Polygenic Score (PGS) ID: PGS000680

Predicted Trait
Reported Trait Cystatin C [mg/L]
Mapped Trait(s) cystatin C measurement (EFO_0004617)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Cystatin_C
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 24,487
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 45.5%
African: 18.2%
East Asian: 18.2%
South Asian: 18.2%
11 Sample Sets

Development Samples

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
223,327 individuals European
(British)
UKB Training
31,929 individuals European
(British)
UKB Validation

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
PPM001408 PSS000677|
African Ancestry|
6,015 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.17697
Spearman's ρ: 0.196
Age, sex, PCs(1-40)
PPM001443 PSS000678|
East Asian Ancestry|
1,082 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.28853
Spearman's ρ: 0.274
Age, sex, PCs(1-40)
PPM001478 PSS000679|
European Ancestry|
23,580 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] Spearman's ρ: 0.391
: 0.30498
Age, sex, PCs(1-40)
PPM001513 PSS000680|
South Asian Ancestry|
7,338 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.26742
Spearman's ρ: 0.323
Age, sex, PCs(1-40)
PPM001548 PSS000681|
European Ancestry|
63,762 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.29509
Spearman's ρ: 0.405
Age, sex, PCs(1-40)
PPM001591 PSS000802|
European Ancestry|
2,116 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] Spearman's ρ: 0.255 Age, sex
PPM007325 PSS007141|
African Ancestry|
6,098 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Cystatin C : 0.11726 [0.10257, 0.13195]
Incremental R2 (full-covars): 0.00628
PGS R2 (no covariates): 0.01457 [0.00879, 0.02036]
age, sex, UKB array type, Genotype PCs
PPM007326 PSS007142|
East Asian Ancestry|
1,617 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Cystatin C : 0.22897 [0.194, 0.26393]
Incremental R2 (full-covars): 0.02178
PGS R2 (no covariates): 0.03277 [0.01618, 0.04936]
age, sex, UKB array type, Genotype PCs
PPM007327 PSS007143|
European Ancestry|
23,779 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Cystatin C : 0.20012 [0.19124, 0.20901]
Incremental R2 (full-covars): 0.07378
PGS R2 (no covariates): 0.07907 [0.07263, 0.0855]
age, sex, UKB array type, Genotype PCs
PPM007328 PSS007144|
South Asian Ancestry|
7,426 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Cystatin C : 0.16627 [0.15122, 0.18132]
Incremental R2 (full-covars): 0.03349
PGS R2 (no covariates): 0.03448 [0.02654, 0.04242]
age, sex, UKB array type, Genotype PCs
PPM007329 PSS007145|
European Ancestry|
64,468 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Cystatin C : 0.21975 [0.21423, 0.22528]
Incremental R2 (full-covars): 0.09316
PGS R2 (no covariates): 0.09133 [0.08718, 0.09548]
age, sex, UKB array type, Genotype PCs

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
PSS000679 23,580 individuals European Non-British White UKB
PSS000680 7,338 individuals South Asian UKB
PSS000681 63,762 individuals European
(British)
UKB
PSS007141 6,098 individuals African unspecified UKB
PSS007142 1,617 individuals East Asian UKB
PSS007143 23,779 individuals European non-white British ancestry UKB
PSS007144 7,426 individuals South Asian UKB
PSS007145 64,468 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS000802 2,116 individuals European Participants self-identifying as white MESA
PSS000677 6,015 individuals African unspecified UKB
PSS000678 1,082 individuals East Asian UKB