Oncofusion

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Proteinstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q5c-interactome2

CDC73 / parafibromin — the PAF1C subunit that was genetically tested, and a second tumour suppressor required by the fusion

also called CDC73 · parafibromin · HRPT2 · hyperparathyroidism 2 protein

CDC73 is one of the four proteins in the PAF1 machine, and it is the only one that has actually been deleted in mice to prove the machine is needed for KMT2A-fusion leukemia. Like menin, it is also a tumour suppressor whose loss causes a parathyroid disease in humans, which is a pattern worth noticing.

The same thing, for a scientist

CDC73 (Q6P1J9, 531 aa) encodes parafibromin, a core PAF1C subunit. Conditional Cdc73 deletion is the genetic evidence that PAFc is required in MLL-fusion AML, and the same work showed that disrupting the MLL-PAFc interface is selective and HSC-sparing. CDC73 is DepMap common-essential (mean Chronos -1.12, depleted in 98.7% of lines), heavily constrained in humans (LOEUF 0.361, pLI ~1.0), and germline loss causes hyperparathyroidism-jaw tumour syndrome. The parallel with MEN1 -- a tumour suppressor of the parathyroid that a leukemia cannot do without -- is the most interesting thing about this entry.

What it looks like
CDC73531 aa
Nuclear localization signal · residues 125–1390200400
loading AF-Q6P1J9-F1…
AlphaFold AF-Q6P1J9-F1 ↗
colourshape

This is a prediction, not a measurement. No one has seen this protein in this shape. The colours say how much the software trusts itself, and that is worth reading before anything else — the orange stretches are places the model is effectively saying this part has no fixed shape.

very high (90+)confident (70–90)low (50–70)very low (<50)
I have never read one of these pictures before

A protein is one long chain of amino acids that folds up. The ribbon traces that chain from one end to the other; it is not a wire, it is a simplification of where the backbone runs. Drag to rotate, scroll to zoom.

Domains are the stretches of chain that do a particular job, and they are what the coloured blocks above the picture mark out. Click one and the view flies to it. In this project the important question about any domain is usually whether the fusion still has it — the labels say lost where it does not.

Anything in yellow sticks is a bound small molecule, which is usually the drug.

Go deeper
The parathyroid parallel is not a coincidence worth ignoring

This graph has already worked hard on the paradox that menin is a parathyroid tumour suppressor and simultaneously an obligate cofactor for KMT2A-fusion leukemia. CDC73 is the same shape of object. Germline CDC73/HRPT2 loss causes hyperparathyroidism-jaw tumour syndrome, and the protein it encodes is called parafibromin for that reason. Yet CDC73 sits in a complex the fusion requires.

Two tumour suppressors of the parathyroid, both physically engaged by the same oncogenic complex, both required by it. Either this is coincidence, or the KMT2A fusion is exploiting a module whose normal job involves restraining proliferation in tissues that are sensitive to exactly that restraint. This graph should record the observation even though it currently has no mechanism to explain it, because it is the kind of pattern that generates a hypothesis. We have not verified a primary citation for the CDC73 hyperparathyroidism-jaw tumour association in this entry and therefore state it as background rather than as evidence.

The one PAF1C subunit with in vivo genetics

Of the five PAF1C subunits, CDC73 is the one that was conditionally deleted to test the complex's requirement. Deletion blocks AML cell proliferation. Crucially, the same study showed PAFc is required indiscriminately across AML — it is not MLL-selective — while disruption of the MLL–PAFc interface selectively inhibits MLL-fusion AML and does not impair normal HSC function 1.

A later paper from the same group showed PAFc regulates Prmt5 to facilitate progression and maintenance of MLL-fusion leukemia 2, and another showed the PAF1/SETDB1 axis repressing HOXA9 and MEIS1 3. PAFc's relationship to the output programme is therefore bidirectional, and CDC73 participates in both arms.

Dependency and tolerability

CDC73 is DepMap common-essential: mean Chronos -1.122, leukemia -1.135, depleted in 98.7% of 1,258 lines 4. Leukemia-restricted correlation with MEN1 is -0.076, crossing zero 5. No window in the protein.

gnomAD: pLI ~1.0, LOEUF 0.361, 21 observed against 83.7 expected loss-of-function variants 4. Strongly constrained, with a well-powered estimate. Expression is flat and low: bone marrow 8.4, thymus 9.9, liver 8.6 nTPM, and notably 0.5 nTPM in both classical monocytes and naive B cells 4.

Structure: two high-resolution crystal structures of the N-terminal region, 5YDE (residues 1–111, 1.02 Å) and 5YDF (residues 1–100, 1.40 Å), plus resolution within Pol II elongation-complex cryo-EM maps (6TED, 7OPC, 8A3Y) 6. A 1.02 Å structure of a tumour-suppressor N-terminus is unusually good starting material if anyone wanted to interrogate that surface.

Facts and figures
uniprotQ6P1J9
gene symbolCDC73
ensemblENSG00000134371
length AA531
alphafold IDAF-Q6P1J9-F1
complexPAF1C (PAF1, CTR9, LEO1, CDC73, WDR61)
rolePAF1C subunit; the one genetically tested in MLL-fusion AML. Also a germline tumour suppressor (hyperparathyroidism-jaw tumour syndrome; stated as background, not verified in this entry).
druggabilityNone in the protein, which is pan-essential. The MLL-PAFc interface is the tractable object and CDC73 is not known to be the subunit that makes that contact.
subnuclear localizationNUCLEOLUS - the best-evidenced subnuclear assignment for any PAF1C subunit in this graph, and it disagrees with the only other one. Three nucleolar localization signals are mapped (76-92, 192-194, 393-409), the bipartite NLS at 125-139 does not confer the nucleolar pool, and the nucleolar pool is separately lost in human parathyroid carcinomas carrying HRPT2 mutations predicted to abolish those three signals while nuclear parafibromin is retained [E_q95_cdc73_loc2][E_q95_cdc73_loc3]. AGAINST THIS: in budding yeast, wild-type Paf1C including Cdc73 is nucleoplasmic and NUCLEOLUS-EXCLUDED, and entering the nucleolus is what happens when the complex is pulled off Pol II (PMID 15643076, recorded on gene-ctr9 by tranche 5). The reconciliation this graph should carry until somebody tests it: the nucleolar parafibromin pool is the pool that is NOT in PAF1C. Do not write 'PAF1C is nucleolar'.
localization shown for fusionNO, in the strict sense - nobody has measured where CDC73 or parafibromin sits in any cell carrying any KMT2A fusion, and the bound is tight: 0 records for the gene clause against a localisation clause AND the fusion clause, and 0 against a subnuclear clause AND the fusion clause, from operand controls of 656 for the gene clause and 4 for the gene-fusion intersection [E_q95_cdc73_loc5]. What makes this absence unusually cheap to close: CDC73 is the PAF1C subunit that HAS been conditionally deleted in MLL-fusion AML, so the mouse and the cells already exist.
identifier note q95Rule 62 hazard already in the registry for the neighbouring subunit: gene_exact:PAF1 returns TWO reviewed human records (Q8N7H5 PAF1 531 aa and P28328 PEX2 305 aa). CDC73 itself is clean - Q6P1J9, 531 aa, primary gene CDC73, synonyms C1orf28 and HRPT2 - but note that CDC73 and PAF1 are BOTH 531 residues, so the length check in verify-accessions.py cannot separate two subunits of the same complex from one another. Verified live 2026-09-22.
PDB verified
[
  "5YDE",
  "5YDF"
]
PDB IDS
[
  "5YDE",
  "5YDF",
  "6TED",
  "7OOP",
  "7OPC",
  "7OPD",
  "7UNC",
  "7UND",
  "8A3Y"
]
domains
[
  {
    "name": "Nuclear localization signal",
    "start": 125,
    "end": 139,
    "pfam": null
  }
]
essentiality
{
  "depmap_common_essential": true,
  "chronos_mean": -1.1215,
  "chronos_mean_leukemia_lines": -1.1348,
  "n_lines": 1258,
  "fraction_lines_depleted": 0.9868,
  "gnomad_pLI": 1,
  "gnomad_loeuf": 0.3613,
  "gnomad_obs_lof": 21,
  "gnomad_exp_lof": 83.7,
  "mouse_ko": "Conditional Cdc73 deletion blocks AML cell proliferation; germline knockout phenotype not verified in this entry",
  "hpa_ntpm": {
    "thymus": 9.9,
    "liver": 8.6,
    "bone_marrow": 8.4,
    "spleen": 8.1,
    "lymph_node": 7,
    "heart_muscle": 6.3,
    "testis": 4.8,
    "classical_monocyte": 0.5,
    "naive_B_cell": 0.5
  },
  "hpa_specificity": "Low tissue specificity"
}
codependency men1
{
  "r_leukemia_lines": -0.0762,
  "ci_leukemia": [
    -0.3063,
    0.1504
  ],
  "crosses_zero": true,
  "p_permutation": 0.59388
}
depmap kmt2a selectivity
{
  "chronos_mean_kmt2a_rearranged": -1.1766,
  "chronos_mean_other_leukaemia": -1.1962,
  "difference": 0.0195,
  "pan_essentiality_all_lines": -1.1215,
  "selectivity_rank": 11645,
  "rank_denominator": 17728,
  "provenance": "Joined 2026-09-21 from analyses/depmap-kmt2a-selective-scan-full (generated 2026-09-19T10:12:06Z), the project's own genome-wide scan over 11 KMT2A-rearranged and 43 other leukaemia DepMap lines. NOT re-fetched and NOT independent of that scan: every caveat it carries applies here, including that the KMT2A-rearranged arm is a small number of lines drawn from nine individuals, that the rank denominator is 17,728 genes, and that a difference is not a dependency. Added because only 26 of 308 gene entries carried this number, which made any KMT2A-selectivity question answerable for 8% of the corpus.",
  "how_to_read": "A negative difference means MORE required in KMT2A-rearranged lines than in other leukaemia lines. A rank near 17,728 is ANTI-selective. Neither is evidence of a fusion-driven dependency on its own: check pan_essentiality_all_lines before calling anything selective, and note that a paralogue-redundant gene can score near zero for reasons that have nothing to do with this disease - see ana-the-paralogue-redundancy-excuse-is-not-tested-and-my-proxy-decided-the-answer."
}
localization
{
  "CONSTITUTIVE": "NUCLEUS AND NUCLEOLUS, and the two are separately addressed. UniProt Q6P1J9 (fetched live 2026-09-22) carries one value, 'Nucleus', on three ECO:0000269 - PubMed 15580289, 15632063 and 15923622, all 2005 papers on parafibromin's PAF1-complex membership and cyclin D1 regulation - plus a bipartite NLS mapped at residues 125-139 [E_q95_cdc73_loc1]. The record carries NO nucleolar term, and the nucleolar pool is mapped to three separate NoLS at 76-92, 192-194 and 393-409 [E_q95_cdc73_loc2].",
  "determinants": "NLS 125-139 governs nuclear entry and does NOT mediate nucleolar localisation; the three NoLS govern the nucleolar pool and contribute only minimally to nuclear localisation. Two addresses, two signal sets, one protein [E_q95_cdc73_loc2].",
  "how_shown": "deletion and point mutagenesis of transfected constructs for the signal map [E_q95_cdc73_loc2]; high-power immunohistochemistry of 82 human parathyroid tumours for the endogenous nucleolar pool [E_q95_cdc73_loc3]; co-immunoprecipitation plus subcellular localisation of the germline L95P mutant [E_q95_cdc73_loc3].",
  "systems": "transfected cell lines, NIH-3T3, HEK293, and human parathyroid carcinoma and adenoma tissue. NOTHING HAEMATOPOIETIC AND NOTHING LEUKAEMIC."
}
cell type
{
  "measured_in": "HAEMATOPOIETIC, in mouse, and by requirement rather than by imaging. CDC73 is required for fetal and adult haematopoiesis; loss in haematopoietic cells is lethal through bone marrow failure, and the requirement is cell-autonomous in the adult HSC in vivo [E_q95_cdc73_loc4]. For LOCALISATION the cell types are parathyroid tumour tissue, NIH-3T3 and HEK293 - no haematopoietic cell has ever been imaged for this protein [E_q95_cdc73_loc2][E_q95_cdc73_loc3].",
  "expression": "HPA low tissue specificity; bone marrow 8.4 nTPM, thymus 9.9, and notably LOW in mature blood cells (classical monocyte 0.5, naive B cell 0.5) - a progenitor-weighted profile, already recorded in this entry's essentiality block.",
  "the_split_that_matters": "the one cell type with a requirement measurement (mouse HSC) and the cell types with a compartment measurement (parathyroid, fibroblast, HEK293) do not overlap at all."
}
cell state
{
  "SELF_RENEWAL": "CDC73 regulates self-renewal gene programmes and does so DIFFERENTLY in normal progenitors and in AML cells: the Hoxa9/Meis1 programme is differentially regulated between the two, which the authors read as a disease-specific function [E_q95_cdc73_loc4]. Maps to cell-state-stem-like-self-renewal.",
  "CELL_CYCLE": "Cdc73 deletion produces cell-cycle defects in haematopoietic progenitors [E_q95_cdc73_loc4]. Separately, the nucleolar pool is the one whose loss confers a growth phenotype: the L95P mutant that cannot reach the nucleolus enhances cell-cycle progression and survival by dominant interference [E_q95_cdc73_loc3].",
  "state_dependence_of_the_COMPARTMENT": "UNMEASURED in any mammalian cell. The only conditional relocalisation of a Paf1C subunit anywhere is the yeast result where dissociation from Pol II admits the complex to the nucleolus; nobody has asked whether human parafibromin's nucleolar fraction changes with proliferative state, differentiation or transcription inhibition."
}
localization bounded absence
{
  "date": "2026-09-22",
  "tool": "NCBI E-utilities esearch, db=pubmed",
  "run_by": "Q95",
  "shape": "one [tiab] tag per term (brief rule 94); every cytogenetic term quoted (brief rule 95); querytranslation read back and stored beside every count (brief rule 90)",
  "absence_class": "never-measured",
  "queries": {
    "gene_clause_alone": {
      "query": "CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]",
      "count": 656,
      "querytranslation": "\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]"
    },
    "gene_AND_loc": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (localization[tiab] OR localisation[tiab] OR subcellular[tiab] OR immunofluorescence[tiab] OR nuclear[tiab] OR cytoplasmic[tiab] OR compartment[tiab])",
      "count": 100,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"localization\"[Title/Abstract] OR \"localisation\"[Title/Abstract] OR \"subcellular\"[Title/Abstract] OR \"immunofluorescence\"[Title/Abstract] OR \"nuclear\"[Title/Abstract] OR \"cytoplasmic\"[Title/Abstract] OR \"compartment\"[Title/Abstract])"
    },
    "gene_AND_subnuclear": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (\"nuclear speckle\"[tiab] OR \"nuclear speckles\"[tiab] OR nucleolus[tiab] OR nucleolar[tiab] OR \"PML body\"[tiab] OR \"PML bodies\"[tiab] OR \"nuclear matrix\"[tiab] OR \"Polycomb bodies\"[tiab] OR \"Polycomb body\"[tiab] OR subnuclear[tiab] OR \"nuclear bodies\"[tiab] OR \"nuclear body\"[tiab] OR chromocent*[tiab] OR heterochromat*[tiab])",
      "count": 10,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"nuclear speckle\"[Title/Abstract] OR \"nuclear speckles\"[Title/Abstract] OR \"nucleolus\"[Title/Abstract] OR \"nucleolar\"[Title/Abstract] OR \"PML body\"[Title/Abstract] OR \"PML bodies\"[Title/Abstract] OR \"nuclear matrix\"[Title/Abstract] OR \"Polycomb bodies\"[Title/Abstract] OR \"Polycomb body\"[Title/Abstract] OR \"subnuclear\"[Title/Abstract] OR \"nuclear bodies\"[Title/Abstract] OR \"nuclear body\"[Title/Abstract] OR \"chromocent*\"[Title/Abstract] OR \"heterochromat*\"[Title/Abstract])"
    },
    "gene_AND_fusion": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL1\"[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab] OR \"MLL-ENL\"[tiab] OR \"MLL-AF10\"[tiab] OR \"t(4;11)\"[tiab] OR \"t(11;19)\"[tiab])",
      "count": 4,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL1\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract] OR \"MLL-ENL\"[Title/Abstract] OR \"MLL-AF10\"[Title/Abstract] OR \"t 4 11\"[Title/Abstract] OR \"t 11 19\"[Title/Abstract])"
    },
    "gene_AND_loc_AND_fusion": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (localization[tiab] OR localisation[tiab] OR subcellular[tiab] OR immunofluorescence[tiab] OR nuclear[tiab] OR cytoplasmic[tiab] OR compartment[tiab]) AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL1\"[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab] OR \"MLL-ENL\"[tiab] OR \"MLL-AF10\"[tiab] OR \"t(4;11)\"[tiab] OR \"t(11;19)\"[tiab])",
      "count": 0,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"localization\"[Title/Abstract] OR \"localisation\"[Title/Abstract] OR \"subcellular\"[Title/Abstract] OR \"immunofluorescence\"[Title/Abstract] OR \"nuclear\"[Title/Abstract] OR \"cytoplasmic\"[Title/Abstract] OR \"compartment\"[Title/Abstract]) AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL1\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract] OR \"MLL-ENL\"[Title/Abstract] OR \"MLL-AF10\"[Title/Abstract] OR \"t 4 11\"[Title/Abstract] OR \"t 11 19\"[Title/Abstract])"
    },
    "gene_AND_subnuclear_AND_fusion": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (\"nuclear speckle\"[tiab] OR \"nuclear speckles\"[tiab] OR nucleolus[tiab] OR nucleolar[tiab] OR \"PML body\"[tiab] OR \"PML bodies\"[tiab] OR \"nuclear matrix\"[tiab] OR \"Polycomb bodies\"[tiab] OR \"Polycomb body\"[tiab] OR subnuclear[tiab] OR \"nuclear bodies\"[tiab] OR \"nuclear body\"[tiab] OR chromocent*[tiab] OR heterochromat*[tiab]) AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL1\"[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab] OR \"MLL-ENL\"[tiab] OR \"MLL-AF10\"[tiab] OR \"t(4;11)\"[tiab] OR \"t(11;19)\"[tiab])",
      "count": 0,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"nuclear speckle\"[Title/Abstract] OR \"nuclear speckles\"[Title/Abstract] OR \"nucleolus\"[Title/Abstract] OR \"nucleolar\"[Title/Abstract] OR \"PML body\"[Title/Abstract] OR \"PML bodies\"[Title/Abstract] OR \"nuclear matrix\"[Title/Abstract] OR \"Polycomb bodies\"[Title/Abstract] OR \"Polycomb body\"[Title/Abstract] OR \"subnuclear\"[Title/Abstract] OR \"nuclear bodies\"[Title/Abstract] OR \"nuclear body\"[Title/Abstract] OR \"chromocent*\"[Title/Abstract] OR \"heterochromat*\"[Title/Abstract]) AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL1\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract] OR \"MLL-ENL\"[Title/Abstract] OR \"MLL-AF10\"[Title/Abstract] OR \"t 4 11\"[Title/Abstract] OR \"t 11 19\"[Title/Abstract])"
    },
    "cdc73_nucleolar": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (nucleolus[tiab] OR nucleolar[tiab])",
      "count": 8,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"nucleolus\"[Title/Abstract] OR \"nucleolar\"[Title/Abstract])"
    },
    "cdc73_speckle": {
      "query": "(CDC73[tiab] OR HRPT2[tiab] OR parafibromin[tiab]) AND (\"nuclear speckle\"[tiab] OR \"nuclear speckles\"[tiab] OR speckles[tiab])",
      "count": 0,
      "querytranslation": "(\"CDC73\"[Title/Abstract] OR \"HRPT2\"[Title/Abstract] OR \"parafibromin\"[Title/Abstract]) AND (\"nuclear speckle\"[Title/Abstract] OR \"nuclear speckles\"[Title/Abstract] OR \"speckles\"[Title/Abstract])"
    }
  },
  "title_check": "cdc73_nucleolar, 8 records: 6 are the parafibromin nucleolar literature (17923126, 24340015, 24842573, 21221636, 20304979 and the 2005 yeast Paf1C subnuclear paper 15643076), 2 are parathyroid-tumour reviews. This is the one gene in the tranche where the 'nucleolar' token was NOT contaminated.",
  "aliases_searched": [
    "CDC73",
    "HRPT2",
    "parafibromin"
  ],
  "aliases_not_searched": [
    "C1orf28 - a positional symbol with no literature of its own"
  ]
}
How this could bite us back
  • Essential-function toxicity: CDC73 is required by 98.7% of cell lines. Degrading or inhibiting the protein is not a therapeutic option.
  • Tumour-suppressor risk: CDC73 is a germline tumour suppressor. Chronic partial inhibition in a child raises the same unanswered second-cancer question this graph has already raised for menin, and with even less data.
  • The validated reagent is a dominant-negative fragment, so the entire selectivity argument for MLL-PAFc rests on a tool that cannot be given to a patient.
Still open
  1. Why are two parathyroid tumour suppressors, menin and parafibromin, both required by KMT2A-fusion leukemia? If this is not coincidence it implies a shared restraining function that the fusion subverts, and nobody appears to have asked the question.
  2. Which PAF1C subunit makes the direct contact with the MLL CxxC-flanking region? The interface is genetically validated as a selective target but its subunit-level geometry is undefined, which blocks any structure-based campaign.
  3. Does menin inhibition alter PAFc occupancy at fusion target loci, or vice versa? Two selective interfaces on the same fusion protein are the natural orthogonal combination this project has been looking for, and their interaction is untested.
Every source behind this entry (11)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Conditional Cdc73 deletion blocks AML cell proliferation and establishes the PAF1 complex as required in MLL-fusion AML, while targeted disruption of the MLL-PAFc interaction selectively inhibits MLL-fusion-driven AML without impairing normal haematopoietic stem cell function.

    MLL fusion protein-driven AML is selectively inhibited by targeted disruption of the MLL-PAFc interaction. · Muntean AG, Chen W, Jones M, Granowicz EM, Maillard I, Hess JL · Blood 2013
    What this evidence cannot show

    Mouse AML models and a dominant-negative protein fragment, not infant KMT2A::AFF1 B-ALL and not a drug. The paper states PAFc is required indiscriminately for AML proliferation, so CDC73 loss is not a selective intervention; only the interface is.

    Evidence that argues against this (1)
    • CDC73/parafibromin is a bona fide germline tumour suppressor, which is the reason a CDC73-directed intervention cannot be pursued as written. Thirteen distinct heterozygous germline inactivating mutations were identified in fourteen families with hyperparathyroidism-jaw tumour syndrome, and three somatic inactivating mutations were found among 48 parathyroid adenomas, none in normal controls. The entry acknowledges this framing, but the constraint deserves a resolvable citation attached to the evidence item that asserts the dependency: a compound that reduces CDC73 function is a compound that phenocopies a cancer predisposition allele. Carpten JD et al. 2002
  2. E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    The PAF complex regulates Prmt5 to facilitate the progression and maintenance of MLL-fusion leukemia.

    The PAF complex regulation of Prmt5 facilitates the progression and maintenance of MLL fusion leukemia. · Serio J, Ropa J, Chen W, Mysliwski M, Saha N, Chen L, Wang J, Miao H, Cierpicki T, Grembecka J, Muntean AG · Oncogene 2018
    What this evidence cannot show

    This paper concerns PRMT5, which is a different enzyme from PRMT1; the two are easily conflated in this literature and should not be. Mouse and cell-line models.

    Evidence that argues against this (1)
    • Read this evidence item with the disambiguation that PRMT5 is not PRMT1. The PAF-complex regulation described here is of PRMT5, a type II arginine methyltransferase with a different substrate specificity and a separate inhibitor pipeline, and the same paper is carried in gene-prmt1 E3 explicitly as a disambiguation warning because the two enzymes are routinely conflated in the MLL literature. Anyone building a CDC73-to-arginine-methylation argument from this item should not carry it across to PRMT1, whose case in MLL-fusion leukemia rests on MLL-EEN and on FLT3 methylation, both different mechanisms. Zhu Y et al. 2019
  3. E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of HOXA9 and MEIS1.

    PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia. · Ropa J, Saha N, Chen Z, Serio J, Chen W, Mellacheruvu D, Zhao L, Basrur V, Nesvizhskii AI, Muntean AG · Oncotarget 2018
    What this evidence cannot show

    Oncotarget, weaker editorial reputation. Demonstrated in AML models; the relative weight of the repressive arm in B-ALL is unknown.

    Evidence that argues against this (1)
    • This is PAF1-complex biology acting to REPRESS HOXA9 and MEIS1 through SETDB1, which is the opposite direction from the fusion's programme. An entry placing CDC73 in a fusion interactome has to say which role it is claiming. Cell Reports 2014
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    CDC73 is DepMap common-essential with mean Chronos -1.122 across 1,258 lines and depletion in 98.7% of lines; gnomAD reports pLI ~1.0 and LOEUF 0.361 with 21 observed against 83.7 expected loss-of-function variants; HPA reports low tissue specificity with bone marrow 8.4 nTPM and 0.5 nTPM in classical monocytes and naive B cells.

    What this evidence cannot show

    DepMap release version not stated by the API. Strong LoF constraint in a gene that is also a classical tumour suppressor is expected and does not by itself indicate intolerance to partial pharmacological inhibition.

    Evidence that argues against this (1)
    • CTR9 is a germline tumour suppressor in a childhood cancer, which is a hard constraint on treating it as a target in paediatric leukemia. Inactivating germline CTR9 mutations were found in 3 of 35 Wilms tumour families by exome and Sanger sequencing and in none of 1,000 population controls (P < 0.0001); each mutation segregated with disease and a second mutational event was present in the available tumours, establishing CTR9 as a Wilms tumour predisposition gene acting as a tumour suppressor. A second family with a novel splice-acceptor CTR9 germline variant and tumour loss of heterozygosity was reported subsequently (PMID 29292210). Whatever CTR9 contributes to the MLL-PAFc interaction, pharmacologically reducing CTR9 function in a child is reducing a tumour suppressor. Hanks S et al. 2014
  5. E5moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset

    Across 54 DepMap leukemia lines CDC73 correlates with MEN1 at r = -0.076, confidence interval -0.306 to 0.150, crossing zero.

    Leukemia-restricted co-dependency with MEN1, bootstrap and permutation testing; analyses/wrad-discrimination/ in this project · Broad Institute DepMap; Open Targets Platform; analysis run by this project · Database and derived analysis 2026
    What this evidence cannot show

    Our own computation in 54 lines. A pan-essential gene has no variance to correlate, so this null is uninformative about biology.

    Evidence that argues against this (1)
  6. E6established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    Two high-resolution crystal structures of the CDC73 N-terminal region exist, 5YDE (residues 1-111, 1.02 A) and 5YDF (residues 1-100, 1.40 A), and CDC73 is additionally resolved within Pol II elongation-complex cryo-EM structures.

    What this evidence cannot show

    These entries cover only the first ~110 residues of a 531-residue protein; the bulk of CDC73 including any MLL-proximal surface is not covered by an isolated high-resolution structure.

    Evidence that argues against this (1)
    • Counting PDB entries measures how tractable a protein was to CRYSTALLISE, which correlates with being small, ordered and well-behaved rather than with being druggable. What decides design value is whether the deposited density covers the site that matters, at a resolution that supports modelling, in the relevant state — and this graph has repeatedly found structures described in the direction that overstates what is resolved. 1.02 A and 1.40 A on the N-terminal 111 residues is superb data on a small fragment; CDC73 being otherwise resolved only inside cryo-EM elongation complexes means the rest of it has no independent structure. RCSB PDB 2026
  7. E_q95_cdc73_loc1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    UniProt Q6P1J9 carries exactly ONE subcellular location value for parafibromin - 'Nucleus', on three ECO:0000269 citations, all of them 2005 papers about PAF1-complex membership and cyclin D1 regulation - together with a mapped bipartite nuclear localization signal at residues 125-139, and it carries NO nucleolar term at all, although three nucleolar localization signals have been mapped in the protein and the nucleolar pool is separately measurable in human tumours.

    What this evidence cannot show

    This is a statement about the database record, not about the biology, and the direction of the defect is the OPPOSITE of the one this project usually finds. The three cited papers are real parafibromin papers and none of them is off-topic in the way UniProt's KMT2A or AFF4 citations are; what is missing is precision, not honesty. The feature table does carry the NLS, which is more than MEN1's record does.

    Evidence that argues against this (1)
    • ARGUING AGAINST TREATING THIS AS A DATABASE ERROR: one of the three cited papers is the paper that placed parafibromin in the human PAF1 complex, so 'Nucleus' is exactly the claim those papers support and a curator who wrote only what the cited experiments showed would write only 'Nucleus'. The sharper point is comparative. On CTR9, one subunit away in the same complex, UniProt's single value is the MORE precise 'Nucleus speckle' resting on a source whose own words are 'predominantly in the nucleus' - precision the record gained in transit. Here the record LOST precision that the literature has. Two subunits of one complex, two opposite failures, and only reading the cited papers separates them; no evidence-code filter distinguishes the two cases, because both are ECO:0000269. Rozenblatt-Rosen O et al. 2005
  8. E_q95_cdc73_loc2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Parafibromin's subnuclear address is the NUCLEOLUS, and it is determined by three nucleolar localization signals at residues 76-92, 192-194 and 393-409 that are clusters of arginine and lysine; the bipartite NLS at 125-139 is the primary determinant of NUCLEAR localisation and does not mediate nucleolar localisation, while the three NoLSs play only a minor role in nuclear localisation and are critical for the nucleolar pool - so the two compartments are separately addressed in one protein.

    What this evidence cannot show

    Signal mapping by mutagenesis of transfected constructs is a statement about DETERMINANTS rather than about where the endogenous protein sits, and the abstract does not name the cell line. Independent mapping of three NoLS mutations of CDC73 reaches the same three-signal architecture (PMID 24340015), and a separate missense mutant characterisation adds a fourth (PMID 24842573), so the determinant map is replicated; the endogenous confirmation comes from human tumour tissue and is recorded separately as this entry's nucleolar-loss evidence.

    Evidence that argues against this (1)
    • THIS CONTRADICTS THE ONLY OTHER SUBNUCLEAR MEASUREMENT OF THIS COMPLEX IN THIS GRAPH, AND THE CONTRADICTION IS THE INTERESTING PART. Tranche 5 recorded, on gene-ctr9, that in budding yeast all five wild-type Paf1C components - Paf1, Ctr9, Cdc73, Rtf1 and Leo1 - are present in the NUCLEOPLASM BUT NOT THE NUCLEOLUS, and that pulling the complex off Pol II by paf1 or rtf1 loss is what ADMITS it to the nucleolus. Human parafibromin instead carries three constitutive nucleolar addressing signals. The two results are reconcilable in exactly one way that is testable: the nucleolar parafibromin pool is the pool NOT in Paf1C. The yeast paper measured the complex, the NoLS papers measured the subunit, and the experiment nobody has done is to ask whether nucleolar parafibromin co-purifies with PAF1, CTR9 and LEO1 or with none of them. Until that is done, this graph should not write 'PAF1C is nucleolar'. Porter SE et al. 2005
  9. E_q95_cdc73_loc3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    The nucleolar pool of parafibromin is separately lost in human disease tissue: nucleolar parafibromin immunoreactivity was ABSENT in three of 23 parathyroid carcinomas and one of 16 atypical adenomas scored by high-power microscopy in 82 tumours, all three carcinomas carried HRPT2/CDC73-inactivating mutations predicted to abolish the three nucleolar localization signals, and in those tumours NUCLEAR parafibromin was still expressed - so the nucleolar compartment can be lost while the nuclear compartment is retained.

    Absence of nucleolar parafibromin immunoreactivity in subsets of parathyroid malignant tumours. · Juhlin CC, Haglund F, Obara T, Arnold A, Larsson C, Höög A · Virchows Arch 2011
    What this evidence cannot show

    Immunohistochemistry on parathyroid tumours, n = 4 positive events out of 82 tumours, so the event is rare and the study is an antibody-scoring study rather than a mechanistic one; brief rule 74 applies in that the clone determines what could be seen, and the abstract does not name it. The germline-mutant arm supplies the mechanism independently (PMID 20304979): a HPT-JT L95P missense mutant is markedly deficient in nucleolar localisation, still assembles with endogenous PAF1 complex components by co-immunoprecipitation, and acquires a growth-stimulatory dominant-interfering phenotype in NIH-3T3 and HEK293.

    Evidence that argues against this (1)
    • THE SYSTEM IS WRONG FOR THIS GRAPH AND THAT HAS TO BE SAID IN THE CLAIM, NOT ONLY HERE (brief rule 73): every endogenous measurement of nucleolar parafibromin is in PARATHYROID tissue, in an endocrine tumour syndrome, and the mechanistic arm is in NIH-3T3 fibroblasts and HEK293. There is no haematopoietic cell of any kind in the nucleolar literature for this protein. The countervailing consideration is that it is the same allele series in both arms - mutations abolishing the same three NoLS - which is a stronger form of agreement than two independent systems reporting the same compartment, because the genotype is doing the work. But a nucleolar tumour-suppressor function established in parathyroid cells cannot be assumed in a KMT2A-rearranged blast, where the nucleolar/ribosome-biogenesis module is the single most enriched complex in the fusion interactome and the nucleolar biology may therefore be under completely different control. Panicker LM et al. 2010
  10. E_q95_cdc73_loc4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    CDC73's cell type and cell state are measured, and in mouse rather than human: CDC73 is required for both fetal and adult haematopoiesis, loss of Cdc73 in haematopoietic cells is lethal through extensive bone marrow failure, it has an essential cell-autonomous role for adult haematopoietic stem cell function in vivo, its deletion causes cell-cycle defects in haematopoietic progenitors, and expression profiling shows DIFFERENTIAL regulation of the Hoxa9/Meis1 programme in progenitors compared with AML cells - a leukaemia-specific regulation of self-renewal genes inside a gene the normal stem cell also needs.

    The PAF1c Subunit CDC73 Is Required for Mouse Hematopoietic Stem Cell Maintenance but Displays Leukemia-Specific Gene Regulation. · Saha N, Ropa J, Chen L, Hu H, Mysliwski M, Friedman A, Maillard I, Muntean AG · Stem Cell Reports 2019
    What this evidence cannot show

    Mouse conditional knockout, and the leukaemia arm is MLL-fusion AML rather than infant B-lineage KMT2A::AFF1, so both halves of the result are imported. No compartment was measured in either arm - this is a requirement and gene-expression result, and it is recorded under cell type and cell state rather than localisation for that reason.

    Evidence that argues against this (1)
    • THIS RESULT ARGUES AGAINST TARGETING CDC73 AND THE ENTRY SHOULD NOT READ AS THOUGH A LEUKAEMIA-SPECIFIC GENE PROGRAMME IMPLIED A THERAPEUTIC WINDOW. The same paper that reports leukaemia-specific regulation reports that Cdc73 loss is LETHAL through bone marrow failure and is cell-autonomously required by the adult HSC, and DepMap has CDC73 depleted in 98.7% of 1,258 lines at a mean Chronos of -1.12, which is among the most floor-compressed values in this graph. So the 'window' is a difference in which genes move, in a cell that dies either way. The germline data point the same direction: CDC73 is a tumour-suppressor gene in humans, so reducing its function pharmacologically in a child is reducing a tumour suppressor - the identical objection tranche 5 recorded for CTR9 and Wilms tumour, now the second PAF1C subunit in this graph to carry it. Juhlin CC et al. 2011
  11. E_q95_cdc73_loc5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    Bounded 2026-09-22: no localisation measurement of CDC73 exists in any KMT2A-fusion context. The gene clause over CDC73, HRPT2 and parafibromin returns 656 records and the nine-term KMT2A/MLL fusion clause intersects it at 4; the gene clause with a localisation clause returns 100 and with the fusion clause added returns 0; the gene clause with a subnuclear clause returns 10 and with the fusion clause added returns 0. The nucleolar sub-query returns 8 records of which 6 are the parafibromin nucleolar literature itself and none is in a leukaemic cell, and the speckle sub-query returns 0.

    What this evidence cannot show

    Titles and abstracts only; supporting figures were not searched, which matters here because brief rule 80's worked example is exactly a compartment measurement living in a figure panel. One tag per term and every count stored with its querytranslation. Rule 64 was applied and changes the reading: the complex form is what reaches this protein's real subnuclear literature at all - the yeast Paf1C paper that measures Cdc73 has no CDC73 symbol in its title - so the zero bounds the SUBUNIT-plus-fusion literature and not the question.

    Evidence that argues against this (1)
    • THE ZERO IS WEAKER THAN IT LOOKS IN ONE DIRECTION AND STRONGER IN ANOTHER, AND BOTH SHOULD BE STATED. Weaker: CDC73 is the PAF1C subunit that HAS been genetically tested in MLL-fusion AML, so a fusion-context zero on localisation sits inside a literature that is otherwise active on this exact gene and disease - the absence is of a compartment measurement, not of interest. Stronger: the nucleolar sub-query is the one query in this beat where the contaminated-token hazard the registry records for 'nucleolar' did NOT fire - 6 of 8 hits are genuinely about parafibromin nucleolar localisation, against 2 of 2 off-topic for USP8 and roughly 19 of 20 off-topic for CDK4 in this same tranche. A gene with its own real nucleolar literature is protected from that contamination by having enough true positives to see. Pazienza V et al. 2013
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