Polygenic Score (PGS) ID: PGS003280

Predicted Trait
Reported Trait Cystatin C
Mapped Trait(s) cystatin C measurement (EFO_0004617)
Additional Trait Information Cystatin C (quantile); Quantitative
Released in PGS Catalog: Nov. 23, 2022
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Score Details

Score Construction
PGS Name ExPRSweb_CysC_30720-irnt_PT_MGI_20211120
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (using Plink to calculate LD, MAF >= 1%, r^2 <= 0.1) & P-value threshold <=3.98e-15
Original Genome Build GRCh37
Number of Variants 346
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000393
Citation (link to publication) Ma Y et al. Am J Hum Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
344,264 individuals (100%)
Score Development/Training
European: 100%
19,026 individuals (100%)
PGS Evaluation
Not Reported: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
344,264 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
19,026 individuals European MGI Cystatin C (LOINC: 33863-2); Quantitative

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM015731 PSS010000|
Ancestry Not Reported|
213 individuals
PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C β: -0.0229 (0.0513) : 4e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4

Evaluated Samples

PGS Sample Set ID
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
PSS010000 213 individuals Not reported MGI