Trait: calcium measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004838
Description
  • Is a quantification of calcium, typically in serum. Calcium (Ca2+) plays a pivotal role in the physiology and biochemistry of organisms and the cell. It plays an important role in signal transduction pathways, where it acts as a second messenger, in neurotransmitter release from neurons, contraction of all muscle cell types, and fertilization. Many enzymes require calcium ions as a cofactor, those of the blood-clotting cascade being notable examples. Extracellular calcium is also important for maintaining the potential difference across excitable cell membranes, as well as proper bone formation.
Trait category
Other measurement
Synonyms calcium levels
Mapped term(s) 2 mapped terms
  • NCIt:C64488
  • SNOMEDCT:71878006

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)
PGS000676
(snpnet.Calcium)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Calcium [mmol/L] calcium measurement 12,334
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http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000676/ScoringFiles/PGS000676.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
PPM001404 PGS000676
(snpnet.Calcium)
PSS000657|
African Ancestry|
5,576 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Calcium [mmol/L] : 0.07349
Spearman's ρ: 0.11
Age, sex, PCs(1-40)
PPM001439 PGS000676
(snpnet.Calcium)
PSS000658|
East Asian Ancestry|
987 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Calcium [mmol/L] : 0.10943
Spearman's ρ: 0.225
Age, sex, PCs(1-40)
PPM001474 PGS000676
(snpnet.Calcium)
PSS000659|
European Ancestry|
21,544 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Calcium [mmol/L] : 0.11196
Spearman's ρ: 0.25
Age, sex, PCs(1-40)
PPM001509 PGS000676
(snpnet.Calcium)
PSS000660|
South Asian Ancestry|
6,696 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Calcium [mmol/L] : 0.0961
Spearman's ρ: 0.226
Age, sex, PCs(1-40)
PPM001544 PGS000676
(snpnet.Calcium)
PSS000661|
European Ancestry|
58,264 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Calcium [mmol/L] : 0.11497
Spearman's ρ: 0.26
Age, sex, PCs(1-40)
PPM001590 PGS000676
(snpnet.Calcium)
PSS000796|
European Ancestry|
2,072 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Calcium [mmol/L] Spearman's ρ: 0.202 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
PSS000657 5,576 individuals African unspecified UKB
PSS000658 987 individuals East Asian UKB
PSS000659 21,544 individuals European Non-British White UKB
PSS000660 6,696 individuals South Asian UKB
PSS000661 58,264 individuals European
(British)
UKB
PSS000796 2,072 individuals European Participants self-identifying as white MESA