VAR_PHENOTYPES

Description:

The VAR_PHENOTYPES table contains the external phenotype identifier and the system that defined it.

Primary Key

Column Name	Ordinal Position
VARIANT_ID	1
LINE	2

Column Information

	Name	Type	Discontinued?
1	VARIANT_ID	NUMERIC	No
	The unique identifier for the variant record.
2	LINE	INTEGER	No
	The line number for the information associated with this record. Multiple pieces of information can be associated with this record.
3	PHENOTYPE_SYSTEM_C_NAME	VARCHAR	No
	The coding system category ID for the phenotype. May contain organization-specific values: No Category Entries: MEDGEN OMIM SNOMED CT HPO ICD-9-CM ICD-10-CM
4	PHENOTYPE_CODE	VARCHAR	No
	The external phenotype code assigned by the phenotype coding system.
5	PHENOTYPE_NAME	VARCHAR	No
	Phenotype name of phenotypes associated with the variant
6	MODE_OF_INHERITANCE_C_NAME	VARCHAR	No
	The mode of inheritance category ID for the phenotype associated with the variant May contain organization-specific values: No Category Entries: Autosomal dominant inheritance Autosomal dominant inheritance with maternal imprinting Autosomal dominant inheritance with paternal imprinting Autosomal recessive inheritance Autosomal unknown Codominant Digenic inheritance Genetic anticipation Mitochondrial inheritance Multifactorial inheritance Oligogenic inheritance Pseudoautosomal dominant inheritance Pseudoautosomal recessive inheritance Sex-limited autosomal dominant Somatic mutation Sporadic Unknown mechanism X-linked dominant inheritance X-linked inheritance X-linked recessive inheritance Y-linked inheritance Other
7	PHENOTYPE_SPEC_PENETRANCE	NUMERIC	No
	The penetrance of a particular phenotype
8	PHENOTYPE_SPEC_DESC	VARCHAR	No
	A free-text description of a particular phenotype
9	PHENOTYPE_SPEC_VAR_CLASS_C_NAME	VARCHAR	No
	The category ID corresponding to the variant classification of a phenotype. May contain organization-specific values: No Category Entries: Pathogenic Likely pathogenic Uncertain significance Likely benign Benign Risk allele Tier 1 or 2: Strong or potential significance Tier 1: Strong significance Tier 2: Potential significance Tier 3: Unknown clinical significance Tier 4: Benign or likely benign Drug response Complete Penetrance Incomplete Penetrance Premutation Uncertain Penetrance Intermediate Mutable Normal Allele Recessive Allele Normal Allele Classification not provided
10	PHENOTYPE_EFFECT_TYPE_C_NAME	VARCHAR	No
	Stores the phenotypic effect type of a variant. May contain organization-specific values: No Category Entries: Metabolism Efficacy Risk Transport Enzyme Activity
11	PHENOTYPE_EFFECT_VAL_C_NAME	VARCHAR	No
	Stores the phenotypic effect value of a variant. May contain organization-specific values: No Category Entries: Indeterminate Increased function Normal function Decreased function Uncertain function Unknown function No function Ultrarapid metabolizer Rapid metabolizer Normal metabolizer Intermediate metabolizer Poor metabolizer Likely ultrarapid metabolizer Likely rapid metabolizer Likely normal metabolizer Likely intermediate metabolizer Likely poor metabolizer Possible ultrarapid metabolizer Possible rapid metabolizer Possible normal metabolizer Possible intermediate metabolizer Possible poor metabolizer Resistant Responsive Benign Presumed resistant Presumed responsive Presumed benign Presumed non-responsive Unknown significance Low risk High risk Typical risk Poor function Likely increased function Likely normal function Likely decreased function Likely poor function Possible increased function Possible normal function Possible decreased function Possible poor function Deficient Deficient with CNSHA Normal Variable
12	PHENOTYPE_ACTIVITY_SCORE_LOWER	NUMERIC	No
	The activity score of the pharmacogenomic variant, or the lowest value the activity score can be based on lab input
13	PHENOTYPE_ACTIVITY_SCORE_UPPER	NUMERIC	No
	The highest value the activity score can be based on lab input