Trait: serum alanine aminotransferase measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004735
Description Is a quantification of serum alanine aminotransferase, most commonly found in liver, the test is used in ascertainment of liver function.
Trait category
Liver enzyme measurement
Synonyms 2 synonyms
  • alanine aminotransferase measurement
  • alanine transaminase measurement
Mapped terms 2 mapped terms
  • NCIt:C61017
  • SNOMEDCT:34608000

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)
PGS000668
(snpnet.Alanine_aminotransferase)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Alanine aminotransferase [U/L] serum alanine aminotransferase measurement 12,076
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000668/ScoringFiles/PGS000668.txt.gz - Check Terms/Licenses
PGS000816
(GRS150_ALT)
PGP000201 |
Pazoki R et al. Nat Commun (2021)
Alanine transaminase serum alanine aminotransferase measurement 150
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000816/ScoringFiles/PGS000816.txt.gz
PGS001940
(portability-PLR_log_ALT)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Alanine aminotransferase serum alanine aminotransferase measurement 51,849
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001940/ScoringFiles/PGS001940.txt.gz
PGS002158
(portability-ldpred2_log_ALT)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Alanine aminotransferase serum alanine aminotransferase measurement 774,274
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002158/ScoringFiles/PGS002158.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
PPM001466 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000624|
European Ancestry|
23,569 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.2041
Spearman's ρ: 0.22
Age, sex, PCs(1-40)
PPM001501 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000625|
South Asian Ancestry|
7,325 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.18304
Spearman's ρ: 0.198
Age, sex, PCs(1-40)
PPM001536 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000626|
European Ancestry|
63,766 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.19165
Spearman's ρ: 0.244
Age, sex, PCs(1-40)
PPM001396 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000622|
African Ancestry|
6,017 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.17646
Spearman's ρ: 0.092
Age, sex, PCs(1-40)
PPM001431 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000623|
East Asian Ancestry|
1,081 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.1561
Spearman's ρ: 0.145
Age, sex, PCs(1-40)
PPM007267 PGS000668
(snpnet.Alanine_aminotransferase)
PSS007078|
European Ancestry|
23,758 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alanine aminotransferase : 0.07978 [0.07332, 0.08623]
Incremental R2 (full-covars): 0.00218
PGS R2 (no covariates): 0.03 [0.02583, 0.03418]
age, sex, UKB array type, Genotype PCs
PPM007265 PGS000668
(snpnet.Alanine_aminotransferase)
PSS007076|
African Ancestry|
6,099 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alanine aminotransferase : 0.0977 [0.084, 0.11141]
Incremental R2 (full-covars): 0.00077
PGS R2 (no covariates): 0.00447 [0.00124, 0.00771]
age, sex, UKB array type, Genotype PCs
PPM007266 PGS000668
(snpnet.Alanine_aminotransferase)
PSS007077|
East Asian Ancestry|
1,615 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alanine aminotransferase : 0.08994 [0.06408, 0.11581]
Incremental R2 (full-covars): 0.00177
PGS R2 (no covariates): 0.02382 [0.00954, 0.03809]
age, sex, UKB array type, Genotype PCs
PPM007268 PGS000668
(snpnet.Alanine_aminotransferase)
PSS007079|
South Asian Ancestry|
7,414 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alanine aminotransferase : 0.08504 [0.07323, 0.09685]
Incremental R2 (full-covars): 0.00213
PGS R2 (no covariates): 0.02862 [0.02135, 0.0359]
age, sex, UKB array type, Genotype PCs
PPM007269 PGS000668
(snpnet.Alanine_aminotransferase)
PSS007080|
European Ancestry|
64,440 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Alanine aminotransferase : 0.06901 [0.06532, 0.0727]
Incremental R2 (full-covars): 0.00284
PGS R2 (no covariates): 0.03994 [0.03705, 0.04284]
age, sex, UKB array type, Genotype PCs
PPM002176 PGS000816
(GRS150_ALT)
PSS001062|
European Ancestry|
3,620 individuals
PGP000201 |
Pazoki R et al. Nat Commun (2021)
Reported Trait: Serum alanine transaminase level OR: 1.72 [1.36, 2.07]
PPM002173 PGS000816
(GRS150_ALT)
PSS001060|
European Ancestry|
331 individuals
PGP000201 |
Pazoki R et al. Nat Commun (2021)
Reported Trait: Serum alanine transaminase level β: 3.09 [2.02, 4.17] Unit of measurement = U/L in alanine transaminase
PPM010396 PGS001940
(portability-PLR_log_ALT)
PSS009201|
European Ancestry|
3,950 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2328 [0.203, 0.2622] sex, age, birth date, deprivation index, 16 PCs
PPM010397 PGS001940
(portability-PLR_log_ALT)
PSS008755|
European Ancestry|
6,321 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2248 [0.2012, 0.2481] sex, age, birth date, deprivation index, 16 PCs
PPM010399 PGS001940
(portability-PLR_log_ALT)
PSS008307|
South Asian Ancestry|
5,992 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2205 [0.1963, 0.2445] sex, age, birth date, deprivation index, 16 PCs
PPM010400 PGS001940
(portability-PLR_log_ALT)
PSS008084|
East Asian Ancestry|
1,716 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1841 [0.1377, 0.2297] sex, age, birth date, deprivation index, 16 PCs
PPM010401 PGS001940
(portability-PLR_log_ALT)
PSS007871|
African Ancestry|
2,345 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1008 [0.0604, 0.1409] sex, age, birth date, deprivation index, 16 PCs
PPM010402 PGS001940
(portability-PLR_log_ALT)
PSS008975|
African Ancestry|
3,656 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1054 [0.0731, 0.1374] sex, age, birth date, deprivation index, 16 PCs
PPM010395 PGS001940
(portability-PLR_log_ALT)
PSS009427|
European Ancestry|
18,995 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2633 [0.25, 0.2765] sex, age, birth date, deprivation index, 16 PCs
PPM010398 PGS001940
(portability-PLR_log_ALT)
PSS008529|
Greater Middle Eastern Ancestry|
1,123 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1871 [0.1295, 0.2435] sex, age, birth date, deprivation index, 16 PCs
PPM012112 PGS002158
(portability-ldpred2_log_ALT)
PSS009201|
European Ancestry|
3,950 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2355 [0.2058, 0.2648] sex, age, birth date, deprivation index, 16 PCs
PPM012111 PGS002158
(portability-ldpred2_log_ALT)
PSS009427|
European Ancestry|
18,995 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2622 [0.2489, 0.2754] sex, age, birth date, deprivation index, 16 PCs
PPM012113 PGS002158
(portability-ldpred2_log_ALT)
PSS008755|
European Ancestry|
6,321 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2258 [0.2022, 0.2491] sex, age, birth date, deprivation index, 16 PCs
PPM012114 PGS002158
(portability-ldpred2_log_ALT)
PSS008529|
Greater Middle Eastern Ancestry|
1,123 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1997 [0.1423, 0.2557] sex, age, birth date, deprivation index, 16 PCs
PPM012115 PGS002158
(portability-ldpred2_log_ALT)
PSS008307|
South Asian Ancestry|
5,992 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.2086 [0.1842, 0.2328] sex, age, birth date, deprivation index, 16 PCs
PPM012116 PGS002158
(portability-ldpred2_log_ALT)
PSS008084|
East Asian Ancestry|
1,716 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.194 [0.1478, 0.2394] sex, age, birth date, deprivation index, 16 PCs
PPM012117 PGS002158
(portability-ldpred2_log_ALT)
PSS007871|
African Ancestry|
2,345 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.1063 [0.0659, 0.1463] sex, age, birth date, deprivation index, 16 PCs
PPM012118 PGS002158
(portability-ldpred2_log_ALT)
PSS008975|
African Ancestry|
3,656 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Alanine aminotransferase Partial Correlation (partial-r): 0.088 [0.0557, 0.1202] 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
PSS008529 1,123 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009427 18,995 individuals European UK (+ Ireland) UKB
PSS009201 3,950 individuals European Poland (NE Europe) UKB
PSS008307 5,992 individuals South Asian India (South Asia) UKB
PSS000622 6,017 individuals African unspecified UKB
PSS000623 1,081 individuals East Asian UKB
PSS000624 23,569 individuals European Non-British White UKB
PSS000625 7,325 individuals South Asian UKB
PSS000626 63,766 individuals European
(British)
UKB
PSS008975 3,656 individuals African unspecified Nigeria (West Africa) UKB
PSS008084 1,716 individuals East Asian China (East Asia) UKB
PSS007076 6,099 individuals African unspecified UKB
PSS007077 1,615 individuals East Asian UKB
PSS007078 23,758 individuals European non-white British ancestry UKB
PSS007079 7,414 individuals South Asian UKB
PSS007080 64,440 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS001062 Serum concentrations of alanine transaminase (ALT), alkaline phosphatase (ALP), and gamma-glutamyl transferase (GGT) were measured from stored blood samples using the enzymatic rate analytical method on a Beckman Coulter AU5800. The manufacturer’s analytic range for ALT was 3–500 U/L, for ALP, 5–1500 U/L, and it was 5–1200 U/L for GGT. 3,620 individuals European NFBC
PSS001060 Serum concentrations of alanine transaminase (ALT) and alkaline phosphatase (ALP), were measured from stored blood samples using the enzymatic rate analytical method on a Beckman Coulter AU5800. The manufacturer’s analytic range for ALT was 3–500 U/L, for ALP, 5–1500 U/L, and it was 5–1200 U/L for GGT. 331 individuals European Airwave
PSS008755 6,321 individuals European Italy (South Europe) UKB
PSS007871 2,345 individuals African American or Afro-Caribbean Carribean UKB