Polygenic Score (PGS) ID: PGS003590

Predicted Trait
Reported Trait Cystatin C production
Mapped Trait(s) cystatin C measurement (EFO_0004617)
Additional Trait Information Latent trait, from structural equation model
Released in PGS Catalog: April 28, 2023
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name UKB_cycproduction_EUR_exome
Development Method
Name LDpred2
Parameters exonic variants
Variants
Original Genome Build GRCh37
Number of Variants 352,549
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000463
Citation (link to publication) Kleeman SO et al. Cell Genom (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
381,764 individuals (100%)
Score Development/Training
Multi-ancestry (excluding European): 100%
  • Additional Asian Ancestries
  • South Asian
9,845 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 381,764 individuals European UKB
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 9,845 individuals Central Asian, South Asian UKB — — — — —

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) 		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
PPM018284 PSS010957|
European Ancestry|
50,000 individuals
 PGP000463 |
Kleeman SO et al. Cell Genom (2023)
 Reported Trait: Cystatin C production — — R²: 0.04 Age, sex, PC1-4, recruitment center, genotyping array —

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
PSS010957 — — 50,000 individuals — European — UKB —