Polygenic Score (PGS) ID: PGS005218

Predicted Trait
Reported Trait Hypothyroidism
Mapped Trait(s) hypothyroidism (EFO_0004705)
Released in PGS Catalog: Nov. 10, 2025
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Score Details

Score Construction
PGS Name prsweights_hypothyroidism_excl23
Development Method
Name PRS-CS
Parameters LD-reference from UKB internal to PRS-CS Default global shrinkage parameter Only autosomes
Variants
Original Genome Build GRCh37
Number of Variants 1,110,091
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000733
Citation (link to publication) Rand SA et al. Nat Genet (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,178,661 individuals (100%)
Score Development/Training
European: 100%
1,146,562 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 113,393 cases
  • , 1,065,268 controls
]
 European
(Danish, White British, Finish)		 23andMe, CHB, DBDS, FinnGen, UKB
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
[
  • 98,912 cases
  • , 1,047,650 controls
]
 European
(Danish, Icelandic, Finnish, Estonian)		 CHB, DBDS, EB, FinnGen, deCODE ICD10: E038, E039, E063 ICD9: 2448, 2449 ATC: H03A Cases excluded ICD10:DE05[0-9] Controls excluded ICD10: E0[1-2], E03[0-5], E0[4-7] — — — 23andMe data were included in PRS from the manuscript, but is omitted from the PGS upload due to company policies

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) 		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
PPM022615 PSS012042|
European Ancestry|
441,692 individuals
 PGP000733 |
Rand SA et al. Nat Genet (2025)
 Reported Trait: Incident hypothyroidism — AUROC: 0.698 [0.693, 0.703] — age, sex, PC1, PC2, PC3, PC4 Evaluated in UKB for only incident hypothyroidism
PPM022613 PSS012042|
European Ancestry|
441,692 individuals
 PGP000733 |
Rand SA et al. Nat Genet (2025)
 Reported Trait: Hypothyroidism OR: 2.01 [1.99, 2.03] — — age, sex, PC1, PC2, PC3, PC4 Evaluated in UKB for both incident and prevalent hypothyroidism
PPM022614 PSS012042|
European Ancestry|
441,692 individuals
 PGP000733 |
Rand SA et al. Nat Genet (2025)
 Reported Trait: Hypothyroidism OR: 2.0 [1.95, 2.17] — — age, sex, PC1, PC2, PC3, PC4 Evaluated in GESUS for both incident and prevalent hypothyroidism
PPM022617 PSS012042|
European Ancestry|
441,692 individuals
 PGP000733 |
Rand SA et al. Nat Genet (2025)
 Reported Trait: Incident hypothyroidism — AUROC: 0.859 [0.821, 0.897] — age, sex, TSH, T4, anti-TPO, PC1, PC2, PC3, PC4 Evaluated in GESUS which measured anti-TPO and thyroid hormones at baseline. Prevalent hypothyroidism was excluded
PPM022618 PSS012042|
European Ancestry|
441,692 individuals
 PGP000733 |
Rand SA et al. Nat Genet (2025)
 Reported Trait: Incident hypothyroidism among anti-TPO negative individuals (anti-TPO < 100 U/mL) — — Hazard ratio (HR, high vs middle percentile): 1.97 [1.06, 3.68] age, sex, PC1, PC2, PC3, PC4 Evaluated in GESUS which measured anti-TPO and thyroid hormones at baseline. Only individuals with anti-TPO < 100 u/mL were considered for this analysis. Prevalent hypothyroidism was excluded
PPM022616 PSS012042|
European Ancestry|
441,692 individuals
 PGP000733 |
Rand SA et al. Nat Genet (2025)
 Reported Trait: Progression from subclinical to overt hypothyroidism — — Hazard ratio (HR, high vs middle percentile): 1.43 [1.37, 1.61] age, sex, PC1, PC2, PC3, PC4 Evaluated in UKB primary care date, only in individuals that developed subclinical hypothyroidism after enrollment to UKB. Prevalent hypothyroidism was excluded

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
PSS012042 ICD10: E038, E039, E063 Self-reported hypothyroidism ATC: H03A or dnd codes for levothyroxine Cases excluded ICD10:DE05[0-9] —
[
  • 32,304 cases
  • , 399,000 controls
]
 — European
(White British)		 — UKB —
PSS012042 ICD10: E038, E039, E063 ATC: H03A Excluded individuals with ICD10: E05[0-9] —
[
  • 760 cases
  • , 9,628 controls
]
 — European
(Danish)		 — GESUS —