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
Polygenic inheritance
Genetic anticipation
Mitochondrial inheritance
Multifactorial inheritance
Semidominant 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
Gene of Uncertain Significance
Risk allele
Pseudodeficiency allele
Hypomorphic
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