Oncofusion

start / graph / interface-menin-smad4-declined-single-bret-no-allele-effect

Interfaceweak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.Q128-the-menin-interactome-that-is-not-chromatin

MEN1-SMAD4 is four alleles of ONE BRET assay, all 'mutation with no effect' - declined, and the real menin-TGF-beta literature is elsewhere

also called menin-SMAD4 · SMAD4 mutation with no effect · EBI-63703597

A database lists SMAD4, the central TGF-beta signalling protein, as a menin partner. The basis is one automated screen run over four SMAD4 mutants, none of which changed the signal.

The same thing, for a scientist

**Verdict: DECLINED, and this one needs a second warning.** IntAct curates four MEN1-SMAD4 records from PMID 35512704 - EBI-63703597, EBI-63707938, EBI-63712107, EBI-63716028 - which are four alleles of **one** BRET assay: `p.Asp351His`, `p.Arg361Cys`, `p.Arg361His`, `p.Gly386Asp`, HEK293T, type 'proximity', **Table S2(B)**, intact-miscore **0.27**, all typed **`mutation with no effect`** [E1]. Menin appears nowhere in the paper's prose [E2]. Compartment is compatible - SMAD4 is experimentally cytoplasmic and nuclear [E3]. **The second warning is the one that matters here:** there is a substantial independent literature on menin and TGF-beta/SMAD signalling, and this IntAct row is NOT that literature. Anyone who finds this row and remembers that menin-SMAD is 'a known thing' will read the row as confirmation of something it has no connection to. **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.

Go deeper
Four records, one measurement
IntAct ACallelefeatureTypemethodtablemiscore
EBI-63703597p.Asp351Hismutation with no effectbretST2B0.27
EBI-63707938p.Gly386Aspmutation with no effectbretST2B0.27
EBI-63712107p.Arg361Cysmutation with no effectbretST2B0.27
EBI-63716028p.Arg361Hismutation with no effectbretST2B0.27

All four are MH2-domain substitutions - D351, R361, G386 - the hotspot positions that disrupt SMAD2/3 heteromerisation and are the commonest somatic SMAD4 missense lesions. G386D is the allele the paper carried into its own Figure 4G validation panel, where the tested partners are SMAD3, AXIN2 and GSK3-beta. Menin is not among them.

The trap: a real menin-SMAD literature that this row is not

This is the most likely of the nine to be waved through, and the reason is not the database - it is the reader's memory. Menin's involvement in TGF-beta/BMP signalling, including interaction with receptor-regulated SMADs and with SMAD3 at target promoters, is an established strand of the endocrine-tumour literature, largely developed in parathyroid and pituitary contexts and quite separate from anything in a BRET screen.

A curator who meets MEN1 - SMAD4 in IntAct and recalls that strand will experience the row as already known to be true and will not examine it. That is the failure this project has recorded as 'a deflating caveat needs the same check as a claim', running in the opposite direction: a confirming prior needs the same check as a surprising one.

What this entry asserts is narrow and should be quoted narrowly: the IntAct MEN1-SMAD4 rows come from one BRET assay in a mutation screen and are not evidence for or against the menin-TGF-beta literature. This entry does NOT adjudicate that literature - it was not searched, no paper from it was read, and no claim about it is made here beyond its existence. That is a gap this entry names rather than fills, and naming it is a task for a later beat.

What would make the row informative

The same single number as for FBXW7 and SPOP: the wild-type SMAD4 BRET value against MEN1 in Mo et al. Table S2(A). If wild-type SMAD4 gives a clear signal, the row becomes an allele-independent proximity observation worth one orthogonal experiment. If it does not, IntAct's mutation with no effect type is doing something other than what its name implies and that is a curation problem worth reporting to EBI.

Facts and figures
partner agene-men1
partner bSMAD4
partner b uniprotQ13485
partner b length AA552
partner a uniprotO00255
partner a length AA610
verdictDECLINED
adjudicated byQ128, cycle 91, 2026-09-23
druggabilityNot 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.
allelefour MH2-domain substitutions; see records
n methods1
n records but one assay4
intact miscore0.27
source panelTable S2(B), primary screen CARINA output
not adjudicated herethe independent menin-TGF-beta/SMAD literature, which was not searched and about which this entry makes no claim
absence classmeasured-not-reported
absence class noteWild-type SMAD4 BRET against MEN1 sits in Mo et al. Table S2(A) inside PMC9597701, unread. Separately, whether the published menin-TGF-beta literature has ever been tested in a haematopoietic cell or under a menin inhibitor is unclassified-not-checked by this beat, because that literature was not searched.
interface residues a
[]
structures
[]
ligands
[
  "drug-revumenib",
  "drug-ziftomenib"
]
records
[
  "EBI-63703597 (p.Asp351His)",
  "EBI-63707938 (p.Gly386Asp)",
  "EBI-63712107 (p.Arg361Cys)",
  "EBI-63716028 (p.Arg361His)"
]
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"
}
How this could bite us back
  • TGF-beta signalling is a plausible route by which a menin inhibitor could have effects outside chromatin, and this entry declines the only database row that points at it. If the decline is quoted as 'menin has nothing to do with SMAD', that would be a false inference from a narrow finding about four BRET wells.
  • In the other direction, a combination rationale built on 'menin binds SMAD4' would be built on this row, and the row cannot carry it.
Still open
  1. What is the wild-type SMAD4 BRET value against MEN1 in Table S2(A)?
  2. The menin-TGF-beta/SMAD literature exists and this beat did not search it. Which of its experiments were done in a haematopoietic cell, and has any of them been repeated under a pharmacological menin inhibitor? That is a whole beat and it is a real gap in this corpus.
  3. Why was menin not carried into Figure 4G, the paper's own SMAD4 G386D validation panel, when SMAD3, AXIN2 and GSK3-beta were? The selection criterion for that panel is not stated in the legend and would say what the authors thought of their own menin hit.
Every source behind this entry (3)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    IntAct record(s) EBI-63703597 (p.Asp351His); EBI-63707938 (p.Gly386Asp); EBI-63712107 (p.Arg361Cys); EBI-63716028 (p.Arg361His) curate a MEN1-SMAD4 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 SMAD4, Venus acceptor on MEN1). The SMAD4 side carries feature(s) four MH2-domain 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.

    What 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
  2. 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 2022
    PMID 35512704DOI
    What 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
  3. E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    UniProtKB Q13485 (SMAD4) is 552 aa. Subcellular location: Cytoplasm (ECO:0000269), Nucleus (ECO:0000269). MEN1 (O00255, 610 aa) carries a single subcellular location, Nucleus, with experimental evidence (ECO:0000269), and tissue specificity 'Ubiquitous'.

    What 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
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