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] — — R²: 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] — — R²: 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
R²: 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] — — R²: 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] — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 —