574399b4a7d8fc75c1745fa83564f547ddcb9e8c
chmalee
  Sat Jun 13 00:43:54 2026 -0700
gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
new file mode 100644
index 00000000000..b5d2371fc8a
--- /dev/null
+++ src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
@@ -0,0 +1,221 @@
+track gnomadPLI
+parent gnomadVariants 
+shortLabel gnomAD Constraint Metrics
+longLabel Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores)
+compositeTrack On
+group varRep
+type bigBed 12
+labelFields name,geneName
+dataVersion Release v4.1.1 (March 2026), Release v4.1 (April 19, 2024), Release v4 (November 2023), Release 2.1.1 (March 6, 2019)
+subGroup1 view Views v2=constraintV2 v4=constraintV4 v4_1=constraintV4.1 v4_1_1=constraintV4.1.1
+html gnomadPLI.html
+visibility hide
+
+    track constraintV2
+    parent gnomadPLI off
+    shortLabel Constraint V2
+    longLabel gnomAD Constraint Metrics V2
+    view v2
+    visibility pack
+    type bigBed 12 +
+
+        track pliByGene
+        shortLabel Gene LoF
+        longLabel gnomAD Predicted Loss of Function Constraint Metrics By Gene (LOEUF and pLI) v2.1.1
+        subGroups view=v2
+        type bigBed 12 +
+        itemRgb on
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByGene.bb
+        url https://gnomad.broadinstitute.org/gene/$$?dataset=gnomad_r2_1
+        urlLabel View this Gene on the gnomAD browser
+        labelFields name,geneName
+        defaultLabelFields geneName
+        filter._pli 0:1
+        filterLabel._pli Show only items between this pLI range
+        filterByRange._pli on
+        parent constraintV2 on
+        priority 1
+        mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
+
+        track missenseByGene
+        shortLabel Gene Missense
+        longLabel gnomAD Predicted Missense Constraint Metrics By Gene (Z-scores) v2.1.1
+        subGroups view=v2
+        type bigBed 12 +
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByGene.bb
+        url https://gnomad.broadinstitute.org/gene/$$?dataset=gnomad_r2_1
+        urlLabel View this Gene on the gnomAD browser
+        labelFields name,geneName
+        filter._zscore -19:11
+        itemRgb on
+        filterLabel._zscore Show only items between this Z-score range
+        filterByRange._zscore on
+        parent constraintV2 off
+        priority 2
+        mouseOver Z: $_zscore<br> $synonymous<br> $missense
+
+        track pliByTranscript
+        shortLabel Transcript LoF v2
+        longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v2.1.1
+        subGroups view=v2
+        type bigBed 12 +
+        itemRgb on
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._pli 0:1
+        filterLabel._pli Show only items between this pLI range
+        filterByRange._pli on
+        parent constraintV2 off
+        priority 2
+        mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
+
+        track missenseByTranscript
+        shortLabel Transcript Missense v2
+        longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v2.1.1
+        subGroups view=v2
+        type bigBed 12 +
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._zscore -20:11
+        filterLabel._zscore Show only items between this Z-score range
+        filterByRange._zscore on
+        parent constraintV2 off
+        priority 2
+        mouseOver Z: $_zscore<br> $synonymous<br> $missense
+
+    track constraintV4
+    parent gnomadPLI off
+    shortLabel Constraint V4
+    longLabel gnomAD Constraint Metrics V4
+    view v4
+    visibility hide
+    type bigBed 12 +
+    
+        track pliByTranscriptV4
+        shortLabel Transcript LoF v4
+        longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4
+        subGroups view=v4
+        type bigBed 12 +
+        itemRgb on
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._pli 0:1
+        filterLabel._pli Show only items between this pLI range
+        filterByRange._pli on
+        parent constraintV4
+        priority 2
+        mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
+
+        track missenseByTranscriptV4
+        shortLabel Transcript Missense v4
+        longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4
+        subGroups view=v4
+        type bigBed 12 +
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._zscore -20:11
+        filterLabel._zscore Show only items between this Z-score range
+        filterByRange._zscore on
+        parent constraintV4
+        priority 2
+        mouseOver Z: $_zscore<br> $synonymous<br> $missense
+
+    track constraintV4_1
+    parent gnomadPLI off
+    shortLabel Constraint V4.1
+    longLabel gnomAD Constraint Metrics V4.1
+    view v4_1
+    visibility pack
+    type bigBed 12 +
+
+        track pliByTranscriptV4_1
+        shortLabel Transcript LoF v4.1
+        longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1
+        subGroups view=v4_1
+        type bigBed 12 +
+        itemRgb on
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.1.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._pli 0:1
+        filterLabel._pli Show only items between this pLI range
+        filterByRange._pli on
+        parent constraintV4_1
+        priority 2
+        mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
+
+        track missenseByTranscriptV4_1
+        shortLabel Transcript Missense v4.1
+        longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1
+        subGroups view=v4_1
+        type bigBed 12 +
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.1.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._zscore -20:11
+        filterLabel._zscore Show only items between this Z-score range
+        filterByRange._zscore on
+        parent constraintV4_1
+        priority 2
+        mouseOver Z: $_zscore<br> $synonymous<br> $missense
+
+    track constraintV4_1_1
+    parent gnomadPLI off
+    shortLabel Constraint V4.1.1
+    longLabel gnomAD Constraint Metrics V4.1.1
+    view v4_1_1
+    visibility pack
+    type bigBed 12 +
+
+        track pliByTranscriptV4_1_1
+        shortLabel Transcript LoF v4.1.1
+        longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1.1
+        subGroups view=v4_1_1
+        type bigBed 12 +
+        itemRgb on
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.1.1.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._pli 0:1
+        filterLabel._pli Show only items between this pLI range
+        filterByRange._pli on
+        parent constraintV4_1_1
+        priority 1
+        mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF<br> Gene flags: $geneFlags<br> Constraint flags: $constraintFlags
+
+        track missenseByTranscriptV4_1_1
+        shortLabel Transcript Missense v4.1.1
+        longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1.1
+        subGroups view=v4_1_1
+        type bigBed 12 +
+        searchIndex name,geneName
+        bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.1.1.bb
+        url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
+        urlLabel View this Transcript on the gnomAD browser
+        labelFields name,geneName
+        filter._zscore -20:11
+        filterLabel._zscore Show only items between this Z-score range
+        filterByRange._zscore on
+        parent constraintV4_1_1
+        priority 1
+        mouseOver Z: $_zscore<br> $synonymous<br> $missense<br> Gene flags: $geneFlags<br> Constraint flags: $constraintFlags