Trait: primary hyperthyroidism

Trait Information
Identifier MONDO_1060200
Description A form of hyperthyroidism caused by overproduction of thyroid hormones (T3 and T4) due to pathology within the thyroid gland itself. Primary hyperthyroidism is characterized by low TSH levels and elevated T3/T4 levels. [PMID: 30725738]
Trait category
Other trait
Child trait(s) 2 child traits

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
Note: This table shows PGS for child terms of "primary hyperthyroidism" in the EFO hierarchy.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS005264
(graves_disease_mixed_pt)
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Graves' disease Graves disease 112
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005264/ScoringFiles/PGS005264.txt.gz
PGS005265
(graves_disease_mixed_prscs)
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Graves' disease Graves disease 1,085,173
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005265/ScoringFiles/PGS005265.txt.gz
PGS005266
(graves_disease_eur_prscs)
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Graves' disease Graves disease 1,085,170
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005266/ScoringFiles/PGS005266.txt.gz
PGS018650
(TPMI_241_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Nontoxic nodular goiter toxic multinodular goitre 2,717
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018650/ScoringFiles/PGS018650.txt.gz
PGS018651
(TPMI_241_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Nontoxic nodular goiter toxic multinodular goitre 939,876
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018651/ScoringFiles/PGS018651.txt.gz
PGS018652
(TPMI_241_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Nontoxic nodular goiter toxic multinodular goitre 457,716
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018652/ScoringFiles/PGS018652.txt.gz
PGS018653
(TPMI_241_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Nontoxic nodular goiter toxic multinodular goitre 983,821
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018653/ScoringFiles/PGS018653.txt.gz
PGS018654
(TPMI_241_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Nontoxic nodular goiter toxic multinodular goitre 94,850
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018654/ScoringFiles/PGS018654.txt.gz
PGS018671
(TPMI_242.1_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Graves disease Graves disease 415
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018671/ScoringFiles/PGS018671.txt.gz
PGS018672
(TPMI_242.1_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Graves disease Graves disease 220,843
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018672/ScoringFiles/PGS018672.txt.gz
PGS018673
(TPMI_242.1_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Graves disease Graves disease 37,771
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018673/ScoringFiles/PGS018673.txt.gz
PGS018674
(TPMI_242.1_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Graves disease Graves disease 983,772
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018674/ScoringFiles/PGS018674.txt.gz
PGS018675
(TPMI_242.1_PRSmix+)
 PGP000835 |
Chen HH et al. Nature (2025)
 Graves disease Graves disease 1,071,402
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018675/ScoringFiles/PGS018675.txt.gz
PGS018676
(TPMI_242.1_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Graves disease Graves disease 975,251
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018676/ScoringFiles/PGS018676.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
PPM022747 PGS005264
(graves_disease_mixed_pt)
 PSS012069|
Multi-ancestry (including European)|
94,651 individuals
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Reported Trait: graves' disease OR: 1.008
β: 0.008		 AUROC: 0.6587 — — —
PPM022748 PGS005265
(graves_disease_mixed_prscs)
 PSS012069|
Multi-ancestry (including European)|
94,651 individuals
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Reported Trait: graves' disease OR: 1.62508
β: 0.48556		 AUROC: 0.66522 — — —
PPM022749 PGS005266
(graves_disease_eur_prscs)
 PSS012069|
Multi-ancestry (including European)|
94,651 individuals
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Reported Trait: graves' disease OR: 1.54333
β: 0.43394		 AUROC: 0.66373 — — —
PPM036832 PGS018650
(TPMI_241_Lassosum2)
 PSS012563|
East Asian Ancestry|
18,285 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Nontoxic nodular goiter — AUROC: 0.73122 R²: 0.12994 sex, age, array, PCs 1-10 —
PPM036833 PGS018651
(TPMI_241_LDpred2)
 PSS012562|
East Asian Ancestry|
18,285 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Nontoxic nodular goiter — AUROC: 0.73416 R²: 0.13359 sex, age, array, PCs 1-10 —
PPM036834 PGS018652
(TPMI_241_MegaPRS)
 PSS012564|
East Asian Ancestry|
18,285 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Nontoxic nodular goiter — AUROC: 0.72435 R²: 0.11874 sex, age, array, PCs 1-10 —
PPM036835 PGS018653
(TPMI_241_PRS-CS)
 PSS012565|
East Asian Ancestry|
18,285 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Nontoxic nodular goiter — AUROC: 0.73337 R²: 0.13292 sex, age, array, PCs 1-10 —
PPM036836 PGS018654
(TPMI_241_SBayesR)
 PSS012566|
East Asian Ancestry|
18,285 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Nontoxic nodular goiter — AUROC: 0.73414 R²: 0.13319 sex, age, array, PCs 1-10 —
PPM036853 PGS018671
(TPMI_242.1_Lassosum2)
 PSS012568|
East Asian Ancestry|
17,305 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Graves disease — AUROC: 0.74792 R²: 0.03286 sex, age, array, PCs 1-10 —
PPM036854 PGS018672
(TPMI_242.1_LDpred2)
 PSS012567|
East Asian Ancestry|
17,305 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Graves disease — AUROC: 0.75387 R²: 0.03447 sex, age, array, PCs 1-10 —
PPM036855 PGS018673
(TPMI_242.1_MegaPRS)
 PSS012569|
East Asian Ancestry|
17,305 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Graves disease — AUROC: 0.75062 R²: 0.03216 sex, age, array, PCs 1-10 —
PPM036856 PGS018674
(TPMI_242.1_PRS-CS)
 PSS012570|
East Asian Ancestry|
17,305 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Graves disease — AUROC: 0.74562 R²: 0.03194 sex, age, array, PCs 1-10 —
PPM036857 PGS018675
(TPMI_242.1_PRSmix+)
 PSS012571|
East Asian Ancestry|
17,305 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Graves disease — AUROC: 0.75988 R²: 0.03585 sex, age, array, PCs 1-10 —
PPM036858 PGS018676
(TPMI_242.1_SBayesR)
 PSS012572|
East Asian Ancestry|
17,305 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Graves disease — AUROC: 0.74098 R²: 0.03008 sex, age, array, PCs 1-10 —

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
PSS012069 Cases - ICD-9-CM codes: 193, V10.87, ICD-10-CM billing codes: C73, Z85.850, ICD-9 codes: 193, V10.87, ICD-10 codes: C73, SNOMED: 92767001 Carcinoma in situ of thyroid gland, 363478007 Malignant tumor of thyroid gland, 255028004 Follicular thyroid carcinoma, 423158009 Hurthle cell carcinoma of thyroid, 772992009 Primary differentiated carcinoma of thyroid gland. Controls - ICD-9-CM codes: 241 Nontoxic nodular goiter, 241.0 Nontoxic uninodular goiter, 241.1 Nontoxic multinodular goiter, 241.9 Unspecified nontoxic nodular goiter ICD-10-CM billing codes: E01.1 Iodine-deficiency related multinodular (endemic) goiter, E04.1 Nontoxic single thyroid nodule, E04.2 Nontoxic multinodular goiter, E04.8 Other specified nontoxic goiter, E04.9 Nontoxic goiter, unspecified, ICD-9-CM codes: 241 Nontoxic nodular goiter, 241.0 Nontoxic uninodular goiter, 241.1 Nontoxic multinodular goiter, 241.9 Unspecified nontoxic nodular goiter, ICD-10 codes: E01.1 Iodine-deficiency related multinodular (endemic) goiter, E04.1 Nontoxic single thyroid nodule, E04.2 Nontoxic multinodular goiter, E04.8 Other specified nontoxic goiter, E04.9 Nontoxic goiter, unspecified, SNOMED: 419153005 Nodular goiter, 190236006 Non-toxic nodular goiter, 66392007 Substernal goiter, 60968001 Adenomatous goiter — 94,651 individuals — African American or Afro-Caribbean, Hispanic or Latin American, European — CCPM —
PSS012562 241,E01.1, E04.1, E04.2, E04.8, E04.9 —
[
  • 1,205 cases
  • , 17,080 controls
]
,
47.92 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012563 241,E01.1, E04.1, E04.2, E04.8, E04.9 —
[
  • 1,205 cases
  • , 17,080 controls
]
,
47.92 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012564 241,E01.1, E04.1, E04.2, E04.8, E04.9 —
[
  • 1,205 cases
  • , 17,080 controls
]
,
47.92 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012565 241,E01.1, E04.1, E04.2, E04.8, E04.9 —
[
  • 1,205 cases
  • , 17,080 controls
]
,
47.92 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012566 241,E01.1, E04.1, E04.2, E04.8, E04.9 —
[
  • 1,205 cases
  • , 17,080 controls
]
,
47.92 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012567 242.0,E05.0 —
[
  • 225 cases
  • , 17,080 controls
]
,
49.58 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012568 242.0,E05.0 —
[
  • 225 cases
  • , 17,080 controls
]
,
49.58 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012569 242.0,E05.0 —
[
  • 225 cases
  • , 17,080 controls
]
,
49.58 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012570 242.0,E05.0 —
[
  • 225 cases
  • , 17,080 controls
]
,
49.58 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012571 242.0,E05.0 —
[
  • 225 cases
  • , 17,080 controls
]
,
49.58 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012572 242.0,E05.0 —
[
  • 225 cases
  • , 17,080 controls
]
,
49.58 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —