Documentation / Phenotype Matching / Interpreting Scores
Interpreting Phenotype Matching Scores
Phenotype Matching produces related but different measurements. Read the score label and clinical tier together; a value without its context can be misleading.
Three Result Levels
Individual HPO similarity (0-1)
For each patient term, the closest term in the gene profile and its Lin similarity. Folklore counts an individual match as significant only when it is greater than 0.5.
Phenotype match score (0-100)
The average best match across valid patient HPO terms, scaled to 100. It summarizes semantic overlap only.
Clinical priority score (0-99.99)
A tier-coded ordering value. Its band identifies Tier 1, Tier 2, IF, Tier 3, or Tier 4; evidence then orders results within that band.
A Match Score Is Not a Probability
A phenotype score of 80 does not mean an 80% probability that the variant causes disease. It reflects ontology-based similarity between the selected patient findings and the available gene annotations.
Recommended Review Order
1. Confirm the tier
Start with the rule-based clinical group and read any demotion or inheritance note.
2. Inspect the variant evidence
Review ACMG classification, criteria, population frequency, ClinVar evidence, impact, genotype, and inheritance.
3. Inspect individual HPO matches
Identify which findings drive the score and whether they are specific, independent, and clinically accurate.
4. Check annotation coverage
Consider whether an emerging gene, atypical presentation, or incomplete phenotype profile could distort the ranking.
Factors That Change the Score
Specificity
Specific terms usually discriminate better than broad system-level findings.
Additional patient terms
Every valid selected term contributes to the directional average; an unmatched term can lower it.
Redundant terms
Selecting both a broad parent and a specific child can over-weight one feature.
Gene annotation coverage
Sparse or outdated gene-phenotype profiles can understate a real clinical relationship.
Atypical presentation
A patient outside the established disease spectrum may receive a lower score.
Invalid identifiers
Terms that cannot be resolved in the loaded ontology are ignored.
Clinical Boundary
Use phenotype matching to focus review, not to exclude a gene or make a diagnosis by itself. Final interpretation remains with a qualified professional and should incorporate the full patient, family, laboratory, and literature context.
Improve the input profile with the HPO Term Selection Guide.