Trait: cataract

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001059
Description Partial or complete opacity of the crystalline lens of one or both eyes that decreases visual acuity and eventually results in blindness. Some cataracts appear in infancy or in childhood, but most develop in older individuals. (Sternberg Diagnostic Surgical Pathology, 3rd ed.) [NCIT: C26713]
Trait category
Other disease
Synonyms 36 synonyms
  • CATARACT NEC
  • CATARACT W RADIATION
  • CATARACT W SYNDROME NEC
  • Cat. - Cataract
  • Cataract (M-54510)
  • Cataract (disorder)
  • Cataract (morphologic abnormality)
  • Cataract NOS
  • Cataract NOS (disorder)
  • Cataract associated with other disorders
  • Cataract associated with other syndromes
  • Cataract associated with other syndromes (disorder)
  • Cataract associated with radiation and other physical influences
  • Cataract form
  • Cataract form (observable entity)
  • Cataract, Membranous
  • Cataracts
  • Cataracts, Membranous
  • Lens Opacities
  • Lens Opacity
  • Lenticular opacity
  • Membranous Cataract
  • Membranous Cataracts
  • Opacities, Lens
  • Opacity, Lens
  • Other cataract
  • Other cataract (disorder)
  • Other cataract NOS
  • Other cataract NOS (disorder)
  • Pseudoaphakia
  • Pseudoaphakias
  • Unspecified cataract
  • cataract
  • cataract (disease)
  • cataracts
  • opacity of the lens
Mapped terms 22 mapped terms
  • DOID:83
  • HP:0000518
  • ICD10:H26
  • ICD9:366
  • ICD9:366.44
  • ICD9:366.8
  • ICD9:366.9
  • MESH:D002386
  • MONDO:0005129
  • MeSH:D002386
  • MedDRA:10007739
  • NCIT:C26713
  • NCIt:C26713
  • OMIM:115900
  • OMIM:116100
  • OMIM:616279
  • OMIM:616509
  • OMIM:618415
  • OMIMPS:116200
  • SCTID:193570009
  • SNOMEDCT:128306009
  • SNOMEDCT:193570009

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)
PGS001302
(GBE_HC25)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Cataract cataract 1,214
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001302/ScoringFiles/PGS001302.txt.gz
PGS001303
(GBE_HC872)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Other cataract (time-to-event) cataract 480
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001303/ScoringFiles/PGS001303.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
PPM009014 PGS001303
(GBE_HC872)
PSS004681|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.72387 [0.71653, 0.73121] : 0.09993
Incremental AUROC (full-covars): 0.00356
PGS R2 (no covariates): 0.0043
PGS AUROC (no covariates): 0.54593 [0.53685, 0.555]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009013 PGS001303
(GBE_HC872)
PSS004680|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.79821 [0.78425, 0.81216] : 0.23261
Incremental AUROC (full-covars): 0.00152
PGS R2 (no covariates): 0.00238
PGS AUROC (no covariates): 0.52897 [0.51011, 0.54783]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009012 PGS001303
(GBE_HC872)
PSS004679|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.75268 [0.74071, 0.76465] : 0.12486
Incremental AUROC (full-covars): 0.00345
PGS R2 (no covariates): 0.00455
PGS AUROC (no covariates): 0.5485 [0.53327, 0.56373]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009011 PGS001303
(GBE_HC872)
PSS004678|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.81597 [0.77997, 0.85198] : 0.21513
Incremental AUROC (full-covars): 0.00031
PGS R2 (no covariates): 0.00012
PGS AUROC (no covariates): 0.50879 [0.45096, 0.56661]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009010 PGS001303
(GBE_HC872)
PSS004677|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.81396 [0.7961, 0.83182] : 0.23163
Incremental AUROC (full-covars): 5e-05
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50326 [0.47798, 0.52854]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009009 PGS001302
(GBE_HC25)
PSS004383|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.73692 [0.73039, 0.74345] : 0.12068
Incremental AUROC (full-covars): 0.00566
PGS R2 (no covariates): 0.00657
PGS AUROC (no covariates): 0.55468 [0.5465, 0.56286]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009008 PGS001302
(GBE_HC25)
PSS004382|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.81674 [0.80411, 0.82937] : 0.28207
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00627
PGS AUROC (no covariates): 0.54731 [0.52945, 0.56518]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009007 PGS001302
(GBE_HC25)
PSS004381|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.76448 [0.75374, 0.77523] : 0.14636
Incremental AUROC (full-covars): 0.00517
PGS R2 (no covariates): 0.00768
PGS AUROC (no covariates): 0.56031 [0.5466, 0.57402]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009006 PGS001302
(GBE_HC25)
PSS004380|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.81531 [0.78353, 0.84709] : 0.22081
Incremental AUROC (full-covars): 0.00025
PGS R2 (no covariates): 0.00037
PGS AUROC (no covariates): 0.48894 [0.43818, 0.53971]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009005 PGS001302
(GBE_HC25)
PSS004379|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.81842 [0.80148, 0.83536] : 0.25176
Incremental AUROC (full-covars): -0.00057
PGS R2 (no covariates): 0.00041
PGS AUROC (no covariates): 0.51203 [0.48858, 0.53548]
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
PSS004380
[
  • 140 cases
  • , 1,564 controls
]
East Asian UKB
PSS004381
[
  • 1,738 cases
  • , 23,167 controls
]
European non-white British ancestry UKB
PSS004382
[
  • 1,165 cases
  • , 6,666 controls
]
South Asian UKB
PSS004383
[
  • 5,153 cases
  • , 62,272 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004677
[
  • 561 cases
  • , 5,936 controls
]
African unspecified UKB
PSS004678
[
  • 115 cases
  • , 1,589 controls
]
East Asian UKB
PSS004679
[
  • 1,448 cases
  • , 23,457 controls
]
European non-white British ancestry UKB
PSS004680
[
  • 986 cases
  • , 6,845 controls
]
South Asian UKB
PSS004681
[
  • 4,189 cases
  • , 63,236 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004379
[
  • 637 cases
  • , 5,860 controls
]
African unspecified UKB