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
PGS002732
(GRS_77)
PGP000341 |
Vujkovic M et al. Nat Genet (2022)
Chronic elevation of alanine aminotransferase serum alanine aminotransferase measurement 77
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002732/ScoringFiles/PGS002732.txt.gz
PGS003342
(CVGRS_ALT)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Alanine aminotransferase level serum alanine aminotransferase measurement 51
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003342/ScoringFiles/PGS003342.txt.gz
PGS003351
(ALLGRS_ALT)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Alanine aminotransferase level serum alanine aminotransferase measurement 57
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003351/ScoringFiles/PGS003351.txt.gz
PGS003522
(cont-decay-log_ALT)
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Alanine aminotransferase serum alanine aminotransferase measurement 979,739
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003522/ScoringFiles/PGS003522.txt.gz
PGS004329
(X30620.score)
PGP000561 |
Jung H et al. Commun Biol (2024)
Alanine aminotransferase (U/L) serum alanine aminotransferase measurement 1,059,939
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004329/ScoringFiles/PGS004329.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
PPM014820 PGS002732
(GRS_77)
PSS009901|
Multi-ancestry (including European)|
45,007 individuals
PGP000341 |
Vujkovic M et al. Nat Genet (2022)
Reported Trait: Non-alcoholic fatty liver disease Risk difference: 0.604 [0.418, 0.79] age, gender, 3-5 ancestry PCs
PPM016181 PGS003342
(CVGRS_ALT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Alanine aminotransferase level β: 0.1213
PPM016198 PGS003342
(CVGRS_ALT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.04754
PPM016190 PGS003351
(ALLGRS_ALT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Alanine aminotransferase level β: 0.16161
PPM017450 PGS003522
(cont-decay-log_ALT)
PSS010885|
European Ancestry|
19,106 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.07 sex, age, deprivation index, PC1-16
PPM017534 PGS003522
(cont-decay-log_ALT)
PSS010801|
European Ancestry|
3,939 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.05 sex, age, deprivation index, PC1-16
PPM017702 PGS003522
(cont-decay-log_ALT)
PSS010549|
Greater Middle Eastern Ancestry|
1,094 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.04 sex, age, deprivation index, PC1-16
PPM017786 PGS003522
(cont-decay-log_ALT)
PSS010213|
European Ancestry|
2,238 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.07 sex, age, deprivation index, PC1-16
PPM017870 PGS003522
(cont-decay-log_ALT)
PSS010465|
South Asian Ancestry|
5,938 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.04 sex, age, deprivation index, PC1-16
PPM017954 PGS003522
(cont-decay-log_ALT)
PSS010381|
East Asian Ancestry|
1,705 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.03 sex, age, deprivation index, PC1-16
PPM018038 PGS003522
(cont-decay-log_ALT)
PSS010297|
African Ancestry|
2,333 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.01 sex, age, deprivation index, PC1-16
PPM018122 PGS003522
(cont-decay-log_ALT)
PSS010717|
African Ancestry|
3,627 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.01 sex, age, deprivation index, PC1-16
PPM017618 PGS003522
(cont-decay-log_ALT)
PSS010633|
European Ancestry|
6,169 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Alanine aminotransferase partial-R2: 0.05 sex, age, deprivation index, PC1-16
PPM020444 PGS004329
(X30620.score)
PSS011364|
European Ancestry|
56,192 individuals
PGP000561 |
Jung H et al. Commun Biol (2024)
Reported Trait: Alanine aminotransferase (U/L) PGS R2 (no covariates): 0.17221

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
PSS010055 22,608 individuals East Asian KBA, KoGES
PSS010801 3,939 individuals,
38.0 % Male samples
Mean = 54.4 years
Sd = 7.5 years
European Polish UKB
PSS010549 1,094 individuals,
60.0 % Male samples
Mean = 51.9 years
Sd = 7.9 years
Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB
PSS010297 2,333 individuals,
37.0 % Male samples
Mean = 52.5 years
Sd = 8.1 years
African American or Afro-Caribbean Caribbean UKB
PSS009201 3,950 individuals European Poland (NE Europe) UKB
PSS008307 5,992 individuals South Asian India (South Asia) UKB
PSS010717 3,627 individuals,
46.0 % Male samples
Mean = 51.9 years
Sd = 8.1 years
African unspecified Nigerian UKB
PSS010465 5,938 individuals,
54.0 % Male samples
Mean = 53.3 years
Sd = 8.4 years
South Asian Indian 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
PSS010213 2,238 individuals,
45.0 % Male samples
Mean = 58.1 years
Sd = 7.1 years
European Ashkenazi UKB
PSS008084 1,716 individuals East Asian China (East Asia) UKB
PSS011364 56,192 individuals European UKB
PSS009901
[
  • 2,829 cases
  • , 41,391 controls
]
European U.S. BioVU, CAP, EPOS PIVENS, FLINT, NASH
PSS009901
[
  • 444 cases
  • , 343 controls
]
Hispanic or Latin American U.S. NR LQTS, NASH
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
PSS010885 19,106 individuals,
46.0 % Male samples
Mean = 56.9 years
Sd = 7.9 years
European white British UKB
PSS010381 1,705 individuals,
33.0 % Male samples
Mean = 52.4 years
Sd = 7.8 years
East Asian Chinese UKB
PSS010633 6,169 individuals,
45.0 % Male samples
Mean = 54.5 years
Sd = 8.4 years
European Italian UKB
PSS007871 2,345 individuals African American or Afro-Caribbean Carribean UKB