CLCN4 encodes ClC-4, a voltage-dependent chloride:proton exchanger of intracellular membranes. Association with ClC-3 shapes its stability and routes it to endosomal, recycling-endosomal and lysosomal compartments, while unpartnered ClC-4 can accumulate in the endoplasmic reticulum. TMEM9-family partners further couple transporter stability to regulation of transport activity. ClC-4 supports neuronal endomembrane ion homeostasis. Pathogenic CLCN4 variants cause an X-linked neurodevelopmental disorder with intellectual disability and variable epilepsy and behavioral features; their effects on transport depend on voltage, pH and the associated ClC-3 partner.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005247 voltage-gated chloride channel activity | IEA GO_REF:0000002 | MODIFY | Summary: The channel-family mapping is better represented by chloride:proton exchange. Reason: The InterPro assignment identifies a CLC-family transport protein, but CLCN4 directly exchanges chloride and protons rather than simply providing a chloride-conducting channel. Voltage dependence remains real; the later proton-flux experiments resolve the transport mechanism more precisely. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: InterPro:IPR002246 SUPPORTS TRANSFER The family association is genuine, but its channel label does not distinguish this exchanger from CLC channels. Proposed replacements: chloride:proton antiporter activity |
| GO:0005247 voltage-gated chloride channel activity | TAS PMID:8069296 A gene from the Xp22.3 region shares homology with voltage-g... | MODIFY | Summary: Refine the historical channel classification to chloride:proton antiporter activity. Reason: The complete 1994 abstract identifies a 760-residue protein by cloning and homology to voltage-gated chloride channels; its full body was not recovered. Later direct CLCN4 proton-flux experiments supply the mechanistic refinement, without attributing that assay to the original reference. Proposed replacements: chloride:proton antiporter activity |
| GO:0005254 chloride channel activity | IBA GO_REF:0000033 | MODIFY | Summary: The inherited CLC transport function is more accurately described as exchange. Reason: The authenticated PAINT assertion includes experimental grounding on CLCN4 itself. Direct chloride/proton coupling supports a mechanistic term correction, not a claim that self-inclusion is circular or that the target was placed in the wrong family. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: PANTHER:PTN002905616 UNRESOLVED The historical tree, MSA and IBD placement were not reconstructed. Current target evidence resolves exchange rather than channel conduction, but does not establish where that distinction arose in the family. Proposed replacements: chloride:proton antiporter activity |
| GO:0005254 chloride channel activity | IDA PMID:10564087 Identification of an acid-activated Cl(-) channel from human... | MODIFY | Summary: Preserve the reported currents while refining their molecular interpretation to exchange. Reason: The authentic abstract reports acid-activated outward currents after expression of a human skeletal-muscle clone in CHO cells. The full original Methods and Results remain inaccessible; later direct CLCN4 proton-transport work justifies the exchange term without claiming that the 1999 assay measured proton coupling or that its positive observation was misattributed. Proposed replacements: chloride:proton antiporter activity |
| GO:0005254 chloride channel activity | IEA GO_REF:0000117 | MODIFY | Summary: The current ARBA rule reaches CLCN4, but its channel output needs mechanistic refinement. Reason: Current target InterPro/FunFam and taxon conditions match ARBA00026476 condition sets 1 and 9, using zero-based numbering. That verified route emits a channel term; direct CLCN4 chloride/proton exchange supports the more accurate antiporter term. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: ARBA:ARBA00026476 SUPPORTS TRANSFER The current condition matches are authenticated. The concern is the channel-versus-exchanger meaning of the emitted term, not an unexplained propagation route. Proposed replacements: chloride:proton antiporter activity |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | KEEP AS NON CORE | Summary: Retain the source-specific CLCN4–ABHD5 interaction outside the transport core. Reason: Three exact positive IntAct records link human CLCN4 and ABHD5 in array, prey-pooling and validated yeast two-hybrid assays. These support the reported binding pair at assay scope; they do not establish a native compartment encounter or a CLCN4 regulatory mechanism. No more specific activity is demonstrated by this pair. The ClinGen project policy explicitly retains supported generic interactions as non-core when a more specific activity has not been established (projects/CLINGEN_MENDELIAN.md, Curation instructions). Supporting Evidence: |
| GO:0005765 lysosomal membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Lysosomal membrane localization is part of the partner-dependent endolysosomal distribution. Reason: The curated PAINT placement is corroborated by human long ClC-4 localization with ClC-3a/b and current experimental mouse Clcn3 records. This is a conditional compartment distribution rather than localization of every CLCN4 product in every cell. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002269383 SUPPORTS TRANSFER Authenticated curated propagation and experimental endolysosomal localization support retention. Historical node placement was not independently reconstructed; target self-inclusion is legitimate experimental grounding. |
| GO:0005765 lysosomal membrane | IDA PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | ACCEPT | Summary: ClC-3 association directs human ClC-4 to late endosomal and lysosomal membranes. Reason: The study expressed the long human ClC-4 construct with mouse ClC-3 splice variants and observed redistribution from the ER to late endosomal/lysosomal compartments with ClC-3a/b. These construct and partner conditions delimit the positive localization. Supporting Evidence: |
| GO:0005765 lysosomal membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Retain the lysosomal membrane vocabulary mapping. Reason: The UniProt subcellular-location mapping agrees with directly observed partner-dependent lysosomal targeting of human long ClC-4. It does not imply constitutive lysosomal residence of the unpartnered or shorter product. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0157 SUPPORTS TRANSFER The mapped compartment has independent target localization support under defined ClC-3 coexpression conditions. |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:17023393 The human ClC-4 protein, a member of the CLC chloride channe... | KEEP AS NON CORE | Summary: ER membrane residence is a genuine expression and retention context. Reason: The recovered original Methods and Results show full-length human GFP/FLAG-ClC-4 in HEK293 ER fractions and with ER markers; separate mouse-brain fractionation also supports an ER pool. The early N-terminal targeting model is not treated as the only determinant because later work maps additional retention behavior and partner-dependent export. |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:27550844 De novo and inherited mutations in the X-linked gene CLCN4 a... | KEEP AS NON CORE | Summary: Retain the observed ER localization in the heterologous assay. Reason: Wild-type and tested mutant human ClC-4 localized predominantly to the ER in COS-7 cells. This positive observation is retained separately from the endosomal transport core; it does not require assuming that all physiological CLCN4 is ER resident. |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | KEEP AS NON CORE | Summary: Unpartnered human long ClC-4 is predominantly retained in the ER. Reason: The human long construct displayed ER localization when expressed alone, whereas ClC-3 splice variants promoted endosomal sorting. In primary mouse astrocytes expressing the fluorescent human construct, WT cells showed predominantly Rab7-positive localization and Clcn3-null cells showed ER retention. Expression-level controls supported partner-dependent sorting; this was not an endogenous human-neuron localization experiment. Supporting Evidence: |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Retain the ER membrane vocabulary mapping as a contextual localization. Reason: Independent human-expression studies directly support ER residence. Partner-dependent redistribution explains why this valid mapped compartment is not the organizing location of the endosomal exchange core. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB-SubCell:SL-0097 SUPPORTS TRANSFER The mapped ER location is experimentally supported, with the distribution conditioned by expression and partner availability. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Retain the plasma membrane assertion at its supported contextual scope. Reason: The authenticated PAINT node draws on experimentally annotated CLC-family members, and human ClC-4 produces surface currents in expression systems. This supports a functional surface pool under assay conditions, while partner-dependent intracellular sorting prevents treating plasma membrane as the principal physiological location. The 2017 paper also discusses earlier endogenous apical localization in human Caco-2 cells, separately from its own heterologous and mouse-astrocyte experiments. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000189250 SUPPORTS TRANSFER Current donor experimental records and target surface transport corroborate the curated assertion. The historical IBD placement remains uninspected; donor number is not used to judge support. |
| GO:0006821 chloride transport | IDA PMID:10564087 Identification of an acid-activated Cl(-) channel from human... | MODIFY | Summary: Specify chloride movement across a membrane. Reason: The original abstract reports human ClC-4-dependent CHO-cell currents; later direct coupled transport establishes the transmembrane step. The preserved acts_upstream_of_or_within qualifier is not silently strengthened while the process term is made more specific. Proposed replacements: chloride transmembrane transport |
| GO:0006821 chloride transport | IEA GO_REF:0000002 | MODIFY | Summary: The domain-based transport annotation can specify transmembrane chloride movement. Reason: The genuine CLC-family mappings agree with measured ClC-4 chloride/proton exchange. Chloride transmembrane transport describes the actual membrane-crossing work performed by the protein. Proposed replacements: chloride transmembrane transport |
| GO:0006821 chloride transport | IMP PMID:23647072 Exome sequencing reveals new causal mutations in children wi... | MODIFY | Summary: Specify the transmembrane chloride transport tested by the human variant experiment. Reason: Human wild-type and G544R ClC-4 constructs were examined in HeLa cells and Xenopus oocytes; the variant nearly abolished the measured currents. The chloride transmembrane term is supported, while direct proton coupling is established by the independent exchange study rather than by these current measurements alone. Proposed replacements: chloride transmembrane transport |
| GO:0006821 chloride transport | IMP PMID:25644381 X-exome sequencing of 405 unresolved families identifies sev... | MODIFY | Summary: Specify chloride transmembrane transport. Reason: The paper measured effects of human CLCN4 variants on oocyte currents. Its separate mouse neuronal knockdown/rescue and knockout-morphology experiments are not substituted for that direct transport assay or used to manufacture another developmental process. Proposed replacements: chloride transmembrane transport |
| GO:0010008 endosome membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Endosomal membrane localization is central to ClC-4 transport. Reason: The curated PAINT assertion is corroborated by partner-dependent targeting of the human long protein and current experimental donor records. Endosomal sorting is supported without assuming that the historical phylogenetic placement has been reconstructed. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002269368 SUPPORTS TRANSFER Authenticated experimental grounding and direct target localization support this compartment. The target appearing among descendants is not circular evidence. |
| GO:0010008 endosome membrane | IDA PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | ACCEPT | Summary: ClC-3 partners route human ClC-4 to endosomal membranes. Reason: The full-length human construct associates with mouse ClC-3 splice variants, which determine its late/endolysosomal or recycling distribution. The unpartnered ER pool and the low-expressing short construct are separate experimental contexts. Supporting Evidence: |
| GO:0010008 endosome membrane | TAS Reactome:R-HSA-2730692 | ACCEPT | Summary: The Reactome target entity is explicitly in the endosome membrane. Reason: The reaction catalyst set resolves to the P51793 protein entity with residues 1–760 and the endosome membrane compartment. CLCN4, CLCN5 and CLCN6 are alternatives in that set, not an asserted obligate three-protein complex. Supporting Evidence: Reactome:R-HSA-2730692 |
| GO:0015108 chloride transmembrane transporter activity | IEA GO_REF:0000002 | MODIFY | Summary: Specify coupled chloride:proton antiporter activity. Reason: The InterPro assignment correctly identifies a chloride transporter. Direct proton flux and transport against the proton gradient distinguish the coupled antiporter mechanism from this broader activity. Proposed replacements: chloride:proton antiporter activity |
| GO:0015297 antiporter activity | IDA PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | MODIFY | Summary: Specify the substrates of ClC-4 antiport. Reason: This study measures human ClC-4 currents, assembly and sorting; it does not independently quantify proton flux. The original antiporter assertion is refined with the direct chloride/proton-coupling evidence from the earlier mechanistic study. Proposed replacements: chloride:proton antiporter activity |
| GO:0015297 antiporter activity | IMP PMID:23647072 Exome sequencing reveals new causal mutations in children wi... | MODIFY | Summary: Specify chloride:proton exchange for the variant-sensitive transporter. Reason: The human G544R functional assay supports loss of ClC-4 current, with mutant expression/localization examined separately. Later interpretation of that current is grounded in direct ClC-4 exchange experiments rather than a claim that this clinical study measured H+ coupling. Proposed replacements: chloride:proton antiporter activity |
| GO:0015297 antiporter activity | IMP PMID:27550844 De novo and inherited mutations in the X-linked gene CLCN4 a... | MODIFY | Summary: Specify chloride:proton exchange. Reason: The human constructs produced strongly rectifying currents in oocytes, with most tested disease variants reducing or abolishing currents while Asp15Asn was WT-like. Their exchange mechanism comes from independent proton-transport experiments; the study’s algal structural model is not a human structure. Proposed replacements: chloride:proton antiporter activity |
| GO:0015297 antiporter activity | TAS Reactome:R-HSA-2730692 | MODIFY | Summary: The Reactome reaction supports substrate-specific antiporter activity. Reason: The target is an alternative catalyst for exchange of endosomal chloride and cytosolic proton into the opposite pools. It performs transport rather than serving as a transported substrate, so the explicit reaction supports chloride:proton antiporter activity. Proposed replacements: chloride:proton antiporter activity |
| GO:0016020 membrane | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Retain the valid broad membrane mapping outside the compartment-specific core. Reason: The InterPro CLC-family mappings support a membrane protein but do not determine its organelle. This broad source assertion is retained at that scope. Independent human ClC-4 localization experiments support the separately reviewed endosomal, lysosomal, ER and surface annotations; they are not attributed to the domain mapping. Supporting Evidence: GO_REF:0000002 |
| GO:0031901 early endosome membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Retain the mapped early endosome membrane compartment. Reason: The UniProt subcellular mapping agrees with a genuine rat Clcn4 experimental annotation and the conserved endosomal distribution of the human transporter. The more recent human sorting experiments mainly resolve late and recycling pools; they are not mislabeled as a direct replication of the rat early-endosome assay. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0093 SUPPORTS TRANSFER The current rat P51794 record carries experimental early-endosome localization from PMID:16222710. Its original body was not separately reread; the curated compartment is retained with ortholog and assay scope explicit. |
| GO:0031901 early endosome membrane | ISS GO_REF:0000024 | ACCEPT | Summary: Retain the curated rat-to-human early-endosomal localization transfer. Reason: P51794 is the rat Clcn4 ortholog, and its current early endosome membrane record is experimental with PMID:16222710. Human partner-dependent endosomal targeting corroborates the biological compartment without pretending to have independently reconstructed the original rat localization assay. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P51794 SUPPORTS TRANSFER The donor identity and experimental term record are authenticated. No wrong-paralog or donor-count objection is supported. |
| GO:0031902 late endosome membrane | EXP PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | ACCEPT | Summary: Retain directly observed late endosomal targeting. Reason: Human long ClC-4 is redirected to late endosomal/lysosomal compartments by mouse ClC-3a/b. The source distinguishes those partners from ClC-3c, which produces a recycling-endosomal distribution. Supporting Evidence: |
| GO:0031902 late endosome membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Retain the late endosome membrane vocabulary mapping. Reason: The specific compartment agrees with the human long-protein localization experiment under ClC-3a/b coexpression. It remains conditional on the partner-dependent sorting context. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0151 SUPPORTS TRANSFER The mapped compartment has direct target support in the primary sorting study. |
| GO:0034220 monoatomic ion transmembrane transport | TAS Reactome:R-HSA-983712 | MODIFY | Summary: Specify chloride transmembrane transport within the broad Reactome pathway. Reason: The pathway resolves through its CLC exchange reaction to the P51793 catalyst entity. Although the parent pathway is named Ion channel transport, this target performs chloride/proton exchange; the chloride transmembrane process captures its own transport step. Proposed replacements: chloride transmembrane transport Supporting Evidence: Reactome:R-HSA-983712 Reactome:R-HSA-2730692 |
| GO:0055037 recycling endosome | IDA PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | MODIFY | Summary: Specify the membrane of the recycling endosome. Reason: The fluorescent human long ClC-4 construct is a membrane protein routed to recycling endosomes by mouse ClC-3c. The membrane term makes the supported localization more precise without altering the original source or evidence. Proposed replacements: recycling endosome membrane Supporting Evidence: |
| GO:0055038 recycling endosome membrane | EXP PMID:28972156 Preferential association with ClC-3 permits sorting of ClC-4... | ACCEPT | Summary: Retain the recycling endosome membrane localization. Reason: ClC-3c-dependent sorting of the human long construct supports this compartment. It is distinct from the late/endolysosomal routing produced by ClC-3a/b in the same study. Supporting Evidence: |
| GO:0055038 recycling endosome membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Retain the specific recycling-endosome membrane mapping. Reason: The UniProt vocabulary mapping agrees with the observed human ClC-4 distribution under ClC-3c coexpression. No all-products localization claim is needed. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0231 SUPPORTS TRANSFER The source mapping is corroborated by the target-specific partner-dependent localization experiment. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: Specify the chloride substrate of transmembrane transport. Reason: The family-based broad process is correct but underspecified. Direct ClC-4 exchange experiments establish chloride movement across a membrane, which is already independently represented among the original source assertions. Proposed replacements: chloride transmembrane transport |
| GO:1902476 chloride transmembrane transport | IBA GO_REF:0000033 | ACCEPT | Summary: Retain chloride transmembrane transport as the protein’s performed process. Reason: Experimental CLC-family descendant annotations support the curated PAINT placement, and direct ClC-4 exchange independently establishes this target’s transport step. No new developmental or channel-trafficking process is inferred from mutant or knockout phenotypes. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000189250 SUPPORTS TRANSFER The inherited chloride-transport function has authenticated experimental grounding and direct target corroboration. Historical tree/MSA/IBD reconstruction was not performed. |
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Download this section (compressed HTML)Q: How do endogenous ClC-3 isoforms, TMEM9-family occupancy, voltage and luminal pH jointly set ClC-4 transport in human neuronal endosomes?
Q: What are the abundance, localization and transport roles of the shorter human CLCN4 product under native expression conditions?
Q: Which neuronal consequences of CLCN4 loss follow directly from altered organellar chloride/proton exchange, and which reflect secondary changes in partner stability or membrane trafficking?
Experiment: Measure chloride and proton flux together in defined human ClC-4 assemblies with matched ClC-3 isoforms and TMEM9-family occupancy, using physiological endosomal voltage and pH ranges and independent surface/compartment abundance controls.
Experiment: Quantify endogenous long and short CLCN4 products in human neurons, then perform product-specific rescue with organellar ion sensors and compartment-resolved localization.
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