bf62c01cee8dc176445aa131e2fd6ea847a4eb68
lrnassar
  Thu May 28 11:32:52 2026 -0700
Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648

Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a
bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity
classification. Filters: pathogenicity, variantClassification, variantType,
tumor frequency. Search by HGVS cDNA name and canonical protein change via
extraIndex + trix. Linkouts to COSMIC and dbSNP.

Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips
actually change. Cron-silent on no-op so unchanged weeks don't email.

Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema),
src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza),
src/hg/makeDb/trackDb/human/umdTp53.html (description page),
src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition).

Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated).
Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict
trackDb checker resolves the parent in the same include chain as the
existing mucins children. Drops the redundant locusSpec stanza from
human/mucins.ra now that it lives in its own file.

diff --git src/hg/utils/otto/umdTp53/umdTp53.as src/hg/utils/otto/umdTp53/umdTp53.as
new file mode 100644
index 00000000000..67bfc6700f9
--- /dev/null
+++ src/hg/utils/otto/umdTp53/umdTp53.as
@@ -0,0 +1,56 @@
+table umdTp53
+"UMD TP53 Variant Database (p53.fr) — one row per unique TP53 variant"
+    (
+    string  chrom;             "Chromosome"
+    uint    chromStart;        "Start position"
+    uint    chromEnd;          "End position"
+    string  name;              "HGVS cDNA nomenclature (NM_000546.5)"
+    uint    score;             "Unused"
+    char[1] strand;            "Strand (TP53 is on minus strand)"
+    uint    thickStart;        "Display thick start"
+    uint    thickEnd;           "Display thick end"
+    uint    reserved;          "RGB color reflecting pathogenicity"
+    lstring cDnaFull;          "Full HGVS cDNA nomenclature (when the displayed name was shortened)"
+    string  proteinChange;     "Protein change on canonical TP53 alpha (NP_000537.3)"
+    string  pathogenicity;     "Curator pathogenicity classification"
+    string  variantClassification; "Effect class (Missense / Nonsense / Synonymous / Frameshift / Splice / ...)"
+    string  variantType;       "Variant type (SNP / DEL / INS / DNP / TNP / ONP)"
+    string  domain;            "TP53 protein domain"
+    string  structure;         "Structural motif (Cho et al. 1994)"
+    string  ptm;               "Post-translational modification site, if any"
+    string  umdId;             "UMD database identifier"
+    string  cosmicId;          "COSMIC mutation ID"
+    string  snpId;             "dbSNP rs ID"
+    lstring activityComment;   "Residual transactivation activity summary (Kato et al. 8-promoter assay)"
+    string  waf1Pct;           "WAF1 promoter activity (% of WT)"
+    string  mdm2Pct;           "MDM2 promoter activity (% of WT)"
+    string  baxPct;            "BAX promoter activity (% of WT)"
+    string  p14333sPct;        "14-3-3-sigma promoter activity (% of WT)"
+    string  aipPct;            "AIP promoter activity (% of WT)"
+    string  gadd45Pct;         "GADD45 promoter activity (% of WT)"
+    string  noxaPct;           "NOXA promoter activity (% of WT)"
+    string  p53r2Pct;          "p53R2 promoter activity (% of WT)"
+    float   tumorFreq;         "Frequency in tumors (%)"
+    string  cellLineFreq;      "Frequency in cell lines (%)"
+    string  somaticFreq;       "Frequency among somatic cases (%)"
+    string  germlineFreq;      "Frequency among germline cases (%)"
+    uint    recordsNumber;     "Total occurrences in the database"
+    string  siftScore;         "SIFT score"
+    string  siftPrediction;    "SIFT prediction"
+    string  polyphenHumVar;    "Polyphen-2 HumVar prediction"
+    string  polyphenHumDiv;    "Polyphen-2 HumDiv prediction"
+    string  mutAssessorScore;  "MutationAssessor score"
+    string  mutAssessorPrediction; "MutationAssessor prediction"
+    string  proveanScore;      "PROVEAN score"
+    string  proveanPrediction; "PROVEAN prediction"
+    string  condel;            "Condel prediction"
+    string  condelScore;       "Condel score"
+    string  mutpredSpliceScore; "MutPred Splice general score"
+    string  mutpredSplicePrediction; "MutPred Splice prediction label"
+    lstring mutpredSpliceHypotheses; "MutPred Splice confident hypotheses"
+    lstring commentFrequency;  "Curator note on variant frequency"
+    lstring commentOutliers;   "Curator note on outlier publications"
+    lstring commentSplicing;   "Curator note on splicing"
+    lstring finalComment;      "Curator final summary"
+    lstring _mouseOver;        "Pre-built hover text"
+    )