Trait: mineral metabolism disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009556
Description Abnormal levels of minerals in the blood.
Trait category
Metabolic disorder
Synonyms 3 synonyms
  • disease of mineral metabolism
  • disorder of mineral metabolism
  • mineral metabolism disease
Mapped terms 5 mapped terms
  • ICD10:E83
  • ICD9:275.8
  • ICD9:275.9
  • MONDO:0000226
  • SCTID:45744005

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001023
(GBE_HC703)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Disorders of mineral metabolism (time-to-event) mineral metabolism disease 2
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001023/ScoringFiles/PGS001023.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM007878 PGS001023
(GBE_HC703)
PSS004605|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE disorders of mineral metabolism AUROC: 0.70572 [0.64003, 0.77141] : 0.04772
Incremental AUROC (full-covars): -0.00243
PGS R2 (no covariates): 0.00257
PGS AUROC (no covariates): 0.49279 [0.49133, 0.49424]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007879 PGS001023
(GBE_HC703)
PSS004606|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE disorders of mineral metabolism AUROC: 0.72332 [0.56417, 0.88247] : 0.06686
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.00038
PGS AUROC (no covariates): 0.49882 [0.49767, 0.49998]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007880 PGS001023
(GBE_HC703)
PSS004607|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE disorders of mineral metabolism AUROC: 0.70459 [0.66766, 0.74152] : 0.07164
Incremental AUROC (full-covars): 0.05404
PGS R2 (no covariates): 0.07064
PGS AUROC (no covariates): 0.63902 [0.6046, 0.67344]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007881 PGS001023
(GBE_HC703)
PSS004608|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE disorders of mineral metabolism AUROC: 0.60481 [0.54255, 0.66706] : 0.01967
Incremental AUROC (full-covars): -0.00045
PGS R2 (no covariates): 0.00194
PGS AUROC (no covariates): 0.50905 [0.4878, 0.5303]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007882 PGS001023
(GBE_HC703)
PSS004609|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE disorders of mineral metabolism AUROC: 0.65351 [0.63175, 0.67527] : 0.03407
Incremental AUROC (full-covars): 0.05096
PGS R2 (no covariates): 0.02793
PGS AUROC (no covariates): 0.57843 [0.55918, 0.59767]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS004605
[
  • 49 cases
  • , 6,448 controls
]
African unspecified UKB
PSS004606
[
  • 8 cases
  • , 1,696 controls
]
East Asian UKB
PSS004607
[
  • 225 cases
  • , 24,680 controls
]
European non-white British ancestry UKB
PSS004608
[
  • 65 cases
  • , 7,766 controls
]
South Asian UKB
PSS004609
[
  • 613 cases
  • , 66,812 controls
]
European white British ancestry UKB Testing cohort (heldout set)