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
Synonym calcium levels
Mapped terms 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 Scoring File (FTP Link)
PGS000676
(snpnet.Calcium)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Calcium [mmol/L] calcium measurement 12,334
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000676/ScoringFiles/PGS000676.txt.gz - Check Terms/Licenses
PGS001893
(portability-PLR_calcium)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Calcium calcium measurement 48,395
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001893/ScoringFiles/PGS001893.txt.gz
PGS002106
(portability-ldpred2_calcium)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Calcium calcium measurement 702,009
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002106/ScoringFiles/PGS002106.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
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
PPM007305 PGS000676
(snpnet.Calcium)
PSS007121|
African Ancestry|
5,658 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Calcium : 0.03291 [0.02438, 0.04144]
Incremental R2 (full-covars): 0.01221
PGS R2 (no covariates): 0.01435 [0.00861, 0.02009]
age, sex, UKB array type, Genotype PCs
PPM007306 PGS000676
(snpnet.Calcium)
PSS007122|
East Asian Ancestry|
1,475 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Calcium : 0.05488 [0.0339, 0.07586]
Incremental R2 (full-covars): 0.02744
PGS R2 (no covariates): 0.03682 [0.01931, 0.05434]
age, sex, UKB array type, Genotype PCs
PPM007307 PGS000676
(snpnet.Calcium)
PSS007123|
European Ancestry|
21,751 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Calcium : 0.0574 [0.05179, 0.06301]
Incremental R2 (full-covars): 0.04912
PGS R2 (no covariates): 0.05876 [0.05309, 0.06442]
age, sex, UKB array type, Genotype PCs
PPM007308 PGS000676
(snpnet.Calcium)
PSS007124|
South Asian Ancestry|
6,790 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Calcium : 0.04643 [0.03734, 0.05553]
Incremental R2 (full-covars): 0.03689
PGS R2 (no covariates): 0.04361 [0.03477, 0.05246]
age, sex, UKB array type, Genotype PCs
PPM007309 PGS000676
(snpnet.Calcium)
PSS007125|
European Ancestry|
59,074 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Calcium : 0.06293 [0.05938, 0.06648]
Incremental R2 (full-covars): 0.05233
PGS R2 (no covariates): 0.06188 [0.05836, 0.06541]
age, sex, UKB array type, Genotype PCs
PPM010031 PGS001893
(portability-PLR_calcium)
PSS008491|
Greater Middle Eastern Ancestry|
1,035 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2261 [0.1669, 0.2837] sex, age, birth date, deprivation index, 16 PCs
PPM010028 PGS001893
(portability-PLR_calcium)
PSS009389|
European Ancestry|
17,443 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2668 [0.2529, 0.2805] sex, age, birth date, deprivation index, 16 PCs
PPM010029 PGS001893
(portability-PLR_calcium)
PSS009163|
European Ancestry|
3,592 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2822 [0.2517, 0.3121] sex, age, birth date, deprivation index, 16 PCs
PPM010030 PGS001893
(portability-PLR_calcium)
PSS008717|
European Ancestry|
5,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.252 [0.2277, 0.276] sex, age, birth date, deprivation index, 16 PCs
PPM010032 PGS001893
(portability-PLR_calcium)
PSS008269|
South Asian Ancestry|
5,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.241 [0.2159, 0.2658] sex, age, birth date, deprivation index, 16 PCs
PPM010033 PGS001893
(portability-PLR_calcium)
PSS008047|
East Asian Ancestry|
1,563 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2155 [0.1674, 0.2626] sex, age, birth date, deprivation index, 16 PCs
PPM010034 PGS001893
(portability-PLR_calcium)
PSS007833|
African Ancestry|
2,161 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.1173 [0.0753, 0.1589] sex, age, birth date, deprivation index, 16 PCs
PPM010035 PGS001893
(portability-PLR_calcium)
PSS008937|
African Ancestry|
3,403 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.1184 [0.085, 0.1515] sex, age, birth date, deprivation index, 16 PCs
PPM011708 PGS002106
(portability-ldpred2_calcium)
PSS008269|
South Asian Ancestry|
5,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2226 [0.1973, 0.2477] sex, age, birth date, deprivation index, 16 PCs
PPM011709 PGS002106
(portability-ldpred2_calcium)
PSS008047|
East Asian Ancestry|
1,563 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2046 [0.1562, 0.2519] sex, age, birth date, deprivation index, 16 PCs
PPM011710 PGS002106
(portability-ldpred2_calcium)
PSS007833|
African Ancestry|
2,161 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.1002 [0.0581, 0.1419] sex, age, birth date, deprivation index, 16 PCs
PPM011711 PGS002106
(portability-ldpred2_calcium)
PSS008937|
African Ancestry|
3,403 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.1167 [0.0833, 0.1498] sex, age, birth date, deprivation index, 16 PCs
PPM011707 PGS002106
(portability-ldpred2_calcium)
PSS008491|
Greater Middle Eastern Ancestry|
1,035 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2067 [0.1471, 0.2649] sex, age, birth date, deprivation index, 16 PCs
PPM011704 PGS002106
(portability-ldpred2_calcium)
PSS009389|
European Ancestry|
17,443 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2672 [0.2533, 0.2809] sex, age, birth date, deprivation index, 16 PCs
PPM011705 PGS002106
(portability-ldpred2_calcium)
PSS009163|
European Ancestry|
3,592 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2911 [0.2608, 0.3208] sex, age, birth date, deprivation index, 16 PCs
PPM011706 PGS002106
(portability-ldpred2_calcium)
PSS008717|
European Ancestry|
5,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Calcium Partial Correlation (partial-r): 0.2562 [0.2319, 0.2801] 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
PSS009163 3,592 individuals European Poland (NE Europe) UKB
PSS008269 5,484 individuals South Asian India (South Asia) UKB
PSS007121 5,658 individuals African unspecified UKB
PSS007122 1,475 individuals East Asian UKB
PSS007123 21,751 individuals European non-white British ancestry UKB
PSS007124 6,790 individuals South Asian UKB
PSS007125 59,074 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS008937 3,403 individuals African unspecified Nigeria (West Africa) UKB
PSS008047 1,563 individuals East Asian China (East Asia) UKB
PSS008717 5,801 individuals European Italy (South Europe) UKB
PSS007833 2,161 individuals African American or Afro-Caribbean Carribean UKB
PSS008491 1,035 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009389 17,443 individuals European UK (+ Ireland) UKB
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