Trait: vitamin B12 deficiency

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000734
Description A disease characterized by low serum levels of vitamin B12, either inherited or acquired. [PMID: 16846473]
Trait category
Metabolic disorder
Synonyms 20 synonyms
  • Cobalamin deficiency
  • Cobalamin deficiency (disorder)
  • DEFIC VITAMIN B 12
  • DEFIC VITAMIN B12
  • Deficiencies, Vitamin B12
  • Deficiency of vitamin B12
  • Deficiency of vitamin B<sub>12</sub>
  • Deficiency of vitamin B>12<
  • Deficiency of vitamin B>12< (disorder)
  • Deficiency, Vitamin B 12
  • Deficiency, Vitamin B12
  • VITAMIN B 12 DEFIC
  • VITAMIN B A 12 DEFICIENCY
  • VITAMIN B12 DEFIC
  • Vitamin B 12 Deficiency
  • Vitamin B12 Deficiencies
  • cobalamin deficiency
  • hypocobalaminemia
  • vitamin B12 deficiency
  • vitamin b12 deficiency
Mapped terms 14 mapped terms
  • DOID:0050731
  • HP:0100502
  • ICD10:D51
  • ICD9:266.2
  • MEDGEN:21880
  • MESH:D014806
  • MONDO:0020696
  • MedDRA:10047609
  • NCIT:C131684
  • OMIM:193090
  • SCTID:190634004
  • SNOMEDCT:190634004
  • UMLS:C0042847
  • icd11.foundation:1366882206

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)
PGS001305
(GBE_HC608)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Vitamin B12 deficiency induced anemia (time-to-event) vitamin B12 deficiency,
anemia		 121
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001305/ScoringFiles/PGS001305.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
PPM009020 PGS001305
(GBE_HC608)
 PSS004536|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitamin b12 deficiency anaemia — AUROC: 0.66063 [0.54547, 0.77579] R²: 0.02699
Incremental AUROC (full-covars): 0.01762
PGS R2 (no covariates): 0.00536
PGS AUROC (no covariates): 0.5839 [0.43974, 0.72805]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009021 PGS001305
(GBE_HC608)
 PSS004538|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitamin b12 deficiency anaemia — AUROC: 0.65118 [0.60827, 0.69409] R²: 0.02729
Incremental AUROC (full-covars): 0.02555
PGS R2 (no covariates): 0.00865
PGS AUROC (no covariates): 0.59612 [0.5552, 0.63704]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009022 PGS001305
(GBE_HC608)
 PSS004539|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitamin b12 deficiency anaemia — AUROC: 0.72387 [0.6834, 0.76434] R²: 0.06747
Incremental AUROC (full-covars): 0.01252
PGS R2 (no covariates): 0.00966
PGS AUROC (no covariates): 0.57469 [0.52685, 0.62252]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009023 PGS001305
(GBE_HC608)
 PSS004540|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitamin b12 deficiency anaemia — AUROC: 0.64482 [0.61972, 0.66993] R²: 0.02374
Incremental AUROC (full-covars): 0.02212
PGS R2 (no covariates): 0.0068
PGS AUROC (no covariates): 0.57972 [0.55331, 0.60612]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004540 — —
[
  • 447 cases
  • , 66,978 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004536 — —
[
  • 19 cases
  • , 6,478 controls
]
 — African unspecified — UKB —
PSS004538 — —
[
  • 160 cases
  • , 24,745 controls
]
 — European non-white British ancestry UKB —
PSS004539 — —
[
  • 138 cases
  • , 7,693 controls
]
 — South Asian — UKB —