Trait: deafness

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001063
Description
  • A partial or complete loss o f hearing in one or both ears; the level of impairment varies from a mild but important loss of sensitivity to a total loss of hearing.
  • An inherited or acquired condition characterized by a partial or complete loss of hearing in one or both ears. The level of impairment varies from a mild but important loss of sensitivity to a total loss of hearing.
  • An inherited or acquired condition characterized by the complete loss of the ability to hear from one or both ears.
Trait category
Neurological disorder
Synonyms 8 synonyms
  • Bilateral Deafness
  • Bilateral deafness (finding)
  • Complete deafness (finding)
  • Deafness NOS
  • Deafness NOS (disorder)
  • Deafness NOS (finding)
  • Total Deafness
  • complete hearing loss
Mapped terms 5 mapped terms
  • MeSH:D003638
  • MedDRA:10011878
  • NCIt:C27644
  • OMIM:301018
  • SNOMEDCT:162344009

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)
PGS001252
(GBE_BIN_FC3002247)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Hearing difficulty and deafness deafness,
hearing loss		 3,731
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001252/ScoringFiles/PGS001252.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
PPM008769 PGS001252
(GBE_BIN_FC3002247)
 PSS003899|
African Ancestry|
6,123 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.58635 [0.56411, 0.60859] R²: 0.01752
Incremental AUROC (full-covars): -0.00041
PGS R2 (no covariates): 0.00138
PGS AUROC (no covariates): 0.52307 [0.50054, 0.54561]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008770 PGS001252
(GBE_BIN_FC3002247)
 PSS003900|
East Asian Ancestry|
1,568 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62777 [0.58865, 0.66688] R²: 0.04973
Incremental AUROC (full-covars): 0.00284
PGS R2 (no covariates): 0.00305
PGS AUROC (no covariates): 0.53516 [0.49316, 0.57716]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008771 PGS001252
(GBE_BIN_FC3002247)
 PSS003901|
European Ancestry|
23,697 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62252 [0.61446, 0.63058] R²: 0.05132
Incremental AUROC (full-covars): 0.00531
PGS R2 (no covariates): 0.00527
PGS AUROC (no covariates): 0.53867 [0.53034, 0.54699]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008772 PGS001252
(GBE_BIN_FC3002247)
 PSS003902|
South Asian Ancestry|
7,266 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.61586 [0.5994, 0.63232] R²: 0.04282
Incremental AUROC (full-covars): 0.00304
PGS R2 (no covariates): 0.00345
PGS AUROC (no covariates): 0.53204 [0.5154, 0.54867]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008773 PGS001252
(GBE_BIN_FC3002247)
 PSS003903|
European Ancestry|
65,065 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62548 [0.62074, 0.63023] R²: 0.05558
Incremental AUROC (full-covars): 0.00728
PGS R2 (no covariates): 0.00646
PGS AUROC (no covariates): 0.54216 [0.53723, 0.54709]		 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
PSS003900 — —
[
  • 214 cases
  • , 1,354 controls
]
 — East Asian — UKB —
PSS003901 — —
[
  • 6,214 cases
  • , 17,483 controls
]
 — European non-white British ancestry UKB —
PSS003902 — —
[
  • 1,425 cases
  • , 5,841 controls
]
 — South Asian — UKB —
PSS003903 — —
[
  • 18,231 cases
  • , 46,834 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003899 — —
[
  • 699 cases
  • , 5,424 controls
]
 — African unspecified — UKB —