOutcomeFor, associatedWithWorseOutcomeFor

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Inherited Attributes

All ClinVar proposition types inherit from the VA-Spec ClinicalVariantProposition, which provides:

• subjectVariant — the variant being classified
• geneContextQualifier — the gene impacted by the variant
• alleleOriginQualifier — germline, somatic, or mosaic origin

See the individual class pages for the complete information model including all inherited fields.