c9446936b026a803d97e7f5128404a327829fe2e
max
  Sun Jul 19 00:01:22 2026 -0700
ClinVar Mapped: add Pfam-domain mapping method

Maps ClinVar coding variants through Pfam protein domains as a second method
under the clinvarMapped container. Each Pfam family's profile HMM gives a shared
coordinate, so a variant inside a domain is projected to the residue in the same
HMM match-state column in every other MANE Select gene carrying that domain, then
mapped back to that gene's genomic codon. This links genes that share a domain
without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium
channels via Ion_trans). Each variant is shown at its 25 most conserved
equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants,
Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and
description page, refs #37883

diff --git src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfam.as src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfam.as
new file mode 100644
index 00000000000..9c548479d1a
--- /dev/null
+++ src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfam.as
@@ -0,0 +1,32 @@
+table clinvarMappedPfam
+"ClinVar variants projected onto other genes sharing the same Pfam domain, at the equivalent domain position"
+    (
+    string chrom;         "Reference sequence chromosome"
+    uint   chromStart;    "Start position of the equivalent codon in this gene"
+    uint   chromEnd;      "End position of the equivalent codon in this gene"
+    string name;          "Source gene and variant"
+    uint   score;         "Review status scaled 0-1000 (stars x 250)"
+    char[1] strand;       "Strand of this gene"
+    uint   thickStart;    "Coding start (equal to chromStart)"
+    uint   thickEnd;      "Coding end (equal to chromEnd)"
+    uint   reserved;      "Color (itemRgb) by clinical significance of the source variant"
+    int    blockCount;    "Number of codon blocks (2 if the codon spans an intron)"
+    int[blockCount] blockSizes;  "Codon block sizes"
+    int[blockCount] chromStarts; "Codon block starts relative to chromStart"
+    string sourceGene;    "Source gene|Gene the ClinVar variant is annotated in"
+    string thisGene;      "This gene|Gene carrying the equivalent domain position"
+    string sourceVariant; "Source variant|ClinVar protein change in the source gene"
+    uint   sourceAaPos;   "Source residue #|Residue position in the source gene"
+    char[1] srcRes;       "Source residue|Reference residue in the source gene"
+    char[1] thisRes;      "This-gene residue|Residue at the equivalent domain position"
+    string residueMatch;  "Residue match|identical, similar or different vs the source residue"
+    string clinSign;      "Clinical significance|ClinVar significance of the source variant"
+    string clinSignCode;  "Significance code"
+    uint   reviewStars;   "Review stars|ClinVar review status, 0-4 stars"
+    string molConseq;     "Consequence|Molecular consequence in the source gene"
+    string pfamId;        "Pfam domain|Pfam domain name"
+    string pfamAcc;       "Pfam accession|Pfam family accession"
+    uint   domainColumn;  "Domain position|Pfam HMM match-state column (shared coordinate)"
+    string vcvId;         "ClinVar VCV|ClinVar variant accession"
+    string sourceLocus;   "Source position|Position of the source variant on hg38"
+    )