AFG2A / SPATA5 (Q8NB90) - a 55LCC replisome-proteostasis ATPase that co-purifies with KMT2A and menin, and whose CURRENT symbol cannot retrieve its own source paper or any of its function literature

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.

• AFG2A is required in 90.5% of DepMap lines, and leukaemia lines are marginally MORE tolerant than average (-0.7899 versus -0.8275). Any intervention would be an anti-proliferative with no window, and the direction of the leukaemia number argues against even a modest one.
• The human loss-of-function phenotype is a severe neurodevelopmental encephalopathy with drug-resistant infantile epileptic spasms in two thirds of affected children. A systemic 55LCC inhibitor in an infant leukaemia population - the index population for this project - would be acting on a pathway whose partial loss in infancy is already known to produce exactly that.
• Inhibiting a complex whose job is replisome proteostasis raises replication stress and chromosome instability. In a leukaemia defined by a translocation, deliberately increasing chromosome instability is a plausible route to additional rearrangements and to therapy-related second malignancy.
• The protein also has a pre-60S ribosome-maturation function separate from its replisome one, so any inhibitor has at least two essential-pathway liabilities and no way to separate them pharmacologically without a domain-selective tool that does not exist.

1. Do C1orf109 and CINP co-purify with KMT2A, menin or PSIP1? The 55LCC coherence test currently fails on two of four subunits, and this is the single measurement that would settle whether the two rows record a complex association or two individual ATPases in a TAP eluate.
2. Is the 55LCC coherence test different against IntAct REST? The union it was run on comes from PSICQUIC, which returns 64% of the rows REST returns for the same six accessions, so the absence of C1orf109/CINP should be re-checked on the fuller endpoint before it is treated as settled.
3. Does 55LCC loss change the frequency or the breakpoint distribution of KMT2A rearrangements? The complex's loss-of-function phenotype is severe chromosome instability, and the KMT2A breakpoint cluster region is the most studied translocation hotspot in paediatric leukaemia - but no experiment links them and no patient in the 51-person AFG2A-RE cohort has a reported malignancy.
4. Where is AFG2A in the nucleus, if anywhere? UniProt codes no nuclear localisation at all while calling the complex chromatin-associated, and the coded cytoplasm/spindle assignments come from a 2008 paper that predates the complex's discovery.
5. Is there a KMT2A-rearranged-specific replication-stress phenotype that a 55LCC hypomorph would modify? This would be the cheapest way to convert a HeLa co-purification into a leukaemia-relevant test, and it has never been attempted under any of the symbols tried.

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

   The 55LCC complex comprises the AAA+ ATPases SPATA5 (AFG2A) and SPATA5L1 (AFG2B) together with the heterodimer C1orf109-CINP; the ATPases' N-terminal domains interact with C1orf109-CINP to form a funnel-like structure above a cylindrical ATPase motor; 55LCC deficiency elicits ubiquitin-independent proteotoxicity, replication stress and severe chromosome instability; and its ATPase activity is specifically enhanced by replication fork DNA and coupled to cysteine-protease-dependent cleavage of replisome substrates in response to fork damage.

   The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity. · Krishnamoorthy V, et al. · Cell 2024
   PMID 38554706DOI
   ▸What this evidence cannot show

   Read from the abstract only; the structural model, the fork-DNA ATPase stimulation and the protease coupling are the abstract's own statements and no figure or PDB entry was opened. The two PDB cross-references on Q8NB90 (8RHN, 9LGO) were NOT fetched, so no coordinates, residue ranges or interface claims are taken from them. SYSTEM: human cell lines, including the HeLa S3 tandem affinity purification that produced this entry's IntAct rows; no haematopoietic cell, no leukaemia, no fusion. TITLE NOMENCLATURE TRAP: the paper is titled with the PREVIOUS official symbols SPATA5 and SPATA5L1, which is why a query on the current symbols AFG2A/AFG2B does not retrieve it - see E6.

   ▸Evidence that argues against this (1)

   • The paper's own rationale for its clinical relevance is 'pathogenic variants seen in associated human neurodevelopmental disorders' - not cancer. A complex whose loss causes severe chromosome instability in cells and a non-neoplastic developmental syndrome in 51 humans is a warning that the cellular instability phenotype does not translate into a tumour-predisposition phenotype, which is the inference a leukaemia project would be tempted to draw. Nou-Fontanet L et al. 2026
2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   IntAct holds exactly two rows placing AFG2A (Q8NB90) against this project's scaffold proteins - one against KMT2A (Q03164) and one against MEN1 (O00255) - both from PMID 38554706, both tandem affinity purification (MI:0676), both in HeLa S3, both at IntAct MI-score 0.35, and in both rows the experimental role of AFG2A is bait while the scaffold protein is prey.

   IntAct PSICQUIC, MITAB2.7 rows for Q03164 (KMT2A) and O00255 (MEN1), filtered on Q8NB90 · EMBL-EBI IntAct 2026
   ▸What this evidence cannot show

   Queried live 2026-09-22; experimental role, host organism, detection method and MI-score read out of MITAB2.7 columns 19/20, 29, 7 and 15 rather than assumed. ONE PUBLICATION, ONE EXPERIMENT: the '2 baits' that put this gene in the read queue are two rows of the same tandem affinity purification, so the queue's independence criterion is satisfied by two prey hits in one experiment and NOT by two studies. MI-score 0.35 is the LOWEST band in the read queue apart from RPS11, and far below IntAct's 0.6 conventional high-confidence cut. HOST HeLa S3: an epithelioid cervical carcinoma line, not haematopoietic, not B-lineage, no fusion. DIRECTION: AFG2A is the bait in both rows, so neither KMT2A nor menin has ever been used as the bait in an experiment that recovered it. Rule 93 endpoint caveat: PSICQUIC returns 218 rows for KMT2A and 62 for MEN1 against 376 and 137 from IntAct REST, so these counts are floors.

   ▸Evidence that argues against this (1)

   • A tandem affinity purification from HeLa nuclear extract with an AAA+ ATPase as bait recovers chromatin-associated proteins broadly, and KMT2A and menin are both abundant chromatin proteins in HeLa. The discriminating test is whether the rest of the complex comes along, and it does not: C1orf109 and CINP are absent from the entire 217-partner union. Krishnamoorthy V et al. 2024
3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset

   Neither C1orf109 nor CINP - the two heterodimeric partners that complete the 55LCC complex - appears anywhere in the 217-partner IntAct union of the six scaffold proteins KMT2A, MEN1, PSIP1, AFF4, DOT1L and AFF1: they are not among the 95 partners with their own entry, not among the 10 mentioned-only, and not among the 112 absent entirely, and no node gene-c1orf109 or gene-cinp exists in this graph.

   analyses/core-complex-interactome-gap/results.json (generated 2026-09-22), all_missing and union fields, checked against the full node-id listing · this repository / EMBL-EBI IntAct 2026
   ▸What this evidence cannot show

   Checked by this beat on 2026-09-22 two ways: the 122-member all_missing list in results.json was searched for C1orf109 and CINP (absent), and the complete 2,019-id node listing was searched for gene-c1orf109 and gene-cinp (absent). WHAT THIS IS NOT: it is not a claim that C1orf109 and CINP do not bind these proteins. It is a claim that the curated IntAct record does not contain such a row, and IntAct curation of one paper reflects what the depositors submitted. The endpoint is PSICQUIC, which returns fewer rows than IntAct REST (376 versus 218 for KMT2A), so a C1orf109 or CINP row could exist and be invisible to this instrument - the coherence test should be re-run against REST before it is treated as settled.

   ▸Evidence that argues against this (1)

   • The endpoint caveat is a real one and cuts directly against this item: the instrument that produced the 217-partner union sees 651 of the 1,015 rows IntAct REST returns for the same six accessions, i.e. 64%. A subunit missing from a 64%-complete record is weaker evidence of complex incoherence than a subunit missing from a complete one, and the coherence test is exactly the kind of measurement that should be re-run after the endpoint migration. EMBL-EBI IntAct 2026
4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   AFG2A-related encephalopathy, previously called SPATA5-related encephalopathy, is an ultra-rare autosomal recessive disorder; in the largest series to date (systematic review of 45 published patients plus 6 new, n = 51, 29 male, mean age 8.35 years) intellectual disability was present in 97.92%, hearing loss in 93.62%, microcephaly in 85.71%, visual impairment in 79.49%, hypotonia in 71.74%, spasticity in 60.87% and epilepsy in 74.71% of whom 82.35% were drug-resistant, with infantile epileptic spasms syndrome the predominant onset syndrome (66.67%); the presentation may mimic mitochondrial disease and no genotype-epilepsy-phenotype association was found.

   AFG2A-related encephalopathy, expanding the neurodevelopmental and epileptic spectrum. · Nou-Fontanet L, et al. · Orphanet J Rare Dis 2026
   PMID 41933351DOI
   ▸What this evidence cannot show

   Read from the abstract only; all percentages are the abstract's own. A SYSTEMATIC-REVIEW-PLUS-CASE-SERIES design, so the denominators differ per feature (hearing loss 93.62% of 47 assessed, microcephaly 85.71% of 42, and so on) and the percentages are not all over n = 51 - the abstract does not give per-feature denominators and this beat did not reconstruct them, so each figure should be read as 'of those in whom it was assessed'. Publication bias is the dominant limitation of any pooled rare-disease series: severe cases are reported. CRITICALLY FOR THIS GRAPH: no cancer, no leukaemia and no malignancy of any kind is reported in these 51 individuals, which is a constraint on any chromosome-instability-to-translocation inference and is recorded here as such.

   ▸Evidence that argues against this (1)

   • The absence of reported malignancy in 51 patients is a weak negative rather than a strong one: mean age is 8.35 years, the cohort is small, and the disorder is severe enough that competing mortality and ascertainment for neurological features would both suppress a cancer signal. A biallelic-hypomorph genotype also need not phenocopy the complete loss that produced chromosome instability in cells. Nou-Fontanet L et al. 2025
5. E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   In DepMap release 26Q2 as served by Open Targets, AFG2A (ENSG00000145375) has a mean gene effect of -0.8275 across 1,258 screens, a minimum of -1.826, 90.5% of lines below -0.5, and a mean of -0.7899 across the 57 leukaemia-annotated screens.

   Open Targets Platform GraphQL, target.depMapEssentiality (DepMap 26Q2) · Open Targets Platform / DepMap 2026
   ▸What this evidence cannot show

   RELEASE RECORDED per rule 83: meta.dataVersion = {year: 26, month: 06} = DepMap 26Q2, fetched 2026-09-22. 1,258 is this gene's own screen count. All 29 tissue blocks concatenated before averaging. Ensembl id resolved through the HGNC primary ensembl_gene_id per rule 78 and the readback control passed (Open Targets returned approvedSymbol AFG2A for ENSG00000145375, confirming the symbol migration is reflected in the platform). The leukaemia subset is a substring match on diseaseFromSource and was NOT stratified by KMT2A rearrangement. NOTE THE DIRECTION OF THE LEUKAEMIA NUMBER: -0.7899 is LESS negative than the panel mean of -0.8275, i.e. leukaemia lines are marginally more tolerant, which is the opposite of selectivity. No median-split proportion is reported here, per rule 84.

   ▸Evidence that argues against this (1)

   • Near-pan-essentiality at 90.5% of lines is the same double-edged number as for PES1: it rules out a therapeutic window and it simultaneously makes the co-purification less interpretable, because a protein required by nine lines in ten is abundant and present everywhere. It also sits oddly beside the human genetics - biallelic pathogenic variants are compatible with survival to at least 8 years, so the cell-line requirement must be partly a proliferation requirement rather than an absolute one. Open Targets Platform / DepMap 2026
6. E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   PubMed esearch 2026-09-22: AFG2A[tiab] returns 7 records of which 4 are aflatoxin papers and 3 are AFG2A-related encephalopathy, none is about the protein's molecular function, and PMID 38554706 is NOT among them; SPATA5[tiab] returns 40 records and does include 38554706; AFG2B[tiab] returns 2 and SPATA5L1[tiab] returns 14; "55LCC"[tiab] returns exactly 1, the source paper; and SPATA5[tiab] AND KMT2A[tiab], SPATA5[tiab] AND MLL[tiab] and SPATA5[tiab] AND leukemia[tiab] are all parsed zeros.

   NCBI PubMed esearch, symbol-generation recall test and bounded-absence queries with querytranslation recorded · NCBI E-utilities 2026
   ▸What this evidence cannot show

   All 7 AFG2A records and all 3 zeros were handled properly: each zero carries a non-empty querytranslation (e.g. `"SPATA5"[Title/Abstract] AND "KMT2A"[Title/Abstract]`) and warninglist.outputmessages = ["No items found."]. Each operand separately tagged, no `(A OR B)[tiab]` form, per rule 94. ALL SEVEN AFG2A RECORDS WERE TITLE-CHECKED INDIVIDUALLY - this is not a sampled estimate: 15810799 aflatoxins in Egyptian infants, 10788571 aflatoxins on guinea-pig trachea, 30978883 monoclonal antibodies to aflatoxin B1/M1, 42073338 aflatoxin B1 degradation by a multicopper oxidase, 40846618 / 40712368 / 41933351 AFG2A-related encephalopathy. BOTH KMT2A SYMBOL GENERATIONS were run against the productive gene symbol. NOT TRIED: SPAF (the third UniProt synonym), 'SPATA5' paired with MLL-AF4/MLL-AF9/'t(4;11)', C1orf109 or CINP paired with anything. Bounded by titles and abstracts only. data/symbol-collisions.json (147 rows) was grepped for AFG2A, AFG2B, SPATA5, SPATA5L1, 55LCC and AFG2 before the first query per rule 88: no row for any of them, so this is a NEW trap.

   ▸Evidence that argues against this (1)

   • The trap's most dangerous property is that the recall failure and the precision failure PARTLY CANCEL in a way that makes the symbol look serviceable: AFG2A[tiab] returns 7 records, not 0, so a beat running it gets a non-empty result set and no signal that it is missing 33 records and the source paper. An empty result would have been safer. The same shape applies to AFG2B, where 2 records stand in for 14. NCBI E-utilities 2026
7. E7strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   UniProt resolves gene_exact:AFG2A in reviewed human records to exactly one entry, Q8NB90 (AFG2A_HUMAN, 893 aa, 'ATPase family gene 2 protein homolog A'), whose gene-names field carries the synonyms SPAF and SPATA5; the record describes the protein as an ATP-dependent chaperone of the chromatin-associated 55LCC heterohexameric ATPase complex and also as essential for cytoplasmic maturation of pre-60S ribosomal particles; its subcellular-location comments are Cytoplasm (ECO:0000269, PubMed 18445686), Mitochondrion (ECO:0000250, by similarity to Q3UMC0) and Cytoplasm/cytoskeleton/spindle (ECO:0000269, PubMed 18445686) - and NO nuclear location is annotated; and the disease comment is Neurodevelopmental disorder with hearing loss, seizures and brain abnormalities (NEDHSB).

   UniProtKB - Q8NB90 (AFG2A_HUMAN), ATPase family gene 2 protein homolog A · UniProt Knowledgebase 2026
   ▸What this evidence cannot show

   Fetched live 2026-09-22. THE CONTRADICTION INSIDE THE RECORD IS THE POINT AND IS NOT RESOLVED HERE: the FUNCTION comment calls the 55LCC complex CHROMATIN-ASSOCIATED and cites PubMed 38554706, while the SUBCELLULAR LOCATION comments annotate NO nucleus at all - the only experimentally coded locations are cytoplasm and spindle, both from PubMed 18445686, a 2008 paper this beat did NOT open. Per rule 91 the evidence code says a curator read an experiment, not that the paper is about the fact, and here the coded localisation paper predates the complex's discovery by sixteen years. So the nuclear pool that the two IntAct rows presuppose is NOT supported by any coded UniProt localisation for this protein. Also NOT verified: the pre-60S maturation function (cited to PubMed 35354024 and 38554706, neither opened for that claim), the feature table has NO Domain features so no AAA+ boundary is asserted, and the two PDB entries (8RHN, 9LGO) were not fetched.

   ▸Evidence that argues against this (1)

   • The absent nuclear localisation is the strongest internal argument against the two IntAct rows meaning what they appear to mean. A protein with no experimentally coded nuclear pool, whose coded locations are cytoplasm and spindle, co-purifying from HeLa nuclear-extract TAP with two chromatin proteins, is the pattern this project's cycle-54 queue adjudication used to reject CAMKV and EPB41L1 - and it applies here with the difference that the FUNCTION comment does call the complex chromatin-associated, which is why this entry was written rather than rejected. Krishnamoorthy V et al. 2024

• co-occurs with →KMT2A / MLL1 — the gene that breaks

  one HeLa S3 tandem affinity purification (PMID 38554706); AFG2A is the BAIT and KMT2A the prey; IntAct MI-score 0.35

• co-occurs with →MEN1 / menin — the adaptor the fusion cannot work without

  same single HeLa S3 TAP (PMID 38554706); AFG2A bait, menin prey; MI-score 0.35

• ← part ofAFG2B / SPATA5L1 (Q9BVQ7) - the second 55LCC ATPase, the only read-queue member with an annotated nuclear pool, pan-essential in 95.5% of lines, and the one that touches PSIP1

  both AAA+ ATPases of the 55LCC complex with C1orf109-CINP; the two missing subunits are absent from the entire 217-partner union, so the complex-coherence test fails 2 of 4

• related to →SETD2 (Q9BYW2) - the H3K36 trimethyltransferase that binds all seven MLL fusions, and the only one of them with a published KMT2A::AFF1 dependency test

  both reach this project through genome-integrity biology rather than elongation: SETD2 safeguards genomic integrity in MLL-fusion leukaemia, 55LCC loss causes severe chromosome instability. No experiment connects them

• ← supportsIn all 24 read-queue rows inspected, the candidate is the BAIT and this project's protein is the prey - nobody has ever tagged KMT2A, AFF4, menin or PSIP1 and found any of them; plus seven bounded rejections

  both AFG2A rows read per row: candidate bait, scaffold prey, HeLa S3, MI-score 0.35, one publication and one purification