ATG9B is the vertebrate-specific, tissue-restricted paralog of the core autophagy protein ATG9A, expressed mainly in placental trophoblast and pituitary. Like ATG9A, it is a multispanning membrane protein that forms a homotrimer and acts as a phospholipid scramblase. It binds the lipid-transfer protein ATG2A. At steady state it is mostly on the Golgi, with some on early and recycling endosomes. In starvation, ATG9B vesicles join LC3-positive sites of autophagosome formation, where ATG9-family scramblases equilibrate lipids delivered by ATG2 across the growing phagophore. ATG9B can replace ATG9A in starvation-induced autophagy. The ATG9B locus overlaps NOS3 antisense.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000045 autophagosome assembly | IDA PMID:15755735 Endothelial nitric-oxide synthase antisense (NOS3AS) gene en... | ACCEPT | Summary: Autophagosome assembly (IDA). ATG9B complements ATG9A knockdown in starvation-induced autophagosome formation, and in ATG9A-knockout cells it restores autophagy flux with ATG9A-like trafficking. As an ATG9-family scramblase that delivers and redistributes phagophore lipids, it does part of the work of assembly. Core process. Reason: [PMID:15755735 "In addition, APG9L2 can functionally complement APG9L1 in this process."] [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] [PMID:37938170 "Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase."] Supporting Evidence: PMID:15755735 In addition, APG9L2 can functionally complement APG9L1 in this process. PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. PMID:37938170 Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. |
| GO:0000139 Golgi membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Golgi membrane (ISS, from the paralog ATG9A). In HEK293A cells, ATG9B colocalizes mainly with the Golgi marker GM130, and to a lesser extent with EEA1-positive early endosomes and RAB11-positive recycling endosomes, matching the ATG9A pattern. Accepted as non-core steady-state locations. Reason: [PMID:37938170 "Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A)."] Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q7Z3C6 SUPPORTS TRANSFER Human ATG9A (paralog); ATG9B's own Golgi/endosome colocalization (PMID:37938170) corroborates the transfer. Supporting Evidence: PMID:37938170 Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A). |
| GO:0000407 phagophore assembly site | IBA GO_REF:0000033 | ACCEPT | Summary: Phagophore assembly site (IBA). ATG9B-containing dots colocalize with LC3 under starvation, and ATG9B substitutes for ATG9A at the site of autophagosome formation. Accepted. Reason: [PMID:15755735 "In transient transfection assays we found that both proteins were primarily localized to the perinuclear region and also scattered throughout the cytosol as dots, a subset of which colocalized with an autophagosome-specific marker LC3 under starvation conditions."] [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000315580 SUPPORTS TRANSFER ATG9 family node; consistent with ATG9B behaviour in human cells (PMID:15755735, PMID:37938170). Supporting Evidence: PMID:15755735 In transient transfection assays we found that both proteins were primarily localized to the perinuclear region and also scattered throughout the cytosol as dots, a subset of which colocalized with an autophagosome-specific marker LC3 under starvation conditions. PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. |
| GO:0000423 mitophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Mitophagy (IBA). This selective autophagy pathway uses the core ATG9 machinery. It is plausible for ATG9B wherever it is expressed, but not tested in the cited sources, and ATG9B is largely confined to placenta and pituitary. Kept as non-core, as for ATG9A. Reason: [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] [PMID:37938170 "ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role"] Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000315580 SUPPORTS TRANSFER Node seeded by yeast and fly Atg9 selective-autophagy data. Supporting Evidence: PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. PMID:37938170 ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role |
| GO:0005737 cytoplasm | IEA GO_REF:0000107 | ACCEPT | Summary: Cytoplasm (IEA, mouse ortholog projection). Correct but broad; ATG9B is on cytoplasmic membranes (Golgi, endosomes, vesicles). Accepted. Reason: [PMID:37938170 "Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A)."] Supporting Evidence: PMID:37938170 Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A). |
| GO:0005776 autophagosome | IBA GO_REF:0000033 | ACCEPT | Summary: Autophagosome (IBA). A subset of ATG9B dots colocalizes with LC3 under starvation. As for ATG9A, this probably reflects transient association with forming autophagosomes. Accepted. Reason: [PMID:15755735 "In transient transfection assays we found that both proteins were primarily localized to the perinuclear region and also scattered throughout the cytosol as dots, a subset of which colocalized with an autophagosome-specific marker LC3 under starvation conditions."] Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000315580 SUPPORTS TRANSFER ATG9 family node seeded by mouse Atg9a/Atg9b data. Supporting Evidence: PMID:15755735 In transient transfection assays we found that both proteins were primarily localized to the perinuclear region and also scattered throughout the cytosol as dots, a subset of which colocalized with an autophagosome-specific marker LC3 under starvation conditions. |
| GO:0005776 autophagosome | IEA GO_REF:0000107 | ACCEPT | Summary: Autophagosome (IEA, mouse ortholog projection). A subset of ATG9B dots colocalizes with LC3 under starvation. As for ATG9A, this probably reflects transient association with forming autophagosomes. Accepted. Reason: [PMID:15755735 "In transient transfection assays we found that both proteins were primarily localized to the perinuclear region and also scattered throughout the cytosol as dots, a subset of which colocalized with an autophagosome-specific marker LC3 under starvation conditions."] Supporting Evidence: PMID:15755735 In transient transfection assays we found that both proteins were primarily localized to the perinuclear region and also scattered throughout the cytosol as dots, a subset of which colocalized with an autophagosome-specific marker LC3 under starvation conditions. |
| GO:0005789 endoplasmic reticulum membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Endoplasmic reticulum membrane (ISS, from the paralog ATG9A). ATG9A acts at ER-phagophore contacts with ATG2. ATG9B binds ATG2A, but its own localization studies report Golgi and endosomes, not ER. Plausible by analogy only; kept as non-core. Reason: [PMID:37938170 "Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A)."] [PMID:37938170 "Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A."] Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q7Z3C6 UNRESOLVED Human ATG9A (paralog) acts at ER-phagophore contacts; no ER localization has been reported for ATG9B, so the transfer is plausible but untested. Supporting Evidence: PMID:37938170 Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A). PMID:37938170 Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. |
| GO:0005802 trans-Golgi network | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Trans-golgi network (ISS, from the paralog ATG9A). In HEK293A cells, ATG9B colocalizes mainly with the Golgi marker GM130 (a cis-Golgi marker; the trans-Golgi network is not separately tested), and to a lesser extent with EEA1-positive early endosomes and RAB11-positive recycling endosomes, matching the ATG9A pattern. Accepted as non-core steady-state locations. Reason: [PMID:37938170 "Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A)."] Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q7Z3C6 SUPPORTS TRANSFER Human ATG9A (paralog); ATG9B's own Golgi/endosome colocalization (PMID:37938170) corroborates the transfer. Supporting Evidence: PMID:37938170 Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A). |
| GO:0006914 autophagy | IEA GO_REF:0000002 | ACCEPT | Summary: Autophagy (IEA, InterPro ATG9 family). Correct; ATG9B supports starvation-induced autophagy. Accepted. Reason: [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] Supporting Evidence: PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. |
| GO:0017121 plasma membrane phospholipid scrambling | IEA GO_REF:0000108 | MARK AS OVER ANNOTATED | Summary: Plasma membrane phospholipid scrambling (IEA, derived from scramblase activity). ATG9-family scramblases act in Golgi-derived vesicles and the growing phagophore, not at the plasma membrane. The automatic process inference picks the wrong compartment. Over-annotation, as in the ATG9A review. Reason: [PMID:37938170 "Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase."] [PMID:37938170 "Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A)."] Supporting Evidence: PMID:37938170 Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. PMID:37938170 Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A). |
| GO:0017128 phospholipid scramblase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phospholipid scramblase activity (IBA). Human ATG9B forms the conserved ATG9 homotrimer and is a functional lipid scramblase in vitro. It also forms a complex with the lipid-transfer protein ATG2A, as ATG9A does. Core function. Reason: [PMID:37938170 "Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase."] [PMID:37938170 "Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein."] [PMID:37938170 "Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A."] Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000315580 SUPPORTS TRANSFER ATG9 family node; scramblase activity is now shown directly for ATG9B (PMID:37938170). Supporting Evidence: PMID:37938170 Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. PMID:37938170 Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. PMID:37938170 Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. |
| GO:0017128 phospholipid scramblase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Phospholipid scramblase activity (ISS). Human ATG9B forms the conserved ATG9 homotrimer and is a functional lipid scramblase in vitro. It also forms a complex with the lipid-transfer protein ATG2A, as ATG9A does. Core function. The ISS source is the paralog ATG9A, but the activity has since been measured for ATG9B itself. Reason: [PMID:37938170 "Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase."] [PMID:37938170 "Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein."] [PMID:37938170 "Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A."] Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q7Z3C6 SUPPORTS TRANSFER Human ATG9A (paralog); scramblase activity independently shown for ATG9B (PMID:37938170), so the paralog transfer is correct here. Supporting Evidence: PMID:37938170 Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. PMID:37938170 Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. PMID:37938170 Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. |
| GO:0034045 obsolete phagophore assembly site membrane | EXP PMID:18936157 Kinase-inactivated ULK proteins inhibit autophagy via their ... | MODIFY | Summary: Phagophore assembly site membrane (EXP). This term is now obsolete. As in the ATG9A review, the localization is better stated as phagophore. UniProt cites this ULK study for ATG9B's starvation-induced redistribution, which depends on ULK1 and ATG13; the cached abstract speaks only of Atg9 trafficking, so I defer to the curator on the assay. Reason: [file:human/ATG9B/ATG9B-uniprot.txt "CC -!- SUBCELLULAR LOCATION: Preautophagosomal structure membrane"] [PMID:18936157 "Atg13 is required for autophagy and Atg9 trafficking during autophagy."] Proposed replacements: phagophore Supporting Evidence: file:human/ATG9B/ATG9B-uniprot.txt CC -!- SUBCELLULAR LOCATION: Preautophagosomal structure membrane PMID:18936157 Atg13 is required for autophagy and Atg9 trafficking during autophagy. |
| GO:0034045 obsolete phagophore assembly site membrane | IEA GO_REF:0000044 | MODIFY | Summary: Phagophore assembly site membrane (IEA). This term is now obsolete. As in the ATG9A review, the localization is better stated as phagophore. UniProt cites this ULK study for ATG9B's starvation-induced redistribution, which depends on ULK1 and ATG13; the cached abstract speaks only of Atg9 trafficking, so I defer to the curator on the assay. Reason: [file:human/ATG9B/ATG9B-uniprot.txt "CC -!- SUBCELLULAR LOCATION: Preautophagosomal structure membrane"] [PMID:18936157 "Atg13 is required for autophagy and Atg9 trafficking during autophagy."] Proposed replacements: phagophore Supporting Evidence: file:human/ATG9B/ATG9B-uniprot.txt CC -!- SUBCELLULAR LOCATION: Preautophagosomal structure membrane PMID:18936157 Atg13 is required for autophagy and Atg9 trafficking during autophagy. |
| GO:0034497 protein localization to phagophore assembly site | IBA GO_REF:0000033 | ACCEPT | Summary: Protein localization to phagophore assembly site (IBA). ATG9-family vesicles help recruit autophagy machinery to the nucleation site, and ATG9B reproduces ATG9A trafficking and function. Accepted. Reason: [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000315580 SUPPORTS TRANSFER Node seeded by yeast Atg9; ATG9B functionally replaces ATG9A (PMID:37938170). Supporting Evidence: PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. |
| GO:0034727 piecemeal microautophagy of the nucleus | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Piecemeal microautophagy of the nucleus (IBA). The donor is yeast Atg9. This process happens at the yeast nucleus-vacuole junction, which mammals do not have. Over-annotation, as in the ATG9A review. Reason: [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN000315580 SUPPORTS SOURCE BUT NOT TARGET Yeast nucleus-vacuole-junction process; the structure has no mammalian counterpart. Supporting Evidence: PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. |
| GO:0055038 recycling endosome membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Recycling endosome membrane (ISS, from the paralog ATG9A). In HEK293A cells, ATG9B colocalizes mainly with the Golgi marker GM130, and to a lesser extent with EEA1-positive early endosomes and RAB11-positive recycling endosomes, matching the ATG9A pattern. Accepted as non-core steady-state locations. Reason: [PMID:37938170 "Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A)."] Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q7Z3C6 SUPPORTS TRANSFER Human ATG9A (paralog); ATG9B's own Golgi/endosome colocalization (PMID:37938170) corroborates the transfer. Supporting Evidence: PMID:37938170 Like ATG9A, ATG9B was mainly co-localized with the Golgi marker GOLGA2/GM130, to a lesser extent with early endosomes, positive for EEA1, and recycling endosomes labeled using RAB11 (Figure 6A). |
| GO:0060349 bone morphogenesis | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Bone morphogenesis (ISS). The source (Q68FE2) is mouse Atg9a, a paralog, and the annotation is a phenotype of that ubiquitously expressed gene. ATG9B is tissue-restricted (placenta, pituitary), and no such phenotype is reported for it. The same term is marked over-annotated on ATG9A itself. Over-annotation. Reason: [PMID:37938170 "ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role"] [PMID:15755735 "In human adult tissues, APG9L1 was ubiquitously expressed, whereas APG9L2 was highly expressed in placenta (trophoblast cells) and pituitary gland."] Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:Q68FE2 SUPPORTS SOURCE BUT NOT TARGET Mouse Atg9a (paralog, not ortholog). A knockout phenotype of the ubiquitous paralog does not transfer to the tissue-restricted ATG9B. Supporting Evidence: PMID:37938170 ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role PMID:15755735 In human adult tissues, APG9L1 was ubiquitously expressed, whereas APG9L2 was highly expressed in placenta (trophoblast cells) and pituitary gland. |
| GO:0061709 reticulophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Reticulophagy (IBA). This selective autophagy pathway uses the core ATG9 machinery. It is plausible for ATG9B wherever it is expressed, but not tested in the cited sources, and ATG9B is largely confined to placenta and pituitary. Kept as non-core, as for ATG9A. Reason: [PMID:37938170 "We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization."] [PMID:37938170 "ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role"] Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000315580 SUPPORTS TRANSFER Node seeded by yeast and fly Atg9 selective-autophagy data. Supporting Evidence: PMID:37938170 We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. PMID:37938170 ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role |
| GO:0097300 programmed necrotic cell death | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Programmed necrotic cell death (ISS). The source (Q68FE2) is mouse Atg9a, a paralog, and the annotation is a phenotype of that ubiquitously expressed gene. ATG9B is tissue-restricted (placenta, pituitary), and no such phenotype is reported for it. The same term is marked over-annotated on ATG9A itself. Over-annotation. Reason: [PMID:37938170 "ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role"] [PMID:15755735 "In human adult tissues, APG9L1 was ubiquitously expressed, whereas APG9L2 was highly expressed in placenta (trophoblast cells) and pituitary gland."] Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:Q68FE2 SUPPORTS SOURCE BUT NOT TARGET Mouse Atg9a (paralog, not ortholog). A knockout phenotype of the ubiquitous paralog does not transfer to the tissue-restricted ATG9B. Supporting Evidence: PMID:37938170 ATG9B is described as a vertebrate specific paralog and, in contrast to the ubiquitously expressed ATG9A, is enriched in the placenta and pituitary gland suggesting a specialized role PMID:15755735 In human adult tissues, APG9L1 was ubiquitously expressed, whereas APG9L2 was highly expressed in placenta (trophoblast cells) and pituitary gland. |
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Experiment: Delete ATG9B in trophoblast organoids or in mouse placenta and pituitary, measure autophagy flux and tissue function, and test whether ATG9A can rescue.
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