PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)

- DB build resolves the PGX-007 tag variants from the manifest's probes; coverage over all gene kinds.
- Variant-based genes reported per variant (rs.. REF/ALT | Reference) with the CPIC lowest-activity diplotype;
  tagging genes as positive/negative with the population caveat; GSTM1/GSTT1/UGT2B17 *0 from targeted CN.
- Case-insensitive phenotype keys (MT-RNR1). GeT-RM check extended to VKORC1 and the CN genes:
  131/144 gene calls (docs/validation/V2_pgx_star.md).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

docs/validation/V2_pgx_star.md

@@ -37,7 +37,11 @@ Status: **implemented for CPIC star-allele genes, interim validation** (2026-09-
 | CYP4F2 | 8/9 | 8/9 |
 | NAT2 | 8/9 | 8/9 |
 | NUDT15 | 1/1 | 1/1 |
-| **total** | **100/109 (91.7 %)** | **103/109 (94.5 %)** |
+| VKORC1 (rs9923231, c.-1639G>A) | 13/15 | 13/15 |
+| GSTM1 (CN: DEL/DEL vs present) | 9/9 | 9/9 |
+| GSTT1 (CN 0/1/2) | 7/9 | 7/9 |
+| UGT2B17 (CN) | 2/2 | 2/2 |
+| **total** | **131/144 (91.0 %)** | **134/144 (93.1 %)** |
 
 PGX-032 target (≥ 90 % for CYP2D6/CYP2C19/CYP2C9 against truth): **41/45 = 91 %** (top solution).
 Details and every discordant call: `V2_pgx_star_getrm16.json`.
@@ -70,5 +74,10 @@ so the per-call error is 1e-3 (GS ≥ 0.15) and errors are handled by the probe
   `variants_not_covered.tsv`, per-allele supporting/unresolved sites for **both** alleles of every candidate,
   `variant_change` vs the top solution (`distant_alternative` above 3 changes), `unexplained_variants`, full HGVS on
   GRCh38 RefSeq accessions.
-* Not yet: named-haplotype (G6PD), variant-based and tagging genes; CYP2D6 hybrids (*13, *36, *68); PharmVar-only
+* All CPIC gene kinds are called: star alleles, G6PD (named haplotypes; males hemizygous from the VCF ploidy),
+  variant-based genes (ABCG2, CACNA1S, CFTR, DPYD, IFNL3, MT-RNR1, RYR1, VKORC1; genotype as `rs… REF/ALT` or
+  `Reference`, phenotype diplotype from the two lowest-activity carried variants), HLA-A/B tag variants (PGX-007,
+  positions resolved from the manifest's probes, flag `tag_caveat`), and GSTM1/GSTT1/UGT2B17 `*0` genotypes from
+  the targeted CN (PGX-006).
+* Not yet: CYP2D6 hybrids (*13, *36, *68); PharmVar-only
   genes (CYP2A6, CYP3A4, CYP1A2, …); DPWG tables.

docs/validation/V2_pgx_star_getrm16.json

@@ -32,6 +32,16 @@
    "top": 8,
    "equivalent": 8
   },
+  "GSTM1": {
+   "n": 9,
+   "top": 9,
+   "equivalent": 9
+  },
+  "GSTT1": {
+   "n": 9,
+   "top": 7,
+   "equivalent": 7
+  },
   "NAT2": {
    "n": 9,
    "top": 8,
@@ -56,6 +66,16 @@
    "n": 9,
    "top": 0,
    "equivalent": 1
+  },
+  "UGT2B17": {
+   "n": 2,
+   "top": 2,
+   "equivalent": 2
+  },
+  "VKORC1": {
+   "n": 15,
+   "top": 13,
+   "equivalent": 13
   }
  },
  "legacy_nomenclature_genes": [
@@ -63,9 +83,9 @@
   "UGT1A1"
  ],
  "total": {
-  "n": 109,
-  "top": 100,
-  "equivalent": 103
+  "n": 144,
+  "top": 131,
+  "equivalent": 134
  },
  "discordant": [
   {
@@ -110,6 +130,13 @@
    "call": "*1/*1",
    "within_equivalents": false
   },
+  {
+   "individual": "NA06991",
+   "gene": "VKORC1",
+   "truth": "AA",
+   "call": "rs9923231 T/T",
+   "within_equivalents": false
+  },
   {
    "individual": "NA12878",
    "gene": "CYP2D6",
@@ -145,6 +172,20 @@
    "call": "*28/*80",
    "within_equivalents": false
   },
+  {
+   "individual": "NA12003",
+   "gene": "VKORC1",
+   "truth": "AA",
+   "call": "rs9923231 T/T",
+   "within_equivalents": false
+  },
+  {
+   "individual": "NA12003",
+   "gene": "GSTT1",
+   "truth": "(*A/*A)",
+   "call": "*1/*0",
+   "within_equivalents": false
+  },
   {
    "individual": "NA07029",
    "gene": "CYP2B6",
@@ -229,6 +270,13 @@
    "call": "*80/*80",
    "within_equivalents": false
   },
+  {
+   "individual": "NA12813",
+   "gene": "GSTT1",
+   "truth": "(*A/*A)",
+   "call": "*1/*0",
+   "within_equivalents": false
+  },
   {
    "individual": "NA11881",
    "gene": "SLCO1B1",