MEN1-FBXW7 is four alleles of ONE BRET assay, all typed 'mutation with no effect' - declined, and it is the most insidious class
also called menin-FBXW7 · FBXW7 mutation with no effect · EBI-63685884
A database lists the ubiquitin-ligase adaptor FBXW7 as a menin partner. The basis is one automated screen run over four FBXW7 mutants, none of which changed anything, so the row looks like an ordinary interaction while resting on a single assay.
The same thing, for a scientist
**Verdict: DECLINED.** IntAct curates four MEN1-FBXW7 records from PMID 35512704 - EBI-63685884, EBI-63690742, EBI-63695122, EBI-63699348 - and they are **four alleles of one BRET assay**, not four experiments: `p.Arg465Cys`, `p.Arg465His`, `p.Arg479Gln`, `p.Arg505Cys`, all in HEK293T, all type 'proximity', all annotated to **Table S2(B)**, all intact-miscore **0.27** [E1]. Every one is typed **`mutation with no effect`** - IntAct MI:2226 - meaning the variant did not change a signal that the assay detected. **This is the insidious class**: a `mutation with no effect` row carries no warning label and reads like an ordinary wild-type interaction, which is exactly how a future beat would write it in. Menin appears nowhere in the paper's prose [E2]. Compartment is compatible - FBXW7 is nucleoplasmic, nucleolar and chromosome-associated with experimental evidence [E3] - so the decline is entirely about the single assay. **Criterion C2: fails (a), (b) and (c).** **`confidence_overall` on this entry rates the INTERACTION, not the adjudication.** The adjudication is strong; the interaction is what is weak, and a reader scanning the field should see the weak thing.
Four records, one measurement
| IntAct AC | allele | featureType | method | table | miscore |
|---|---|---|---|---|---|
| EBI-63685884 | p.Arg465Cys | mutation with no effect | bret | ST2B | 0.27 |
| EBI-63690742 | p.Arg465His | mutation with no effect | bret | ST2B | 0.27 |
| EBI-63695122 | p.Arg479Gln | mutation with no effect | bret | ST2B | 0.27 |
| EBI-63699348 | p.Arg505Cys | mutation with no effect | bret | ST2B | 0.27 |
Counting these as four publications-worth of support, or even as four experiments, would be wrong. They are four wells of the same plate, on the same platform, in the same paper, differing only in which FBXW7 arginine was substituted. This is the shape rule 92 warns about from the other direction: a row count is not an evidence count.
All four substitutions are the canonical FBXW7 WD40 substrate-binding arginines - R465, R479, R505 - the hotspot residues that contact the phosphodegron. That the screen chose them is sensible; that none of them changed the menin signal is the finding.
What 'mutation with no effect' does and does not license
IntAct MI:2226 says the variant did not alter the interaction relative to the comparison the curator read. Two readings follow and they point opposite ways.
The generous reading: a signal was present for both wild-type and mutant FBXW7, so unlike the mutation causing rows this is not an allele artefact - it is an ordinary, allele-independent interaction that happens to have been found in a mutation screen.
The strict reading, which this entry takes: it is still one detection method, in one publication, between two tagged proteins co-overexpressed in HEK293T, with no region mapped, no stoichiometry, no orthogonal assay and no appearance in the paper's own validation arm. The fact that four substitutions all failed to move it is equally consistent with the signal being insensitive to anything - which is what a non-specific proximity signal looks like.
The two readings are separated by one number that already exists: the wild-type FBXW7 BRET value in Table S2(A). Nobody in this project has read it. Until somebody does, the strict reading is the honest default, and cycle 72's entry said the same thing in one sentence: 'treating those five as validated wild-type partners because the mutation did nothing would be the mirror error.'
The interesting version of this hypothesis, if anyone wants to test it
FBXW7 is the substrate-recognition subunit of an SCF E3 ubiquitin ligase. A real menin-FBXW7 association would most naturally mean menin is an SCF-FBXW7 substrate, i.e. that menin abundance is controlled by phosphodegron-dependent ubiquitination. That is a sharp, cheap, falsifiable claim: menin protein should rise on FBXW7 loss, fall on FBXW7 overexpression, and carry a CPD-like phosphodegron.
It is also worth noticing, because it is a pattern and not a coincidence, that three of this beat's nine declined partners are E3 ubiquitin-ligase substrate receptors - FBXW7 (SCF), SPOP (CUL3-BTB) and ZC3HC1/NIPA (SCF). See hyp-q128-three-of-menins-nine-declined-partners-are-e3-ligase-substrate-receptors, which treats that as a hypothesis about menin turnover AND as a candidate artefact signature, because substrate receptors are notoriously promiscuous when overexpressed.
| partner a | gene-men1 |
|---|---|
| partner b | FBXW7 |
| partner b uniprot | Q969H0 |
| partner b length AA | 707 |
| partner a uniprot | O00255 |
| partner a length AA | 610 |
| verdict | DECLINED |
| adjudicated by | Q128, cycle 91, 2026-09-23 |
| druggability | Not assessable. No region, residue or domain is mapped on either protein in any record, so it is not known whether the menin-inhibitor MBM pocket is involved, and no structure exists. |
| allele | four WD40 substrate-binding arginine substitutions; see records |
| n methods | 1 |
| n records but one assay | 4 |
| intact miscore | 0.27 |
| source panel | Table S2(B), primary screen CARINA output |
| absence class | measured-not-reported |
| absence class note | The wild-type FBXW7 BRET value against MEN1 is in Mo et al. Table S2(A) inside PMC9597701 and is the single number that separates the generous from the strict reading of 'mutation with no effect'. It has never been read in this project. |
interface residues a
[]
structures
[]
ligands
[ "drug-revumenib", "drug-ziftomenib" ]
records
[ "EBI-63685884 (p.Arg465Cys)", "EBI-63690742 (p.Arg465His)", "EBI-63695122 (p.Arg479Gln)", "EBI-63699348 (p.Arg505Cys)" ]
intact feature types
[ "mutation with no effect" ]
c2
{
"a_second_method": false,
"b_endogenous_side": false,
"c_wild_type": false,
"admitted": false,
"failing_clause": "a, b and c"
}- If menin turnover were FBXW7-dependent, FBXW7-mutant leukaemias would carry more menin protein, and the dose of a menin inhibitor needed to occupy it would differ. FBXW7 is recurrently mutated in T-ALL, which overlaps the menin-inhibitor population - so this is a bite-back with a real patient group behind it even though the database row is weak.
- The opposite bite-back is about this entry rather than the biology: a 'mutation with no effect' row is the most likely of all nine to be written in by a future agent as a plain menin partner, because nothing in the label warns them. If that happens, the graph acquires a false partner with no visible provenance problem.
- What is the wild-type FBXW7 BRET value against MEN1 in Table S2(A)? This is the highest-value unread number in the whole beat, because it governs three entries (FBXW7, SMAD4, SPOP) at once.
- Is menin an SCF-FBXW7 substrate? Menin protein level after FBXW7 knockout, and after MLN4924 neddylation inhibition, would answer it in a week with no new reagents.
- Does menin carry a CDC4 phosphodegron-like motif? A sequence scan of O00255 against the CPD consensus is free and has apparently never been done.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
IntAct record(s) EBI-63685884 (p.Arg465Cys); EBI-63690742 (p.Arg465His); EBI-63695122 (p.Arg479Gln); EBI-63699348 (p.Arg505Cys) curate a MEN1-FBXW7 interaction from PMID 35512704. Detection method bioluminescence resonance energy transfer (BRET), interaction type 'proximity', host Homo sapiens HEK293T embryonic kidney cell, both partners epitope-tagged (NanoLuc donor on FBXW7, Venus acceptor on MEN1). The FBXW7 side carries feature(s) four WD40 substrate-binding arginine substitutions; see records, typed by IntAct as 'mutation with no effect'. The row is annotated to Table S2(B), primary screen CARINA output of the paper. intact-miscore 0.27.
IntAct molecular interaction database, REST findInteractions on O00255, retrieved 2026-09-23 by Q128 · IntAct (EMBL-EBI) 2026What this evidence cannot show
Read live from the IntAct REST endpoint on 2026-09-23; field names quoted are the REST JSON's own. A miscore of 0.27 is low on IntAct's 0-1 scale and is what a single-method, single-publication row scores by construction, so it is a restatement of the evidence thinness rather than an independent grade of it. The underlying supplementary table was not parsed; the allele and feature type are IntAct's curation of it.
Evidence that argues against this (1)
- IntAct's featureType vocabulary is the curator's reading of the paper, not the paper's own words. 'mutation causing an interaction' (MI:2227) and 'mutation with no effect' (MI:2226) both presuppose that a wild-type comparison was made and interpreted. If IntAct has typed a row wrongly, every verdict built on the type is wrong in the same direction, and the only way to check is the paper's own supplementary table. Mo X et al. 2022
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
PMID 35512704 is a quantitative high-throughput differential BRET screen (qHT-dS) of 17,792 wild-type/mutant interaction pairs in live HEK293T cells, built specifically to find interactions a cancer mutation creates and the parental protein does not make. In its 198,614-character PMC full text (PMC9597701), 'menin' and 'MEN1' occur exactly twice and both are the same key-resources row for a ThermoFisher anti-menin antibody (PA5-79663, RRID:AB_2746778). Menin is discussed in no sentence of the narrative, results or discussion.
Systematic discovery of mutation-directed neo-protein-protein interactions in cancer. · Mo X, Niu Q, Ivanov AA, Tsang YH, Tang C, Shu C, Li Q, Qian K, Wahafu A, Doyle SP, Cicka D, Yang X, Fan D, Reyna MA, Cooper LAD, Moreno CS, Zhou W, Owonikoko TK, Lonial S, Khuri FR, Du Y, Ramalingam SS, Mills GB, Fu H · Cell 2022What this evidence cannot show
Full text retrieved by efetch db=pmc and searched after tag-stripping and entity unescaping, so a mention inside a figure image is invisible to it - and one is: MEN1 is a blotted row in Figure 4D. The supplementary tables that hold every menin number in this paper were not parsed. So 'menin is absent from the paper' would be false; the defensible claim is that menin is absent from the paper's prose.
Evidence that argues against this (1)
- A proximity or affinity signal measured between two tagged, co-overexpressed proteins in a heterologous cell line is a real measurement and is not a demonstration that the complex forms at endogenous stoichiometry in any tissue. The Mo et al. platform is explicitly a co-expression BRET screen in live HEK293T cells, and its own validation arm exists because the primary screen output is a candidate list, not a partner list. Mo X et al. 2022
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
UniProtKB Q969H0 (FBXW7) is 707 aa. Subcellular location: Nucleus nucleoplasm (ECO:0000269), Chromosome (ECO:0000269), Nucleus nucleolus (ECO:0000269), Cytoplasm (ECO:0000269). Tissue specificity: Widely expressed MEN1 (O00255, 610 aa) carries a single subcellular location, Nucleus, with experimental evidence (ECO:0000269), and tissue specificity 'Ubiquitous'.
UniProtKB entry Q969H0, subcellular location and tissue specificity, retrieved 2026-09-23 · UniProt Consortium 2026What this evidence cannot show
UniProt subcellular-location comments are curated pointers, and rule 91 in this project's brief established that an ECO:0000269 code means a curator read AN experiment, not necessarily THE experiment or the best one. The cited papers behind these location lines were not opened here. Uncoded lines are recorded as uncoded and not discarded.
Evidence that argues against this (1)
- A compartment mismatch is a prior, not a refutation. Proteins move: menin's own UniProt record annotates only Nucleus, yet the founding localisation paper (PMID 9465067) maps at least two NLSs and UniProt does not cite it, which this project recorded as rule 91. An argument from UniProt compartments is therefore an argument from an incomplete record on both sides of the pair. UniProt Consortium 2026
IntAct-curated MEN1 partner, adjudicated DECLINED by Q128 (a, b and c)
per-partner adjudication of FBXW7
the cycle-72 summary entry this per-partner entry decomposes
FBXW7 is the strongest of the three candidates and the one with a leukaemia genotype
- ← testsIs menin an SCF-FBXW7 substrate? A one-week immunoblot and a free desk scan that settle Arm A
tests the abundance consequence the declined FBXW7 row would imply if real