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)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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
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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)
Evaluated Score 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 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
PSS000679|
European Ancestry|
23,580 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.30498
Spearman's ρ: 0.391
Age, sex, PCs(1-40)
PPM001513 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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

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
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