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G2P All-Gene Audit Summary

Companion artifacts:

The row-level triage TSV omits fully resolved ROOT_MATCH rows so it can be used directly as a curator worklist.

  • G2P source: https://ftp.ebi.ac.uk/pub/databases/gene2phenotype/G2P_data_downloads/2026_03_28/allG2P_2026-03-28.csv.gz
  • Genes audited: 3144
  • G2P rows audited: 3829
  • Actionable rows: 3810
  • Genes with direct dismech matches: 158
  • Genes with G2P MONDO collisions: 37

Aggregate Row Status Counts

  • EMBEDDED_NOT_ROOTED: 492
  • NO_DISMECH_MATCH: 3170
  • ROOT_MATCH: 19
  • ROOT_MATCH_PMID_GAP: 46
  • SPLIT_ACROSS_DISMECH: 39
  • UNDERREPRESENTED_IN_DISMECH: 63

Genes By Highest Curation Priority

  • CRITICAL: 2707
  • HIGH: 60
  • MEDIUM: 368
  • LOW: 9

Most Common Primary Actions

  • ADD_FIRST_GENE_DISEASE_ANCHOR: 2707
  • REVIEW_NON_ROOT_GENE_MENTION: 279
  • DECIDE_IF_EMBEDDED_CONCEPT_NEEDS_ROOT: 57
  • ADD_MISSING_DISEASE_ROOT: 42
  • BACKFILL_G2P_PMIDS_TO_MATCHED_ROOT: 32
  • RECONCILE_SPECTRUM_ROW_ACROSS_MULTIPLE_ROOTS: 18
  • KEEP_EXISTING_ROOT: 9

Critical Genes: new dismech anchors needed (top 15)

Gene Priority Actionable rows Worst status Primary action Note
DSP CRITICAL 7 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
FLNA CRITICAL 7 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
FGFR1 CRITICAL 5 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
PRPS1 CRITICAL 5 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
TGFBI CRITICAL 5 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
TP63 CRITICAL 5 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
ALDH18A1 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
ANK2 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
BEST1 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
COL11A2 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
CRB1 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
FOXE3 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
GJA1 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
KRT1 CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.
MITF CRITICAL 4 NO_DISMECH_MATCH ADD_FIRST_GENE_DISEASE_ANCHOR No dismech disease anchor currently represents this G2P row.

High-Priority Genes: split or underrepresented coverage (top 15)

Gene Priority Actionable rows Worst status Primary action Note
FGFR3 HIGH 8 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
FGFR2 HIGH 6 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
GJB2 HIGH 6 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
OFD1 HIGH 4 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
ATP1A2 HIGH 3 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
FMR1 HIGH 3 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
PRPH2 HIGH 3 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
SDHB HIGH 3 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
SMARCB1 HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
ATM HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
CARD14 HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
GABRA1 HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
HNF4A HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
MYOC HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.
NOTCH3 HIGH 2 UNDERREPRESENTED_IN_DISMECH ADD_MISSING_DISEASE_ROOT dismech has some direct roots for the gene, but this disease row is still missing.

Medium-Priority Genes: embedded concepts or PMID backfill (top 15)

Gene Priority Actionable rows Worst status Primary action Note
COL2A1 MEDIUM 6 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
KCNQ1 MEDIUM 5 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
RET MEDIUM 5 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
COL1A1 MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
FBN1 MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
KCNJ2 MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
LZTR1 MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
NKX2-5 MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
SCN5A MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
SOX10 MEDIUM 4 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
ATP7A MEDIUM 3 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
BRAF MEDIUM 3 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
CACNA1C MEDIUM 3 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
GNAS MEDIUM 3 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.
LRP5 MEDIUM 3 EMBEDDED_NOT_ROOTED REVIEW_NON_ROOT_GENE_MENTION Gene appears only in non-root mechanistic or secondary contexts.

Low-Priority Genes: existing roots already usable (top 9)

Gene Priority Actionable rows Worst status Primary action Note
ARID1B LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Coffin_Siris_Syndrome.yaml already provides a usable direct disease root.
CFL2 LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Nemaline_Myopathy.yaml already provides a usable direct disease root.
CPLANE1 LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Joubert_syndrome.yaml already provides a usable direct disease root.
EHMT1 LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Kleefstra_Syndrome.yaml already provides a usable direct disease root.
GFAP LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Alexander_Disease.yaml already provides a usable direct disease root.
KDM6A LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Kabuki_Syndrome.yaml already provides a usable direct disease root.
P4HTM LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT HIDEA_Syndrome.yaml already provides a usable direct disease root.
RPGRIP1L LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Meckel_Syndrome.yaml already provides a usable direct disease root.
RPS19 LOW 0 ROOT_MATCH KEEP_EXISTING_ROOT Diamond-Blackfan_Anemia.yaml already provides a usable direct disease root.