AFF1::KMT2A (AF4-MLL), the der(4) product: what it is made of, residue by residue

No three-dimensional model is available for this protein, so the map above is the whole picture. That is itself informative: AlphaFold does not model chains this long, and the parts that have been crystallised are held under the entries for the individual domains.

• This protein has no menin-binding motif at all, so a menin inhibitor cannot engage it at any dose. In a reciprocal-positive patient the drug addresses one of two KMT2A-derived oncoproteins by construction, and no eligibility criterion anywhere records which patients those are.
• It retains the WIN motif and the SET domain, so a WIN-site or SET inhibitor could in principle reach it - but the same modules on the wild-type KMT2A allele are identical in sequence, so selectivity would have to come from somewhere other than the target.
• A FYRC decoy aimed at breaking the heterodimer would break the wild-type KMT2A heterodimer too.
• If the reciprocal product is the initiator rather than the maintainer, a drug aimed at it is a prevention agent for a disease that presents already established - a translational path with no trial design behind it.

1. What is the actual residue at which AFF1 meets KMT2A in a given patient? UniProt annotates KMT2A breakpoint sites for five other partners and none for AFF1, and no paper this beat found states the junction residue for AFF1::KMT2A.
2. Has the reciprocal protein ever been detected in a patient blast, as opposed to a cell line or a transfected construct? Every clinical measurement on this axis is RT-PCR.
3. Does the AFF1 exon 1-3 fragment carry targeting information at all, or is the reciprocal protein positioned entirely by FYRN/FYRC heterodimerisation with a KMT2A-derived partner?
4. If PHD1 is truncated in the infant intron-11 version and intact in the intron-9/10 version, are these two functionally different oncoproteins that the literature has been pooling under one name?

1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   The reciprocal t(4;11) fusion gene AF4-MLL comprises AF4 exons 1-3 fused to MLL exons 12-37, the direct fusion comprises MLL exons 1-10 fused to AF4 exons 4-20, KMT2A breakpoints cluster in introns 9-11 (about 81%) and AF4 breakpoints in introns 3 and 4 (about 86%), and KMT2A intron 11 breaks - commonest in infant ALL - disrupt the first PHD finger of the reciprocal protein.

   The role of reciprocal fusions in MLL-r acute leukemia: studying the chromosomal translocation t(4;11). · Wilhelm A, Marschalek R · Oncogene 2021
   PMID 34489550DOI
   ▸What this evidence cannot show

   The exon composition describes cloned Sleeping Beauty constructs designed to model the infant intron-11 breakpoint, not a survey of patient transcripts; the functional experiments in the same paper are in HEK293T cells, which are neither haematopoietic nor leukaemic.

   ▸Evidence that argues against this (1)

   • The recombinome shows reciprocal allele structure is partner- and breakpoint-specific: about half of KMT2A::MLLT1 cases break upstream of the partner's first exon and make no reciprocal transcript at all, so no single exon formula generalises across KMT2A fusions. Meyer C et al. 2023
2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

   UniProt Q03164 places the KMT2A menin-binding motif at 6-25, LEDGF integrase-binding motifs IBM1 at 123-134 and IBM2 at 147-152, AT-hooks at 169-180, 217-227 and 301-309, the CXXC zinc finger at 1147-1195, recurrent translocation breakpoint sites at 1362/1363, 1406/1407 and 1444/1445, PHD1-3 at 1431-1482, 1479-1533 and 1566-1627, an H3K4me3-interaction region at 1584-1600, the bromodomain at 1635-1765, a C2HC pre-PHD zinc finger at 1870-1910, PHD4 at 1931-1978, FYRN at 2018-2074, Taspase1 cleavage sites at 2666/2667 and 2718/2719, a 9aaTAD at 2847-2855, FYRC at 3666-3747, the WIN motif at 3762-3767 with Arg3765 critical, the SET domain at 3829-3945 and post-SET at 3953-3969, in a 3,969-residue chain.

   UniProt Q03164 (KMT2A_HUMAN), feature table · UniProt Consortium · UniProtKB 2026
   ▸What this evidence cannot show

   Fetched from the UniProt REST record on 2026-09-19 with the primary gene name read back as KMT2A and length 3969. UniProt boundaries are curatorial and differ by a few residues from some structural papers - this graph stores the WIN motif as 3762-3773 where UniProt gives 3762-3767 for the motif proper. The annotated breakpoint sites are named for other partners (AFF4, GAS7, LPP, CENPK, FRYL); UniProt annotates no AFF1 breakpoint site, so these coordinates bound the join region rather than pinpoint it.

   ▸Evidence that argues against this (1)

   • A database annotation is opposable on scope: only about 16% of KMT2A has been observed experimentally and the breakpoint cluster region is almost all of what is missing, so boundaries in 1362-1445 are sequence-based curation rather than observed structure. PDBe 2026
3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

   UniProt P51825 annotates the AFF1 N-terminus as disordered (1-45) with a basic-and-acidic compositional bias at 9-35, and annotates no named domain anywhere before residue 601, in a 1,210-residue chain.

   UniProt P51825 (AFF1_HUMAN), feature table · UniProt Consortium · UniProtKB 2026
   ▸What this evidence cannot show

   Fetched 2026-09-19, primary gene name read back as AFF1, length 1210. Absence of an annotation is not absence of function: the AFF-family N-terminal homology domain is a literature construct defined by alignment rather than a UniProt feature, so silence here is a curation boundary, not a negative result.

   ▸Evidence that argues against this (1)

   • Only 42 of 1,210 AFF1 residues have been resolved experimentally, in PDB 2LM0 (AFF1 738-779 bound to the MLLT3 AHD), so neither presence nor absence of structure in the N-terminal region has been observed. RCSB PDB 2013
4. E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

   The N-terminal portion of AF4 mediates interaction with the E3 ubiquitin ligases SIAH1 and SIAH2, the AF4.MLL fusion protein is protected against proteasomal degradation by that route, and both AF4 wild-type and AF4.MLL show growth-transforming potential.

   Interaction of AF4 wild-type and AF4.MLL fusion protein with SIAH proteins: indication for t(4;11) pathobiology? · Bursen A, Moritz S, Gaussmann A, et al. · Oncogene 2004
   PMID 15221006DOI
   ▸What this evidence cannot show

   2004 transfection and degradation assays in non-haematopoietic cells; the transformation readout is growth-based rather than an in vivo leukaemia model, and the paper frames its own conclusion as an indication rather than a demonstration.

   ▸Evidence that argues against this (1)

   • The strongest published test of whether the reciprocal protein matters in a human t(4;11) cell found it dispensable: siRNA knockdown of AF4-MLL in RS4;11 and SEMK2-M1 had no effect on growth, cell cycle or apoptosis, while knockdown of MLL-AF4 inhibited growth in both. Kumar AR et al. 2011
5. E5moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

   Taspase1-mediated hydrolysis of AF4-MLL produces AF4-MLL-N and MLL-C fragments that heterodimerise through the FYRN and FYRC interaction domains, and expression of FYRC or smaller portions of it blocks heterodimer formation, prevents high-molecular-weight complex assembly and destroys the AF4-MLL oncoprotein.

   The heterodimerization domains of MLL-FYRN and FYRC--are potential target structures in t(4;11) leukemia. · Pless B, Oehm C, Knauer S, et al. · Leukemia 2011
   PMID 21233834DOI
   ▸What this evidence cannot show

   Bacterial two-hybrid and mammalian biosensor assays on over-expressed constructs; oncoprotein destruction is measured on transfected protein, not on an endogenous fusion in a patient-derived line, and no leukaemia model was treated with the decoy.

   ▸Evidence that argues against this (1)

   • The same cleavage and heterodimerisation chemistry applies to wild-type KMT2A, whose FYRN/FYRC pair and Taspase1 sites are the same sequence, so a FYRC decoy is not fusion-selective by construction. UniProt Consortium 2026

• ← analogous toThe reciprocal MLLT1::KMT2A transcript was reported in the paper that discovered KMT2A, and nobody has gone back to it in thirty-four years

  same class of product in t(4;11), where it has been cloned and characterised

• ← bindsDDX6 - the only protein ever proposed to do for a cell what Tat does for the virus, on the strength of one 2016 paper

  reported to be recruited by AF4-MLL, which carries the AF4N module

• ← related toThe two t(4;11) products split AFF1 exactly at the P-TEFb-binding module, and the elongation half goes to the reciprocal

  the reciprocal carries AFF1 1-346, including the cyclin T1-binding sequence

• part of →KMT2A / MLL1 — the gene that breaks

  Carries KMT2A residues from the breakpoint cluster region to 3969, including PHD1-4, bromodomain, FYRN, TAD, FYRC, WIN and SET.

• part of →AFF1 / AF4 — the 3' half of the fusion, and a target with almost no structural footing

  Carries AFF1 exons 1-3, the disordered N-terminus that binds SIAH1/2.

• co-occurs with →KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)

  The two products of one balanced t(4;11); complementary halves of KMT2A with no overlapping module.

• binds →WDR5 — the partner that is not a partner: it binds the half of KMT2A the fusion throws away

  Retains the WIN motif at 3762-3767 (Arg3765), the WDR5-binding element absent from the direct product.

• confers resistance to →MEN1 / menin — the adaptor the fusion cannot work without

  Lacks the menin-binding motif (KMT2A 6-25) entirely, so it is outside the reach of any menin-interface inhibitor.

• confers resistance to →PSIP1 / LEDGF p75 — the tether with the best therapeutic index in the whole interactome

  Lacks both LEDGF integrase-binding motifs (IBM1 123-134, IBM2 147-152).

• supports →Forty-five percent of t(4;11) patients express a KMT2A fusion transcript that keeps the whole WRAD interface

  Supplies the residue-level domain inventory behind that entry's WRAD-competence claim.

• supports →An anti-MLL-C antibody in a t(4;11) cell is looking at two proteins at once

  Both Taspase1 sites (2666/2667, 2718/2719) are retained, so the reciprocal releases a sequence-identical MLL-C fragment.

• arises in →Infant acute lymphoblastic leukaemia (ALL diagnosed under 1 year of age)

  Present in t(4;11) infant B-ALL, the commonest KMT2A rearrangement in that disease.

• ← regulatesTaspase1 is what turns the reciprocal product into an oncoprotein - and it is a conditional oncogene because of it

  Cleavage at KMT2A 2666/2667 and 2718/2719 converts a proteasome substrate into a long-lived complex; without it there is no reciprocal oncoprotein.

• ← part ofFYRN/FYRC: the clip that holds the cut reciprocal protein together, and the only fusion-adjacent interface anyone has tried to break with a decoy

  The interface that re-associates the two Taspase1 cleavage products of the reciprocal oncoprotein.

• ← regulatesSIAH1/SIAH2: the disposal route that destroys wild-type AF4 and that the reciprocal fusion escapes

  Sets the abundance of the reciprocal oncoprotein through the AFF1 N-terminal fragment it retains.

• ← regulatesThe infant breakpoint mutilates the reciprocal protein's first PHD finger - so 'the reciprocal product' is at least two different proteins

  Breakpoint position sets the reciprocal protein's N-terminal KMT2A boundary and whether PHD1 survives.

• ← expressed inAt the DNA level almost every KMT2A-rearranged patient has a reciprocal allele - 94% across partners, and 5% have nothing else

  Quantifies how often the reciprocal allele exists and how often it is transcribed.

• ← related toInfants whose leukaemia expresses the reciprocal fusion survive far better - 62.4% versus 11.7% event-free at four years

  The clinical outcome associated with expressing this protein, and it runs against the second-oncoprotein reading.

• ← related toAbout one KMT2A-rearranged patient in twenty has no direct fusion at all - only the reciprocal one

  The population in which the reciprocal product is the only KMT2A fusion present.

• ← regulatesCompeting model 1: the reciprocal product starts the leukaemia and then leaves

  Model in which this protein is required transiently to establish pre-leukaemic chromatin.

• ← regulatesCompeting model 2: the reciprocal allele is lost as the leukaemia evolves, and losing it selects for something worse

  Model for why the reciprocal product is absent in a large minority of patients.

• ← refutesCompeting model 4: t(4;11) cells are addicted to the direct fusion and completely indifferent to the reciprocal one

  The strongest published negative on this protein's role in established disease.

• ← part ofWhat the reciprocal product assembles: P-TEFb, an H3K4 methyltransferase, an H3K79 methyltransferase, an arginine methyltransferase and an acetyltransferase

  The multiprotein assembly the reciprocal oncoprotein nucleates.

• ← regulatesPut both fusion proteins in the same cell and you get something neither produces alone

  The reciprocal product's phenotype is reported only in combination with the direct one.

• ← related toA tested negative: neither fusion product alters DNA double-strand break repair

  A controlled negative on a phenotype the reciprocal product was suspected of having.

• ← analogous tot(6;11) makes four fusion genes, not two, and the PHD/bromodomain cassette is what opens chromatin in all of them

  Same architecture and same proposed chromatin-opening mechanism in a second KMT2A partner family.

• ← analogous tot(9;11): the reciprocal product is made, is engineered into every genome-editing model, and has never been separately tested

  Same KMT2A portion, same architecture, far less studied.

• ← related toBounded absence: not one menin-inhibitor study, trial or preclinical paper has ever recorded reciprocal fusion status

  The protein whose status has never been recorded in any menin-inhibitor study.

• ← related toEnumeration of the reciprocal KMT2A fusion literature: what was searched, found, rejected and could not be read

  Enumerates the literature from which that entry and the rest of this beat were built.

• ← analogous toKMT2A*: a menin-blind, LEDGF-blind, SET-competent KMT2A protein made from out-of-frame reciprocal alleles

  Same KMT2A content without the partner N-terminus; the two are the in-frame and out-of-frame outcomes of the same allele.

• ← supportsIn the only panel that tested both halves of four translocations, 3 of 4 reciprocal fusions transformed and only 1 of 4 direct ones did

  The only symmetric direct-versus-reciprocal transformation comparison, and it favours reciprocal products.