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 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 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
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000680/ScoringFiles/PGS000680.txt.gz - Check Terms/Licenses
PGS001947
(portability-PLR_log_cystatinC)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Cystatin C cystatin C measurement 84,459
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001947/ScoringFiles/PGS001947.txt.gz
PGS002165
(portability-ldpred2_log_cystatinC)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Cystatin C cystatin C measurement 781,302
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002165/ScoringFiles/PGS002165.txt.gz

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] Spearman's ρ: 0.391
: 0.30498
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
PPM007325 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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 PGS000680
(snpnet.Cystatin_C)
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
PPM010455 PGS001947
(portability-PLR_log_cystatinC)
PSS008321|
South Asian Ancestry|
6,001 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.3057 [0.2826, 0.3285] sex, age, birth date, deprivation index, 16 PCs
PPM010451 PGS001947
(portability-PLR_log_cystatinC)
PSS009441|
European Ancestry|
18,996 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.418 [0.4062, 0.4297] sex, age, birth date, deprivation index, 16 PCs
PPM010452 PGS001947
(portability-PLR_log_cystatinC)
PSS009215|
European Ancestry|
3,953 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.4317 [0.4059, 0.4568] sex, age, birth date, deprivation index, 16 PCs
PPM010454 PGS001947
(portability-PLR_log_cystatinC)
PSS008543|
Greater Middle Eastern Ancestry|
1,126 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.3385 [0.2852, 0.3897] sex, age, birth date, deprivation index, 16 PCs
PPM010457 PGS001947
(portability-PLR_log_cystatinC)
PSS007885|
African Ancestry|
2,342 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.1917 [0.1522, 0.2306] sex, age, birth date, deprivation index, 16 PCs
PPM010458 PGS001947
(portability-PLR_log_cystatinC)
PSS008989|
African Ancestry|
3,658 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.1856 [0.1541, 0.2168] sex, age, birth date, deprivation index, 16 PCs
PPM010453 PGS001947
(portability-PLR_log_cystatinC)
PSS008769|
European Ancestry|
6,319 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.3864 [0.3652, 0.4072] sex, age, birth date, deprivation index, 16 PCs
PPM010456 PGS001947
(portability-PLR_log_cystatinC)
PSS008098|
East Asian Ancestry|
1,718 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.2689 [0.2242, 0.3125] sex, age, birth date, deprivation index, 16 PCs
PPM012167 PGS002165
(portability-ldpred2_log_cystatinC)
PSS009441|
European Ancestry|
18,996 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.4072 [0.3953, 0.419] sex, age, birth date, deprivation index, 16 PCs
PPM012168 PGS002165
(portability-ldpred2_log_cystatinC)
PSS009215|
European Ancestry|
3,953 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.4276 [0.4017, 0.4528] sex, age, birth date, deprivation index, 16 PCs
PPM012169 PGS002165
(portability-ldpred2_log_cystatinC)
PSS008769|
European Ancestry|
6,319 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.371 [0.3495, 0.3921] sex, age, birth date, deprivation index, 16 PCs
PPM012170 PGS002165
(portability-ldpred2_log_cystatinC)
PSS008543|
Greater Middle Eastern Ancestry|
1,126 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.3446 [0.2916, 0.3956] sex, age, birth date, deprivation index, 16 PCs
PPM012171 PGS002165
(portability-ldpred2_log_cystatinC)
PSS008321|
South Asian Ancestry|
6,001 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.3009 [0.2777, 0.3238] sex, age, birth date, deprivation index, 16 PCs
PPM012173 PGS002165
(portability-ldpred2_log_cystatinC)
PSS007885|
African Ancestry|
2,342 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.181 [0.1414, 0.2201] sex, age, birth date, deprivation index, 16 PCs
PPM012174 PGS002165
(portability-ldpred2_log_cystatinC)
PSS008989|
African Ancestry|
3,658 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.1653 [0.1335, 0.1967] sex, age, birth date, deprivation index, 16 PCs
PPM012172 PGS002165
(portability-ldpred2_log_cystatinC)
PSS008098|
East Asian Ancestry|
1,718 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.2565 [0.2115, 0.3004] sex, age, birth date, deprivation index, 16 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
PSS007885 2,342 individuals African American or Afro-Caribbean Carribean UKB
PSS008543 1,126 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009441 18,996 individuals European UK (+ Ireland) 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)
PSS009215 3,953 individuals European Poland (NE Europe) UKB
PSS008321 6,001 individuals South Asian India (South Asia) UKB
PSS008989 3,658 individuals African unspecified Nigeria (West Africa) UKB
PSS008098 1,718 individuals East Asian China (East Asia) UKB
PSS000802 2,116 individuals European Participants self-identifying as white MESA
PSS008769 6,319 individuals European Italy (South Europe) UKB
PSS000677 6,015 individuals African unspecified UKB
PSS000678 1,082 individuals East Asian UKB