Trait: Malabsorption

Trait Information
Identifier HP_0002024
Description Impaired ability to absorb one or more nutrients from the intestine. [HPO: probinson]
Trait category
Other trait
Synonyms 2 synonyms
  • Intestinal malabsorption
  • Malabsorption
Mapped term UMLS:C3714745

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)
PGS000940
(GBE_HC1132)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Intestinal malabsorption (time-to-event) Malabsorption 443
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000940/ScoringFiles/PGS000940.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
PPM007527 PGS000940
(GBE_HC1132)
PSS004149|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE intestinal malabsorption AUROC: 0.77831 [0.68833, 0.86829] : 0.08733
Incremental AUROC (full-covars): 0.1198
PGS R2 (no covariates): 0.02978
PGS AUROC (no covariates): 0.67977 [0.56558, 0.79395]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007528 PGS000940
(GBE_HC1132)
PSS004150|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE intestinal malabsorption AUROC: 0.77961 [0.74665, 0.81258] : 0.11095
Incremental AUROC (full-covars): 0.13283
PGS R2 (no covariates): 0.09823
PGS AUROC (no covariates): 0.76402 [0.72932, 0.79873]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007529 PGS000940
(GBE_HC1132)
PSS004151|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE intestinal malabsorption AUROC: 0.72065 [0.63105, 0.81026] : 0.05999
Incremental AUROC (full-covars): 0.05026
PGS R2 (no covariates): 0.04035
PGS AUROC (no covariates): 0.66531 [0.56469, 0.76593]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007530 PGS000940
(GBE_HC1132)
PSS004152|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE intestinal malabsorption AUROC: 0.75898 [0.73729, 0.78067] : 0.08993
Incremental AUROC (full-covars): 0.18915
PGS R2 (no covariates): 0.08413
PGS AUROC (no covariates): 0.75085 [0.7286, 0.77309]
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
PSS004149
[
  • 18 cases
  • , 6,479 controls
]
African unspecified UKB
PSS004150
[
  • 208 cases
  • , 24,697 controls
]
European non-white British ancestry UKB
PSS004151
[
  • 38 cases
  • , 7,793 controls
]
South Asian UKB
PSS004152
[
  • 553 cases
  • , 66,872 controls
]
European white British ancestry UKB Testing cohort (heldout set)