CLCN5

Summary: Retain a supported Golgi membrane pool.

Reason: The subcellular-location mapping is corroborated by Human Protein Atlas staining in CACO-2 and RH-30 cells. Golgi residence is a contextual distribution of the membrane transporter; it is not substituted for its endosomal exchange function.

Summary: ClC-5 performs ion transport that supports renal tubular handling of filtered material.

Reason: The curated inherited renal role has direct experimental grounding on human CLCN5 and independent mouse exchange-uncoupling evidence. ClC-5 supplies endosomal ion transport rather than merely being a substrate or disease marker; the broad renal process is retained without adding a new developmental process.

Summary: Retain the experimentally grounded renal function.

Reason: The complete original abstract reports CLCN5 mutations in renal stone disorders and reduced or abolished currents for tested variants in Xenopus oocytes. Its full original body was not recovered. Later mouse experiments separate coupled exchange from chloride conductance and show impaired proximal-tubule uptake when coupling is removed, independently supporting the protein’s performed renal role.

Summary: Refine inherited chloride-channel terminology to chloride:proton exchange.

Reason: The PAINT assertion represents a genuine CLC transport function with target experimental grounding. Later direct ClC-5 proton-flux experiments distinguish coupled exchange from a passive chloride channel while preserving the original voltage-dependent current observations.

Proposed replacements: chloride:proton antiporter activity

Summary: The combined CLC-family mapping can specify chloride:proton antiporter activity.

Reason: The rat Clcn5 and InterPro associations identify the correct transporter family. Direct human ClC-5 coupling evidence supplies the mechanistic refinement; no wrong-gene transfer is inferred from the older channel vocabulary.

Proposed replacements: chloride:proton antiporter activity

Summary: Preserve the original positive currents while updating their mechanistic interpretation.

Reason: The 1996 abstract reports outward chloride currents from human ClC-5 expressed in oocytes and their reduction by disease variants. Those experiments are not described as proton-flux measurements. Independent later ClC-5 experiments demonstrate electrogenic chloride/proton exchange and justify the more precise activity.

Proposed replacements: chloride:proton antiporter activity

Summary: The matched ARBA rule emits an older channel term for an exchanger.

Reason: Current target InterPro/FunFam and taxon conditions match ARBA00026476 condition sets 1 and 9, using zero-based indices. The propagation route is therefore resolved; direct ClC-5 proton transport supplies the substrate-specific antiporter interpretation.

Proposed replacements: chloride:proton antiporter activity

Summary: Specify the experimentally supported interaction with the kinesin KIF3B.

Reason: Human ClC-5 cytoplasmic-tail and KIF3B constructs associate in two-hybrid, pull-down and reciprocal co-immunoprecipitation assays; separate endogenous mouse-kidney experiments support a kinesin-2 complex context. The six exact interaction records comprise five association assays and one colocalization assay, not six independent binding tests. This supports kinesin binding without attributing KIF3B motor activity to ClC-5.

Proposed replacements: kinesin binding

Summary: Retain a contextual cytoplasmic localization.

Reason: The current Human Protein Atlas record includes cytosol staining in U-2 OS cells, alongside plasma membrane and Golgi localization in other tested lines. The broad cytoplasm assertion does not imply that ClC-5 is a freely soluble protein. The current ARBA rule snapshot did not reproduce the original target match; that historical-route limit does not negate the independently supported localization.

Summary: Retain positive lysosomal-membrane fraction detection outside the principal endosomal core.

Reason: Official Table 1 identifies human placental ClC5 as IPI00294056 with seven peptides, 12.9% coverage and 31 spectra. Its logarithmic enrichment statistic is 2.44 but the adjusted P value is 1, so detection is positive without significant enrichment by this study’s threshold. Follow-up fluorescence tested other proteins; inaccessible peptide supplements prevent isoform-discriminating claims.

Summary: Retain the curated lysosomal-membrane assignment at its contextual scope.

Reason: The inherited compartment assertion is supported by current experimental Clcn3/CLCN4 donor localization and positive human ClC-5 lysosomal-membrane fraction detection. The original is_active_in relation is preserved; the target proteomics result alone does not measure lysosomal transport or establish exclusive residence. The principal directly characterized target compartment remains endosomal.

Summary: Specify the endosome membrane occupied by this integral transporter.

Reason: The rat Clcn5 orthology mapping is consistent with directly observed human ClC-5 endosomal membrane localization. The membrane refinement describes the protein’s topology within the original organelle rather than replacing an ortholog with a different family member.

Proposed replacements: endosome membrane

Summary: Retain the supported Golgi compartment as a contextual localization.

Reason: Current Human Protein Atlas target staining corroborates a Golgi pool. The original PAINT is_active_in assertion is preserved without claiming that staining itself measured Golgi transport; endosomal exchange remains the organizing function.

Summary: Retain directly observed Golgi localization in the tested human cell lines.

Reason: The Human Protein Atlas record assigns Golgi apparatus and plasma membrane as supported main locations, with Golgi staining in CACO-2 and RH-30. These positive cell-line observations are retained separately from renal endosomal function.

Summary: Retain a functional surface pool without making it the principal physiological compartment.

Reason: Curated CLC-family inheritance and direct human-expression experiments support plasma membrane localization and surface currents. ClC-5 surface abundance depends on trafficking partners and cell polarity, so this genuine compartment is retained as contextual rather than made the sole site of renal function.

Summary: Retain the observed plasma membrane staining.

Reason: Human Protein Atlas images and curated records support a plasma membrane pool in the tested cell lines. Independent surface biotinylation and transport measurements corroborate this pool while leaving its abundance in native renal endosomes distinct.

Summary: Retain the plasma membrane vocabulary mapping.

Reason: The mapped compartment agrees with Human Protein Atlas staining and human ClC-5 surface-expression assays. Surface transport is experimentally real, but its assay context does not establish plasma membrane as the principal physiological location.

Summary: Specify chloride movement across a membrane.

Reason: The ortholog and domain mappings identify a chloride transporter, and direct ClC-5 coupling experiments establish the membrane-crossing step. The refinement preserves all combined-method source fields.

Proposed replacements: chloride transmembrane transport

Summary: Specify the transmembrane chloride movement underlying the original current assay.

Reason: The original abstract reports human wild-type and disease-variant ClC-5 currents in oocytes. Later direct exchange assays independently establish chloride movement across the membrane; they are not attributed to the inaccessible 1996 full text.

Proposed replacements: chloride transmembrane transport

Summary: Endosomal membrane transport is central to ClC-5 function.

Reason: The inherited compartment has direct human localization support and independent renal endosomal physiology. Curated donor evidence is retained without pretending that the historical PAINT tree and ancestral placement have been reconstructed.

Summary: Retain the endosome membrane vocabulary mapping.

Reason: Human ClC-5 localizes in endosomal membranes in epithelial-expression studies, and renal experiments connect coupled exchange with endocytic function. This is a functional compartment of the transporter.

Summary: The Reactome catalyst resolves to endosome-membrane ClC-5.

Reason: The exact target entity is P51795, residues 1–816, in the endosome membrane. CLCN4, CLCN5 and CLCN6 are alternatives in the catalyst set, not an asserted obligate three-protein complex.

Summary: Specify the supported endosomal membrane within the endomembrane system.

Reason: Direct human ClC-5 localization establishes an endosomal membrane pool. The current ARBA conditions do not reproduce the historical target match, but that route uncertainty is separate from the experimentally supported compartment refinement.

Proposed replacements: endosome membrane

Summary: Specify chloride:proton antiporter activity.

Reason: The CLC-domain mapping correctly identifies chloride transport, while direct ClC-5 proton-flux and uncoupling experiments resolve coupled exchange rather than a generic chloride transporter.

Proposed replacements: chloride:proton antiporter activity

Summary: Specify the exchanged chloride and proton substrates.

Reason: The Reactome reaction explicitly resolves to P51795 as an alternative endosomal exchanger. Direct transport experiments corroborate chloride/proton coupling. Reaction direction is retained as modeled without assuming that every physiological voltage and pH condition produces the same net flux.

Proposed replacements: chloride:proton antiporter activity

Summary: The exact ClC-5 result in the NK-cell membrane proteomics source remains unresolved.

Reason: The authentic abstract describes a large YTS-cell membrane proteome, but the original ClC-5 target table and peptide evidence could not be inspected after genuine access attempts. General membrane topology does not resolve this source-specific HDA assertion. No wrong-gene or negative-detection claim is made.

Summary: Retain membrane localization at the resolution of the cited renal study.

Reason: The study detects ClC-5 in human and mouse kidney membrane fractions and maps its segmental distribution by immunostaining. The human preparation is a bulk membrane fraction, and developmental staining does not resolve an endosome-specific membrane compartment. Retain the original membrane assertion; the separately supported endosome annotations remain distinct.

Summary: Specify the functional endosomal membrane compartment.

Reason: The rat ortholog and CLC-domain mappings support membrane association; human ClC-5 endosomal localization provides the more specific functional compartment. Other genuine Golgi and surface pools are retained in their separate source assertions.

Proposed replacements: endosome membrane

Summary: Specify chloride transmembrane transport within the broad pathway.

Reason: The ion-transport pathway contains the CLC exchange reaction and its P51795 endosome-membrane catalyst entity. ClC-5 itself performs ion transport rather than serving as a transported substrate.

Proposed replacements: chloride transmembrane transport

Summary: Retain assay-conditioned self-association of the isolated human cytoplasmic domain.

Reason: Sedimentation of the purified human C-terminal domain shows a weak monomer–dimer equilibrium that is unchanged by 5 mM ATP. Crystal packing supplies possible arrangements, but the paper explicitly leaves the native intersubunit geometry unresolved. This positive interaction is retained without asserting a demonstrated full-length native dimer arrangement.

Summary: Retain the renal apical-cell compartment with developmental and species limits.

Reason: The original study examines human fetal and postnatal kidneys alongside mouse development. Human fetal proximal-tubule staining is less polarized; the detailed apical/subapical comparisons include mouse sections. Independent renal and epithelial localization supports an apical endocytic compartment, without attributing every mouse image or developmental stage to human tissue.

Summary: Specify the chloride substrate of transmembrane transport.

Reason: The family-based process is correct but broad. Direct ClC-5 exchange experiments establish the chloride membrane-crossing step performed by this protein.

Proposed replacements: chloride transmembrane transport

Summary: Retain chloride transmembrane transport as the performed process.

Reason: The curated inherited transport process is independently established by direct human ClC-5 ion-flux measurements. No additional endocytosis process is manufactured from uptake phenotypes alone.

Summary: The human cytoplasmic CBS-domain region directly binds adenyl ribonucleotides.

Reason: Equilibrium dialysis of the purified human C-terminal domain measures ATP, ADP and AMP binding; nucleotide-bound structures and binding-site mutants identify the recognition site. The 746-residue P51795-1 sequence is identical to displayed P51795-2 after its first 70 residues, and the native deposited CBS sequence maps to P51795-1 residues 571–746 / P51795-2 residues 641–816. This shared domain is present in both products, without establishing separate full-length activity for each. UniProt ATP-binding and mutant features curate the same paper, providing corroborating annotation rather than an independent experiment. Wild-type-background mutant currents are unchanged; effects in uncoupled E211A do not prove physiological nucleotide gating or ATP hydrolysis.

Summary: Human ClC-5 can directly contribute to endosomal acidification through its proton-transport activity.

Reason: Full-length human ClC-5 expressed in HEK293 cells enhances acidification of VAMP2-pHluorin-positive endosomes, including a component that persists when V-ATPase is inhibited. E211A and E268A pore mutants localize to those compartments but do not confer that component. These transport-dependent measurements identify ClC-5 as performing proton movement, rather than merely being necessary for an outcome. The opossum knockdown experiment is separate. Mouse E211A knock-in retains bulk ATP-driven acidification despite defective uptake, so this annotation does not assert that ClC-5 always acidifies native renal endosomes. The active term has no ancestor/descendant overlap with existing process annotations; same-role CLCN3 has the term, and GO-CAM provides no contrary modeled target role.