Trait: tooth disorder

Trait Information
Identifier MONDO_0006999
Description A disease involving the calcareous tooth.
Trait category
Other trait
Synonyms 7 synonyms
  • calcareous tooth disease
  • calcareous tooth disease or disorder
  • dental disorder
  • disease of calcareous tooth
  • disease or disorder of calcareous tooth
  • disorder of calcareous tooth
  • tooth disorder

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS019300
(TPMI_523_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Gingival and periodontal diseases tooth disorder 798,545
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019300/ScoringFiles/PGS019300.txt.gz
PGS019301
(TPMI_523_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Gingival and periodontal diseases tooth disorder 939,885
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019301/ScoringFiles/PGS019301.txt.gz
PGS019302
(TPMI_523_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Gingival and periodontal diseases tooth disorder 25,354
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019302/ScoringFiles/PGS019302.txt.gz
PGS019303
(TPMI_523_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Gingival and periodontal diseases tooth disorder 983,820
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019303/ScoringFiles/PGS019303.txt.gz
PGS019304
(TPMI_523_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Gingival and periodontal diseases tooth disorder 937,449
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019304/ScoringFiles/PGS019304.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
PPM037482 PGS019300
(TPMI_523_Lassosum2)
 PSS013213|
East Asian Ancestry|
18,461 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Gingival and periodontal diseases — AUROC: 0.657 R²: 0.08492 sex, age, array, PCs 1-10 —
PPM037483 PGS019301
(TPMI_523_LDpred2)
 PSS013212|
East Asian Ancestry|
18,461 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Gingival and periodontal diseases — AUROC: 0.6568 R²: 0.0849 sex, age, array, PCs 1-10 —
PPM037484 PGS019302
(TPMI_523_MegaPRS)
 PSS013214|
East Asian Ancestry|
18,461 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Gingival and periodontal diseases — AUROC: 0.656 R²: 0.08408 sex, age, array, PCs 1-10 —
PPM037485 PGS019303
(TPMI_523_PRS-CS)
 PSS013215|
East Asian Ancestry|
18,461 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Gingival and periodontal diseases — AUROC: 0.65669 R²: 0.08483 sex, age, array, PCs 1-10 —
PPM037486 PGS019304
(TPMI_523_SBayesR)
 PSS013216|
East Asian Ancestry|
18,461 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Gingival and periodontal diseases — AUROC: 0.65756 R²: 0.08524 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
PSS013213 522.4, 522.6, 523,K03.6, K04.4, K04.5, K05.0, K05.1, K05.2, K05.3, K05.4, K05.5, K05.6, K06.0, K06.1, K06.2, K06.8, K06.9 —
[
  • 1,839 cases
  • , 16,622 controls
]
,
46.14 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013214 522.4, 522.6, 523,K03.6, K04.4, K04.5, K05.0, K05.1, K05.2, K05.3, K05.4, K05.5, K05.6, K06.0, K06.1, K06.2, K06.8, K06.9 —
[
  • 1,839 cases
  • , 16,622 controls
]
,
46.14 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013215 522.4, 522.6, 523,K03.6, K04.4, K04.5, K05.0, K05.1, K05.2, K05.3, K05.4, K05.5, K05.6, K06.0, K06.1, K06.2, K06.8, K06.9 —
[
  • 1,839 cases
  • , 16,622 controls
]
,
46.14 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013216 522.4, 522.6, 523,K03.6, K04.4, K04.5, K05.0, K05.1, K05.2, K05.3, K05.4, K05.5, K05.6, K06.0, K06.1, K06.2, K06.8, K06.9 —
[
  • 1,839 cases
  • , 16,622 controls
]
,
46.14 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013212 522.4, 522.6, 523,K03.6, K04.4, K04.5, K05.0, K05.1, K05.2, K05.3, K05.4, K05.5, K05.6, K06.0, K06.1, K06.2, K06.8, K06.9 —
[
  • 1,839 cases
  • , 16,622 controls
]
,
46.14 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —