PhyloP score¶
PhyloP measures how a DNA position has changed across species compared with a neutral model of evolution. A positive score means the position changed more slowly than expected, which supports conservation. A negative score means it changed more quickly than expected, which supports evolutionary acceleration. The magnitude shows the strength of the evolutionary evidence. A change at a strongly conserved position can be more concerning and deserves closer review, but the score alone does not show that the change is harmful or causes disease.
Score range in Gene Inspector Pro¶
PhyloP is a signed statistical score, not a fixed 0 to 1 scale. Its possible values depend on the reference assembly, alignment, species set, neutral model, and track release. Gene Inspector Pro uses these display bands:
| Score | Display meaning |
|---|---|
| Below -1.6 | Accelerated evolution |
| -1.6 to 1.6 | No clear departure from neutral evolution |
| Above 1.6 | Conserved position |
These values describe evolutionary evidence at one position. They are not clinical thresholds. A high positive score is a reason to inspect a change more closely; it does not establish that the change causes disease. Likewise, a near-zero or negative score does not establish that it is harmless.
Limits of conservation scores¶
PhyloP depends on the alignment, species set, reference assembly, and neutral model used to produce the track. It assesses one base at a time and may be missing at gaps or unaligned positions. Conservation can miss functions that are recent or specific to humans.
How to use it¶
Read PhyloP with the affected transcript and consequence, population frequency, ClinVar submissions, functional studies, inheritance, and genotype quality. Use it as evolutionary context, not as a standalone variant classification.