10c0695c8a4ff88a24ae2f446b4ef705fdbc37d8
lrnassar
  Tue Jun 30 17:57:33 2026 -0700
Add popEVE and EVE to the Deleteriousness Predictions page and related tracks. refs #37791

Document EVE and popEVE on the predictionScoresSuper description page, which previously
listed the other member scores but not these two. Also add reciprocal relatedTracks
cross-links between popEVE and EVE, AlphaMissense, PrimateAI-3D, ClinPred, and REVEL.

diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra
index 978403558ec..7caab13856c 100644
--- src/hg/makeDb/trackDb/relatedTracks.ra
+++ src/hg/makeDb/trackDb/relatedTracks.ra
@@ -135,30 +135,42 @@
 hg38 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure
 
 hg19 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors
 hg19 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure
 
 # ClinPred cross-links:
 hg38 clinPred revel REVEL, an ensemble missense pathogenicity score using a similar machine-learning approach
 hg38 revel clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency
 hg38 clinPred caddSuper CADD, a similar deleteriousness score
 hg38 caddSuper clinPred ClinPred, a missense-only pathogenicity predictor
 hg38 clinPred primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation
 hg38 primateAi clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
 hg38 clinPred alphaMissense AlphaMissense, a deep-learning missense pathogenicity predictor
 hg38 alphaMissense clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
 
+# popEVE cross-links:
+hg38 popEve eve EVE, a missense pathogenicity predictor trained on evolutionary sequence variation, and an input to popEVE
+hg38 eve popEve popEVE, a proteome-wide missense deleteriousness model built on EVE and calibrated with human population data
+hg38 popEve alphaMissense AlphaMissense, a similar deep-learning missense pathogenicity predictor
+hg38 alphaMissense popEve popEVE, a proteome-wide missense deleteriousness model combining evolutionary and human population data
+hg38 popEve primateAi PrimateAI-3D, a similar deep-learning missense pathogenicity predictor using primate variation
+hg38 primateAi popEve popEVE, a proteome-wide missense deleteriousness model combining evolutionary and human population data
+hg38 popEve clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency
+hg38 clinPred popEve popEVE, a proteome-wide missense deleteriousness model combining evolutionary and human population data
+hg38 popEve revel REVEL, an ensemble missense pathogenicity score built from multiple predictors
+hg38 revel popEve popEVE, a proteome-wide missense deleteriousness model combining evolutionary and human population data
+
 hg19 clinPred revel REVEL, an ensemble missense pathogenicity score using a similar machine-learning approach
 hg19 revel clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency
 hg19 clinPred caddSuper CADD, a similar deleteriousness score
 hg19 caddSuper clinPred ClinPred, a missense-only pathogenicity predictor
 hg19 clinPred primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation
 hg19 primateAi clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
 hg19 clinPred alphaMissense AlphaMissense, a deep-learning missense pathogenicity predictor
 hg19 alphaMissense clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
 
 # PromoterAI cross-links:
 hg38 promoterAi primateAi PrimateAI-3D, a companion deep-learning model from Illumina for coding (missense) variants
 hg38 primateAi promoterAi PromoterAI, a companion deep-learning model from Illumina for non-coding promoter variants
 hg38 promoterAi alphaMissense AlphaMissense, a deep-learning predictor of missense (coding) variant pathogenicity
 hg38 alphaMissense promoterAi PromoterAI, a deep-learning predictor of expression-altering variants in promoter regions