Trait: cystatin C measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004617
Description
  • is a quantification of serum cystatin C C (formerly gamma trace, post-gamma-globulin or neuroendocrine basic polypeptide),[1] a protein encoded by the CST3 gene, is mainly used as a biomarker of kidney function and kidney disease.
Trait category
Other measurement
Mapped term(s) NCIt:C92290

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000680 snpnet.Cystatin_C PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
 Cystatin C [mg/L] cystatin C measurement 24,487 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000680/ScoringFiles/PGS000680.txt.gz - Check Terms/Licenses

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 ID) 		Evaluated Score PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001408 PGS000680
(snpnet.Cystatin_C)
 PSS000677 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 PGS000680
(snpnet.Cystatin_C)
 PSS000678 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 PGS000680
(snpnet.Cystatin_C)
 PSS000679 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cystatin C [mg/L] — — R²: 0.30498
Spearman's ρ: 0.391		 Age, sex, PCs(1-40) —
PPM001513 PGS000680
(snpnet.Cystatin_C)
 PSS000680 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 PGS000680
(snpnet.Cystatin_C)
 PSS000681 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 PGS000680
(snpnet.Cystatin_C)
 PSS000802 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cystatin C [mg/L] — — Spearman's ρ: 0.255 Age, sex —

Evaluated Samples

PGS Sample Set ID
(PSS 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
PSS000679 — — 23,580 individuals — European Non-British White UKB —
PSS000680 — — 7,338 individuals — South Asian — UKB —
PSS000681 — — 63,762 individuals — European
(British)		 — UKB —
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 —