Trait: cleft lip

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003959
Description Congenital defect in the upper lip where the maxillary prominence fails to merge with the merged medial nasal prominences. It is thought to be caused by faulty migration of the mesoderm in the head region.
Trait category
Other trait
Synonyms 5 synonyms
  • Cleft Lips
  • Harelip
  • Harelips
  • Lip, Cleft
  • Lips, Cleft
Mapped terms 13 mapped terms
  • DOID:9296
  • ICD10:Q36
  • ICD9:749.1
  • MeSH:D002971
  • MedDRA:10009259
  • MedDRA:10009264
  • MedDRA:10009265
  • MedDRA:10009266
  • MedDRA:10009267
  • MedDRA:10009268
  • MedDRA:10019161
  • NCIt:C87175
  • SNOMEDCT:80281008

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:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
East Asian
South Asian
Additional Asian Ancestries
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
Scoring File (FTP Link)
PGP000295 |
Yu Y et al. Hum Mol Genet (2022)
Nonsyndromic cleft lip with or without cleft palate cleft lip,
Cleft palate

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM012907 PGS002266
European Ancestry|
72,542 individuals
PGP000295 |
Yu Y et al. Hum Mol Genet (2022)
Reported Trait: Nonsyndromic cleft lip with or without cleft palate AUROC: 0.66

Evaluated Samples

PGS Sample Set ID
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
PSS009607 cases diagnosed with cleft lip and palate or cleft lip, unspecified cleft type
  • 46 cases
  • , 72,496 controls
(Non-Hispanic European)