Trait: nephrolithiasis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004253
Description The presence of a calculus in the pelvis of the kidney; this is most often composed of mineral salts and proteins. [NCIT: P378]
Trait category
Other disease
Synonyms 23 synonyms
  • CAON
  • Calculi, Kidney
  • Calculi, Renal
  • Calculus, Kidney
  • Calculus, Renal
  • Kidney Calculi
  • Kidney Calculus
  • Kidney Stones
  • Kidney stones
  • Renal Calculi
  • Renal Calculus
  • Renal calculi
  • Renal stones
  • Stone - kidney/ureter
  • Stone, Kidney
  • Stones, Kidney
  • calculus of kidney and ureter
  • kidney stone
  • kidney stones
  • nephrolithiasis
  • nephrolithiasis, calcium oxalate
  • renal calculi
  • urolithiasis, calcium oxalate
Mapped terms 18 mapped terms
  • DOID:585
  • ICD10:N20
  • ICD9:592
  • MEDGEN:98227
  • MESH:D053040
  • MONDO:0008171
  • MeSH:D007669
  • MeSH:D053040
  • MedDRA:10023436
  • MedDRA:10023437
  • MedDRA:10029148
  • NCIT:C114667
  • NCIt:C114667
  • OMIM:167030
  • OMIM:605990
  • SCTID:266556005
  • SNOMEDCT:95570007
  • UMLS:C0392525

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) nephrolithiasis,
ureterolithiasis		 341
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001250/ScoringFiles/PGS001250.txt.gz
PGS004493
(disease.N20.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 N20 (Calculus of kidney and ureter) nephrolithiasis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004493/ScoringFiles/PGS004493.txt.gz
PGS004563
(meta.N20.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 N20 (Calculus of kidney and ureter) nephrolithiasis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004563/ScoringFiles/PGS004563.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
PPM020608 PGS004493
(disease.N20.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: N20 (Calculus of kidney and ureter) OR: 1.22731 — — — —
PPM020678 PGS004563
(meta.N20.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: N20 (Calculus of kidney and ureter) OR: 1.28304 — — — —

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)
PSS011364 — — 56,192 individuals — European — UKB —