ClinGen DataExchange Model

A statement describing the observed correlation between transmission of a particular allele and a particular genetic condition, across a single family pedigree (i.e. the co-segregation of an allele and a condition as observed across a family pedigree).

SEPIO:0000247
Descended from Statement

Scope and Usage

Co-segregatation' refers to the correlation between the presence of a particular allele and the manifestation of a condition in a family pedigree. When an allele and a condition are only found together in family members, they are said to co-segregate.

When there are no individuals that have the allele without the condition or the condition without the allele, the allele and condition are said to co-segregate.

Attributes

Name	Type	Cardinality	Description	IRI	Defined in
canonicalAllele	CanonicalAllele	1..1	Allele being tested for cosegregation	SEPIO:0000275	FamilyCosegregationStatement
condition	GeneticCondition	1..1	Condition being tested for cosegregation	SEPIO:0000276	FamilyCosegregationStatement
family	@id	1..1	Family in which segregation is being tested	SEPIO:0000282	FamilyCosegregationStatement
phenotypePositiveAllelePositive	integer	0..1	Number of (non-proband) individuals with both the condition and the allele	SEPIO:0000292	FamilyCosegregationStatement
phenotypePositiveAlleleNegative	integer	0..1	Number of (non-proband) individuals with the condition and without the allele	SEPIO:0000290	FamilyCosegregationStatement
phenotypeNegativeAllelePositive	integer	0..1	Number of (non-proband) individuals without the condition and with the allele	SEPIO:0000291	FamilyCosegregationStatement
phenotypeNegativeAlleleNegative	integer	0..1	The number of non-proband family members that have neither the allele nor the phenotype	SEPIO:0000289	FamilyCosegregationStatement
inconsistentSegregationsObserved	@id	0..1	Whether phenotype positive/allele negative or phenotype negative/allele positive individuals are in the family	SEPIO:0000314	FamilyCosegregationStatement
inconsistentSegregationCount	integer	0..1	The number of segregations inconsistent with allele pathogenicity	SEPIO:0000315	FamilyCosegregationStatement
columns	string	0..*	Column names for the pedigree data element	SEPIO:0000316	FamilyCosegregationStatement
pedigree	string	0..*	Detailed information about the family structure, affected status, and genotypes in pedigree/linkage format.	SEPIO:0000318	FamilyCosegregationStatement
genotypeValues	string	0..*	Map describing how genotypes are represented in the pedigree	SEPIO:0000317	FamilyCosegregationStatement
affectedValues	string	0..*	Map describing how affected status is represented in the pedigree	SEPIO:0000313	FamilyCosegregationStatement
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	canonicalAllele	condition	family	phenotypePositiveAllelePositive	phenotypePositiveAlleleNegative	phenotypeNegativeAllelePositive	phenotypeNegativeAlleleNegative	inconsistentSegregationsObserved	inconsistentSegregationCount	columns	pedigree	genotypeValues	affectedValues
CGEX:FamSeg076						CAR:CA090930	CGEX:GenCond056	CGEX:Fam373 (Family #011)	0	0	2		SEPIO-CG:99011 (present)
CGEX:FamSeg103		identified in 1 individual with HCM. Segregation analysis determined 5 other members of the family also carried this variant. However, only 3 of those family members had HCM (aged 48-75). The 2 other family members were young and asymptomatic. So from this paper, only count 3 segregations. The two apparently refuting segregations can be ignored due to the age-dependent penetrance of HCM.				CAR:CA010136	CGEX:GenCond020	CGEX:Fam363 (Family #001)	3		2
CGEX:FamSeg104		In LMM internal family, c.1351+1G>A was identified in 1 individual with HCM. Variant also found in individual’s sister - who also had clinical dx of HCM.				CAR:CA010136	CGEX:GenCond020	CGEX:Fam364 (Family #002)	1
CGEX:FamSeg107		proband and 5 affected family members all homozygous for NM_206933.2(USH2A):c.1000C>G (p.Arg334Gly).				CAR:CA143213	CGEX:GenCond021	CGEX:Fam365 (Family #003)	5
CGEX:FamSeg108		c.1000C>T identified in het state in 1 individual with Usher. Individual compound het with Gly1840Val USH2A variant - confirmed in trans. Gly1840Val called Pathogenic. Individual has 3 affected sibs all of whom are compound het with 1000C>T & Gly1840Val. One additional sib only carried 1000C>T and is unaffected.				CAR:CA143213	CGEX:GenCond021	CGEX:Fam366 (Family #004)
CGEX:FamSeg111						CAR:CA501226	CGEX:GenCond051	CGEX:Fam367 (Family #005)	2
CGEX:FamSeg113						CAR:CA006429	CGEX:GenCond002	CGEX:Fam368 (Family #006)	1		1				[“Family”,”Individual”,”Father”,”Mother”,”Sex”,”Affected”,”Genotype”]	[[Fam006,Fam006.1,0,0,1,2,0/0], [Fam006,Fam006.2,0,0,2,1,0/0], [Fam006,Fam006.3,Fam006.1,Fam006.2,2,3,0/0], [Fam006,Fam006.4,Fam006.1,Fam006.2,1,2,1/2], [Fam006,Fam006.5,Fam006.1,Fam006.2,2,1,1/1], [Fam006,Fam006.6,Fam006.1,Fam006.2,1,2,1/2]]	{0: “Unknown”,1:”Reference”, 2: CA65}	{1: “Unaffected”, 2: “Affected”, 3: “Any Cardiovascular Abnormality”}
CGEX:FamSeg114						CAR:CA006429	CGEX:GenCond002	CGEX:Fam369 (Family #007)	2		3				[“Family”,”Individual”,”Father”,”Mother”,”Sex”,”Affected”,”Genotype”,”ObligateGenotype”]	[[Fam007, Fam007.1, 0, 0, 1, 3, 0/0, 0], [Fam007, Fam007.2, 0, 0, 2, 1, 0/0, 0], [Fam007, Fam007.3, 0, 0, 1, 3, 0/0, 0], [Fam007, Fam007.4, 0, 0, 2, 1, 0/0, 0], [Fam007, Fam007.5, 0, 0, 1, 3, 0/0, 0], [Fam007, Fam007.6, Fam007.1, Fam007.2, 2, 3, 1/2, 1], [Fam007, Fam007.7,0, 0, 1, 1, 0/0, 0], [Fam007, Fam007.8, Fam007.1, Fam007.2, 2, 1, 1/2, 1], [Fam007, Fam007.9,Fam007.3, Fam007.4, 1, 1, 0/0, 0], [Fam007, Fam007.10, 0, 0, 1, 1, 0/0, 0], [Fam007, Fam007.11, Fam007.5, Fam007.6, 2, 2, 1/2, 0], [Fam007, Fam007.12, Fam007.5, Fam007.6, 1,2, 0/0, 0], [Fam007, Fam007.13, Fam007.5, Fam007.6, 2,1, 1/1,0], [Fam007, Fam007.14, Fam007.5, Fam007.6, 1, 1, 1/1, 0], [Fam007, Fam007.15, Fam007.7, Fam007.8, 1, 2, 1/2, 0], [Fam007, Fam007.16, Fam007.8, Fam007.9, 1, 2, 1/2, 0], [Fam007, Fam007.17, Fam007.8, Fam007.9, 1, 2, 0/0,0], [Fam007, Fam007.18, Fam007.8, Fam007.9, 1, 2, 0/0, 0], [Fam007, Fam007.19, Fam007.10, Fam007.11, 1, 2, 0/0,0], [Fam007.20,Fam007.10, Fam007.11, 1,1,1/1,0]]	{0: “Unknown”,1:”Reference”, 2: CA65}	{1: “Unaffected”, 2: “Affected”, 3: “Any Cardiovascular Abnormality”}
CGEX:FamSeg196		observed in one case diagnosed with Familial Hypercholesterolemia, characterized by elevated LDLC levels. Two siblings of the proband also have elevated LDLC levels but neither carry the 313+2T>C variant.				CAR:CA023690	CGEX:GenCond035	CGEX:Fam370 (Family #008)	0	2			SEPIO-CG:99011 (present)
CGEX:FamSeg197		The individual with HCM but without the allele is likely a phenocopy explained by environmental factors (obese, alcohol)				CAR:CA010777	CGEX:GenCond065	CGEX:Fam371 (Family #009)	3	1			SEPIO-CG:99011 (present)

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