ClinGen DataExchange Model

A statement about the mechanism underlying a genetic condition (e.g. if that LOF mutations in a particular gene are a known mechanism of disease).

SEPIO:0000228
Descended from Statement

Scope and Usage

Attributes

Name	Type	Cardinality	Description	IRI	Defined in
condition	GeneticCondition	1..1	The condition whose mechanism is being described	SEPIO:0000276	ConditionMechanismStatement
gene	@id	1..1	Gene in which the given variants occur	SEPIO:0000278	ConditionMechanismStatement
statementOutcome	@id	1..1	SO term for a class of variants	SEPIO:0000197	ConditionMechanismStatement
mechanismConfidence	@id	0..1	Qualifier on the Condition/Mechanism pair	SEPIO:0000167	ConditionMechanismStatement
label	string	0..1	A name given to the resource.	RDFS:label	Entity
description	string	0..1	Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.	DC:description	Entity
userLabelDictionary	UserLabel	0..*	An optional label defined by the user. Used for custom entities or to clarify the preferred user label on existing entities with non-preferred labels.	SEPIO:0000422	Statement
outcomeQualifier	string	0..1	Use “NOT” as the value of this property to assert that the statement is negated.	SEPIO:0000346	Statement
evidenceLine	EvidenceLine	0..*	supporting evidence	SEPIO:0000006	Statement
contribution	Contribution	0..*	The contributions (agent, time and role) made to this entity	SEPIO:0000159	Statement
source	string	0..*	A string indicating the source of a Statement	DC:source	Statement

Instances

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ID	label	description	userLabelDictionary	outcomeQualifier	evidenceLine	condition	gene	statementOutcome	mechanismConfidence
CGEX:CondMech002		HNRNPU is not associated with any conditions, and therefore LOF is not an established mechanism of any condition for this gene.					HGNC:5048 (HNRNPU)	SO:0002054 (loss of function variant)	SEPIO:0000269 (established)
CGEX:CondMech004		This is so well-known that it does not require a citation.				CGEX:GenCond001	HGNC:1101 (BRCA2)	SO:0002054 (loss of function variant)	SEPIO:0000269 (established)
CGEX:CondMech007						CGEX:GenCond047	HGNC:12403 (TTN)	SO:0002054 (loss of function variant)	SEPIO:0000269 (established)
CGEX:CondMech118		Of 178 pathogenic alleles in ClinVar, 149 are missense.					HGNC:7577 (MYH7)	SO:0001583 (missense variant)	SEPIO:0000268 (common)
CGEX:CondMech165						CGEX:GenCond054	HGNC:12403 (TTN)	SO:0001583 (missense variant)	SEPIO:0000268 (common)
CGEX:CondMech199		ClinVar shows 421 variants in BRCA2 that are pathogenic for HBOC. 402 of these (~95%) are frameshift, nonsense, or splice-site variants.				CGEX:GenCond036	HGNC:1101 (BRCA2)	SO:0002054 (loss of function variant)	SEPIO:0000270 (primary)
CGEX:CondMech200		ClinVar shows 61 variants in BRCA2 that are pathogenic for Fanconi Anemia. 55 of these (~90%) are frameshift, nonsense, or splice-site variants.				CGEX:GenCond037	HGNC:1101 (BRCA2)	SO:0002054 (loss of function variant)	SEPIO:0000270 (primary)
CGEX:CondMech202		shown in both humans and mouse models				CGEX:GenCond059	HGNC:26521 (LOXHD1)	SO:0002054 (loss of function variant)	SEPIO:0000270 (primary)
CGEX:CondMech204						CGEX:GenCond053	HGNC:12403 (TTN)	SO:0002054 (loss of function variant)	SEPIO:0000270 (primary)
CGEX:CondMech205		Truncating variants in TTN are associated with DCM. However, if missense variants are located in the A-band, impact the A-band, or are in a highly expressed region, they can also be associated with DCM.				CGEX:GenCond053	HGNC:12403 (TTN)	SO:0001583 (missense variant)	SEPIO:0000269 (established)

Showing 1 to 10 of 11 entries