Trait: ureterolithiasis

Trait Information
Identifier MONDO_0007009
Description The presence of a calculus in the ureter of the kidney; this is most often composed of mineral salts and proteins. [NCIT: P378]
Trait category
Other trait
Synonyms 2 synonyms
  • calculus of ureter
  • ureteric stone

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)
PGS001250
(GBE_HC1304)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Calculus of kidney and ureter (time-to-event) ureterolithiasis,
nephrolithiasis		 341
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001250/ScoringFiles/PGS001250.txt.gz
PGS019485
(TPMI_594.3_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Calculus of ureter ureterolithiasis 127,322
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019485/ScoringFiles/PGS019485.txt.gz
PGS019486
(TPMI_594.3_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Calculus of ureter ureterolithiasis 939,826
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019486/ScoringFiles/PGS019486.txt.gz
PGS019487
(TPMI_594.3_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Calculus of ureter ureterolithiasis 46,910
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019487/ScoringFiles/PGS019487.txt.gz
PGS019488
(TPMI_594.3_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Calculus of ureter ureterolithiasis 983,779
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019488/ScoringFiles/PGS019488.txt.gz
PGS019489
(TPMI_594.3_PRSmix+)
 PGP000835 |
Chen HH et al. Nature (2025)
 Calculus of ureter ureterolithiasis 1,070,068
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019489/ScoringFiles/PGS019489.txt.gz
PGS019490
(TPMI_594.3_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Calculus of ureter ureterolithiasis 993,975
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019490/ScoringFiles/PGS019490.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
PPM008759 PGS001250
(GBE_HC1304)
 PSS004253|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.63458 [0.56104, 0.70812] R²: 0.02267
Incremental AUROC (full-covars): -4e-05
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50619 [0.43811, 0.57426]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008760 PGS001250
(GBE_HC1304)
 PSS004254|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66992 [0.57144, 0.7684] R²: 0.05343
Incremental AUROC (full-covars): 0.02085
PGS R2 (no covariates): 0.01881
PGS AUROC (no covariates): 0.61787 [0.49482, 0.74092]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008761 PGS001250
(GBE_HC1304)
 PSS004255|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.6584 [0.63099, 0.68582] R²: 0.03459
Incremental AUROC (full-covars): 0.00159
PGS R2 (no covariates): 0.00193
PGS AUROC (no covariates): 0.53735 [0.50853, 0.56617]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008762 PGS001250
(GBE_HC1304)
 PSS004256|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66463 [0.62056, 0.7087] R²: 0.03629
Incremental AUROC (full-covars): 0.01093
PGS R2 (no covariates): 0.0077
PGS AUROC (no covariates): 0.57305 [0.52667, 0.61943]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008763 PGS001250
(GBE_HC1304)
 PSS004257|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66491 [0.64839, 0.68143] R²: 0.03503
Incremental AUROC (full-covars): 0.01494
PGS R2 (no covariates): 0.00592
PGS AUROC (no covariates): 0.56681 [0.54876, 0.58486]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM037667 PGS019485
(TPMI_594.3_Lassosum2)
 PSS013382|
East Asian Ancestry|
18,587 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Calculus of ureter — AUROC: 0.67883 R²: 0.04979 sex, age, array, PCs 1-10 —
PPM037668 PGS019486
(TPMI_594.3_LDpred2)
 PSS013381|
East Asian Ancestry|
18,587 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Calculus of ureter — AUROC: 0.68562 R²: 0.05268 sex, age, array, PCs 1-10 —
PPM037669 PGS019487
(TPMI_594.3_MegaPRS)
 PSS013383|
East Asian Ancestry|
18,587 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Calculus of ureter — AUROC: 0.68334 R²: 0.05167 sex, age, array, PCs 1-10 —
PPM037670 PGS019488
(TPMI_594.3_PRS-CS)
 PSS013384|
East Asian Ancestry|
18,587 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Calculus of ureter — AUROC: 0.68482 R²: 0.05243 sex, age, array, PCs 1-10 —
PPM037671 PGS019489
(TPMI_594.3_PRSmix+)
 PSS013385|
East Asian Ancestry|
18,587 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Calculus of ureter — AUROC: 0.69005 R²: 0.05469 sex, age, array, PCs 1-10 —
PPM037672 PGS019490
(TPMI_594.3_SBayesR)
 PSS013386|
East Asian Ancestry|
18,587 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Calculus of ureter — AUROC: 0.68139 R²: 0.05191 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
PSS004253 — —
[
  • 56 cases
  • , 6,441 controls
]
 — African unspecified — UKB —
PSS004254 — —
[
  • 25 cases
  • , 1,679 controls
]
 — East Asian — UKB —
PSS004255 — —
[
  • 384 cases
  • , 24,521 controls
]
 — European non-white British ancestry UKB —
PSS004256 — —
[
  • 146 cases
  • , 7,685 controls
]
 — South Asian — UKB —
PSS004257 — —
[
  • 989 cases
  • , 66,436 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS013381 592.1,N20.1 —
[
  • 510 cases
  • , 18,077 controls
]
,
45.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013382 592.1,N20.1 —
[
  • 510 cases
  • , 18,077 controls
]
,
45.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013383 592.1,N20.1 —
[
  • 510 cases
  • , 18,077 controls
]
,
45.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013384 592.1,N20.1 —
[
  • 510 cases
  • , 18,077 controls
]
,
45.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013385 592.1,N20.1 —
[
  • 510 cases
  • , 18,077 controls
]
,
45.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013386 592.1,N20.1 —
[
  • 510 cases
  • , 18,077 controls
]
,
45.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —