EPG5 is a 2,579-residue cytoplasmic Rab7 effector that coordinates selective fusion of autophagosomes with late endosomes and lysosomes. It associates with the lysosomal surface through Rab7 and VAMP7/8, binds autophagic STX17-SNAP29-containing SNARE assemblies, and engages LC3/GABARAP proteins through tandem LC3-interacting-region motifs, with preferential binding to the GABARAP subfamily. These interactions organize the fusion machinery and restrict inappropriate fusion with other endocytic vesicles; EPG5 deficiency causes accumulation of undegraded autophagic cargo. EPG5 also supports endosome-to-lysosome delivery of internalized nucleic acids, enabling endosomal TLR9 and TLR7 signaling. Biallelic pathogenic variants cause Vici syndrome and a neurodevelopmental disorder with parkinsonism or other movement abnormalities.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | KEEP AS NON CORE | Summary: Human EPG5 associates with RAN in cell extracts. Reason: PMID:29130391 Results EPG5 sequence homology and Figure 7D report reciprocal EPG5/RAN co-immunoprecipitation in human fibroblast and transfected HEK293T extracts; the Co-immunoprecipitation Methods use detergent-solubilized cell lysates. This supports the reported physical association, although it does not establish a purified binary interaction or nuclear import/export activity. The source partner is RAN (P62826), not Rab7. Retain supported generic binding as non-core without assigning an untested karyopherin mechanism. The ClinGen campaign instruction in projects/CLINGEN_MENDELIAN.md retains supported generic protein binding as KEEP_AS_NON_CORE when no evidence-backed specific replacement is established. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: EPG5 has a cytoplasmic pool associated with endolysosomal trafficking. Reason: The actual PTHR31139 tree places human EPG5 PTN002525333 below the cytoplasmic IBD at PTN001579556. Its aligned sequence matches the displayed 2579-residue Q9HCE0 product exactly; the family includes distinct limb-expression-protein branches, so the broad ancestral cytoplasmic claim is not mistaken for EPG5-specific orthology. The current IBD export contains this location assertion and no negated record on the inspected target path. PMID:29130391 Figure 7E and fractionation Methods independently support a human cytoplasmic pool. This does not exclude the separately observed nuclear/perinuclear pool. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001579556 · PTN001579556 SUPPORTS TRANSFER Actual PTHR31139 tree placement, exact human alignment sequence and matching current IBD location assertion were verified. The target self-evidence is legitimate. No negated record occurs on this target path in the inspected IBD export; no family-wide absence-of-loss claim is inferred. Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 |
| GO:0005764 lysosome | IBA GO_REF:0000033 | MODIFY | Summary: Human EPG5 has a lysosomal membrane-associated pool. Reason: PMID:27588602 supplementary Figure S3D shows the acidic LysoTracker-positive compartment inside GFP-hEPG5-labeled structures; S3I-N immunogold microscopy places tagged human EPG5 on late-endosomal and hybrid endosome-lysosome membranes in HeLa cells. The original S3 image and caption were inspected. PMID:29130391 Figure 4B-D independently shows human EPG5-GFP associated with LAMP2-positive compartments. Together these data support refining lysosome to lysosomal membrane (GO:0005765), without implying an integral membrane protein, a luminal enzyme or identical localization of every splice isoform. The verified IBD node PTN001259269 still supports the broad compartment; the narrower target-specific refinement uses the independently inspected human experiments, not a claim that the ancestral assertion was erroneous. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: PANTHER:PTN001259269 · PTN001259269 SUPPORTS TRANSFER Actual PTHR31139 tree placement, exact human alignment sequence and matching current IBD location assertion were verified. The target self-evidence is legitimate. No negated record occurs on this target path in the inspected IBD export; no family-wide absence-of-loss claim is inferred. The source location remains biologically supported; the proposed membrane refinement uses direct target evidence. Proposed replacements: lysosomal membrane Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 PMID:29130391 Analysis confirmed the interaction of EPG5 with LAMP2, but not with EEA1 |
| GO:0005764 lysosome | IDA PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | MODIFY | Summary: Human EPG5 has a lysosomal membrane-associated pool. Reason: PMID:27588602 supplementary Figure S3D shows the acidic LysoTracker-positive compartment inside GFP-hEPG5-labeled structures; S3I-N immunogold microscopy places tagged human EPG5 on late-endosomal and hybrid endosome-lysosome membranes in HeLa cells. The original S3 image and caption were inspected. PMID:29130391 Figure 4B-D independently shows human EPG5-GFP associated with LAMP2-positive compartments. Together these data support refining lysosome to lysosomal membrane (GO:0005765), without implying an integral membrane protein, a luminal enzyme or identical localization of every splice isoform. Proposed replacements: lysosomal membrane Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 PMID:29130391 Analysis confirmed the interaction of EPG5 with LAMP2, but not with EEA1 |
| GO:0005764 lysosome | IEA GO_REF:0000044 | MODIFY | Summary: Human EPG5 has a lysosomal membrane-associated pool. Reason: PMID:27588602 supplementary Figure S3D shows the acidic LysoTracker-positive compartment inside GFP-hEPG5-labeled structures; S3I-N immunogold microscopy places tagged human EPG5 on late-endosomal and hybrid endosome-lysosome membranes in HeLa cells. The original S3 image and caption were inspected. PMID:29130391 Figure 4B-D independently shows human EPG5-GFP associated with LAMP2-positive compartments. Together these data support refining lysosome to lysosomal membrane (GO:0005765), without implying an integral membrane protein, a luminal enzyme or identical localization of every splice isoform. The imported UniProt SL-0158 mapping is retained unchanged; its broad compartment is refined using the human experimental evidence. Proposed replacements: lysosomal membrane Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 |
| GO:0006862 nucleotide transport | IMP PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | MODIFY | Summary: EPG5 enables vesicular delivery of internalized CpG oligodeoxynucleotides to the endolysosomal compartment. Reason: The current GO:0006862 definition concerns movement of nucleotides, whereas PMID:29130391 Figures 2-4 trace an internalized DNA oligonucleotide through endocytic compartments. EPG5 depletion retains CpG in tubular/recycling endosomes and prevents its delivery to LAMP2-positive organelles. The observed work is the vesicular trafficking step, appropriately described by GO:0008333, rather than transport of free nucleotide molecules. That same term already occurs in the imported annotations; this is a source-specific refinement, not an additional row. Proposed replacements: endosome to lysosome transport Supporting Evidence: PMID:29130391 In summary, lack of EPG5 impairs the transport to CpG-FITC to the LEs and lysosomes, where TLR9 is located. PMID:29130391 Here we show that EPG5 also plays autophagy-independent roles in the trafficking of molecules from the EEs to LEs and lysosomes. |
| GO:0008333 endosome to lysosome transport | IMP PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | ACCEPT | Summary: EPG5 supports transport of internalized endocytic cargo to late endosomes and lysosomes. Reason: PMID:29130391 Figures 2-4 and the Cell stimulation, siRNA and Confocal microscopy Methods directly follow fluorescent CpG in patient fibroblasts, patient lymphoblastoid cell lines and human control fibroblasts depleted of EPG5. Cargo accumulates in tubular/recycling endosomes when EPG5 is deficient. ATG7 depletion does not reproduce this trafficking defect (Figure 3D-E), supporting a role separable from autophagosome formation in this assay. Failed transfection rescue is reported and is not described as a successful rescue. The specific molecular tethering mechanism of this endocytic route was not reconstituted. Supporting Evidence: PMID:29130391 In summary, lack of EPG5 impairs the transport to CpG-FITC to the LEs and lysosomes, where TLR9 is located. PMID:29130391 Here we show that EPG5 also plays autophagy-independent roles in the trafficking of molecules from the EEs to LEs and lysosomes. PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 |
| GO:0034162 toll-like receptor 9 signaling pathway | IMP PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | KEEP AS NON CORE | Summary: EPG5-dependent ligand trafficking contributes positively to TLR9 signaling in the tested human cells. Reason: PMID:29130391 Figures 1E and 5 show deficient CpG-induced cytokine production and NFKB nuclear translocation in patient or EPG5-depleted cells, while IL1B responses and several other TLR responses remain functional. Figures 2-4 connect this phenotype to delivery of CpG into the receptor-containing endolysosomal compartment. This is an experimentally supported contextual signaling contribution through trafficking, retained as non-core; it does not establish that EPG5 is a receptor, nucleic-acid sensor or kinase. Supporting Evidence: PMID:29130391 We show that mutations or downregulation of EPG5 impaired signaling by TLR9 and TLR7, thus inhibiting NFKB nuclear translocation PMID:29130391 In summary, lack of EPG5 impairs the transport to CpG-FITC to the LEs and lysosomes, where TLR9 is located. |
| GO:0048471 perinuclear region of cytoplasm | IDA PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | KEEP AS NON CORE | Summary: A human EPG5 pool is observed around the nucleus and nuclear envelope. Reason: PMID:29130391 Figure 7E includes EPG5 staining, three-dimensional reconstruction, emerin costaining and nuclear/cytoplasmic fractionation; the figure caption explicitly identifies perinuclear distribution. This supports the location observation even though its proposed karyopherin function remains unproven. The Discussion describes that functional interpretation as preliminary. Retain the observed compartment as non-core, without dismissing it because a nuclear-transport mechanism has not been established. Supporting Evidence: PMID:29130391 our preliminary experiments indicated that EPG5 was located over the nuclear membrane and interacted with RAN |
| GO:0048471 perinuclear region of cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: A human EPG5 pool is observed around the nucleus and nuclear envelope. Reason: PMID:29130391 Figure 7E includes EPG5 staining, three-dimensional reconstruction, emerin costaining and nuclear/cytoplasmic fractionation; the figure caption explicitly identifies perinuclear distribution. This supports the location observation even though its proposed karyopherin function remains unproven. The Discussion describes that functional interpretation as preliminary. Retain the observed compartment as non-core, without dismissing it because a nuclear-transport mechanism has not been established. The imported SL-0198 mapping is consistent with this independently read human observation. Supporting Evidence: PMID:29130391 our preliminary experiments indicated that EPG5 was located over the nuclear membrane and interacted with RAN |
| GO:0061909 autophagosome-lysosome fusion | IBA GO_REF:0000033 | ACCEPT | Summary: EPG5 participates in productive autophagosome-lysosome fusion and clearance. Reason: PMID:23222957 Results and Figures 3-4 show impaired autophagic clearance and reduced LC3/LAMP1 colocalization in human patient fibroblasts, with rapamycin/bafilomycin treatment distinguishing early induction from downstream clearance. The recovered PMID:27588602 supplement Figure S6T additionally shows reduced endogenous STX17-VAMP7 association in human EPG5-depleted cells; S6O-Q directly establishes human-fragment interaction with SNAREs. Lipid-mixing reconstitution in that paper uses worm EPG-5 and worm SNAREs and is not a purified human assay. The actual PAINT tree places the human target and fish epg5 below PTN001259269. Current QuickGO still reports this fusion IBA, but the downloaded current IBD export lacks its corresponding fusion assertion; record that provenance gap without treating it as biological contradiction or weak donor-count evidence. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN001259269 · PTN001259269 UNRESOLVED Human PTN002525333 and fish epg5 PTN001259293 are verified descendants in the actual tree. The imported/current QuickGO fusion assertion is present, but its exact IBD is absent from the inspected current export; the fish UniProt response contains IBA rather than the underlying experimental ZFIN record. Biological acceptance uses independently read human original evidence, not a claim that the full donor chain was recovered. Supporting Evidence: PMID:27588602 EPG5 stabilizes and facilitates the assembly of STX17-SNAP29-VAMP7/8 trans-SNARE complexes, and promotes STX17-SNAP29-VAMP7-mediated fusion of reconstituted proteoliposomes PMID:27588602 Loss of EPG5 activity causes abnormal fusion of autophagosomes with various endocytic vesicles, in part due to elevated assembly of STX17-SNAP25-VAMP8 complexes PMID:23222957 Further studies showed a severe block in autophagosomal clearance in muscle and fibroblasts from individuals with mutant EPG5, resulting in the accumulation of autophagic cargo in autophagosomes. PMID:20550938 EI24 and mEPG5 are required for formation of degradative autolysosomes. |
| GO:1990786 cellular response to dsDNA | IMP PMID:29130391 The Vici syndrome protein EPG5 regulates intracellular nucle... | UNDECIDED | Summary: The dsDNA-specific response remains unresolved despite access to the original study. Reason: The current GO definition covers cellular changes caused by a double-stranded DNA stimulus, including changes in gene expression; it does not require a particular receptor or immune-signaling readout. In PMID:29130391 (doi:10.1080/15548627.2017.1389356), the Toll-like receptor stimulation Methods explicitly use single-stranded DNA ODN for TLR9, so the cytokine and NF-kappaB experiments (Figures 1E and 5) do not establish the double-stranded stimulus. The separate DNA/RNA-vector Results and Figure 6B do expose human fibroblasts to a dsDNA baculovirus carrying RAB5A/RAB7-GFP reporters. Reporter positivity depends jointly on viral entry, endosomal delivery, DNA release, nuclear access and expression; the assay does not distinguish a dsDNA-elicited cellular response from efficient delivery and expression of a DNA template. EPG5 has positive evidence for trafficking activity, so it is not established that its role categorically excludes participation in a response process. The stimulus-specific attribution is therefore unresolved: the experiments justify neither confident acceptance nor a definitive over-annotation judgment. This uncertainty concerns the interpretation of accessible evidence, not missing main text. The inherited TLR9/TLR7 quotation documents the separate signaling experiments; it is contextual support, not direct evidence of dsDNA specificity. Supporting Evidence: PMID:29130391 We show that mutations or downregulation of EPG5 impaired signaling by TLR9 and TLR7, thus inhibiting NFKB nuclear translocation |
| GO:7770062 vesicle membrane tethering activity | IDA PMID:27588602 The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Deter... | UNDECIDED | Summary: EPG5 is a candidate autophagic membrane tether, but isolated human membrane-bridging activity is not established by the inspected experiments. Reason: GO:7770062 is a current, valid molecular-function term requiring physical bridging of a vesicle and target membrane before docking and fusion. The recovered original supplement to PMID:27588602 directly establishes human Rab7 and SNARE interactions (S4F-G, S6O-Q), while the lipid-mixing Methods and S6U-W concern worm EPG-5 and proteoliposomes. Main-paper Figure 6 is available as an original image and shows SNARE assembly and lipid mixing, but its operative main Results/caption remain inaccessible. These observations support a fusion-associated adaptor model without proving an isolated human tethering assay. Retain this inherited proposal and its quotations as unresolved provenance rather than treating worm reconstitution as human biochemical proof. Independent human structural studies PMID:33674710 Figures 1-2 and 7 and PMID:39809444 Figures 1-3 establish elongated architecture and LC3/GABARAP interaction, but membrane bridging remains a mechanistic model rather than an isolated human activity assay. This uncertainty does not assert that the proposed biological tethering role is false. Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 PMID:27588602 EPG5 also binds to LC3/LGG-1 (mammalian and C. elegans Atg8 homolog, respectively) and to assembled STX17-SNAP29 Qabc SNARE complexes on autophagosomes PMID:27588602 EPG5 stabilizes and facilitates the assembly of STX17-SNAP29-VAMP7/8 trans-SNARE complexes, and promotes STX17-SNAP29-VAMP7-mediated fusion of reconstituted proteoliposomes |
| GO:0031267 small GTPase binding | IDA PMID:27588602 The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Deter... | NEW | Summary: Human EPG5 directly binds the small GTPase Rab7 through an experimentally tested fragment. Reason: Retain the inherited proposed annotation. The actual PMID:27588602 supplementary Figure S4F-G shows GST-Rab7 pulldown of purified human EPG5 fragments 491-599 and 491-575; the Protein expression and purification and In vitro pulldown Methods distinguish purified fragments from lysate-based full-length assays. S4E tests full-length human EPG5 association with wild-type and nucleotide-state Rab7 variants in cell extracts. This directly supports small GTPase binding, with no extrapolation to an untested natural isoform, nucleotide exchange or GTP hydrolysis activity. Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 |
| GO:0000149 SNARE binding | IDA PMID:27588602 The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Deter... | NEW | Summary: Human EPG5 binds SNARE proteins and assembled autophagic SNARE complexes. Reason: Retain the inherited proposed annotation. In the actual PMID:27588602 supplement S6O-Q, purified human EPG5(427-1094) binds individual SNAP29/VAMP7/VAMP8 weakly and assembled STX17-SNAP29-VAMP7/8 complexes more strongly; it does not bind isolated STX17 in S6O. S6J-K and N show corresponding human-cell complex associations, and S6T connects EPG5 depletion to reduced endogenous STX17-VAMP7 association. The operative purification/pulldown Methods and figure pixels were inspected. Do not describe every individual partner as an equally strong binary interaction or the worm lipid-mixing assay as full-length human reconstitution. Supporting Evidence: PMID:27588602 EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8 PMID:27588602 EPG5 also binds to LC3/LGG-1 (mammalian and C. elegans Atg8 homolog, respectively) and to assembled STX17-SNAP29 Qabc SNARE complexes on autophagosomes PMID:27588602 EPG5 stabilizes and facilitates the assembly of STX17-SNAP29-VAMP7/8 trans-SNARE complexes, and promotes STX17-SNAP29-VAMP7-mediated fusion of reconstituted proteoliposomes |
| GO:0032182 ubiquitin-like protein binding | IPI PMID:33674710 Insights on autophagosome-lysosome tethering from structural... | NEW | Summary: Human EPG5 directly binds LC3/GABARAP-family ubiquitin-like proteins, preferentially the GABARAP subfamily. Reason: PMID:33674710 Figure 2 and the recombinant-protein purification and affinity-isolation Methods test purified full-length human EPG5 against all six human LC3/GABARAP proteins. The GABARAP subfamily recovers more EPG5 than the LC3 subfamily, and W550A and W567A substitutions distinguish contributions of the tandem LIR region. PMID:39809444 Figures 2 and 3 separately test human LIR peptides by NMR and full-length human EPG5 in HEK293 co-immunoprecipitations: LIR1 W550 is the principal GABARAP-binding determinant in the intact protein. The two motifs are not asserted to bind the same partner simultaneously. GO:0032182 captures binding to these ubiquitin-like proteins; the inspected current ontology searches did not return a more specific LC3/GABARAP-binding term. This is direct molecular-interaction evidence, not a new process inferred from recruitment or knockout alone, and it does not assign ubiquitin conjugation, cargo recognition or equivalent function to the alternative splice isoform. |
Loading supporting content…
Download this section (compressed HTML)Q: Does EPG5 tether membranes on its own (for example, cluster Rab7- and LC3-decorated liposomes in vitro), or does it act only as a SNARE-assembly chaperone downstream of HOPS-mediated tethering?
Q: Is the endolysosomal CpG-delivery defect of EPG5-deficient cells explained by the same Rab7-effector and fusion-specificity mechanism as the autophagy defect?
Q: Does GO:1990786 encompass host-assisted transduction and expression of a dsDNA viral template in the absence of a demonstrated dsDNA-elicited host response, and which Figure 6B step was intended to support the EPG5 assertion?
Experiment: Reconstitute tethering and fusion of Rab7/VAMP7 proteoliposomes with LC3-PE/STX17-SNAP29 proteoliposomes using purified full-length EPG5, with and without HOPS, to separate tethering from SNARE-chaperone activity.
Hypothesis: EPG5 bridges Rab7- and LC3-containing membranes independently of HOPS.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)