TMEM163

TMEM163 is a proton-coupled zinc efflux transporter of the cation diffusion facilitator family that operates at the plasma membrane, synaptic vesicles, endosomes, and lysosome-related organelles to regulate cellular and vesicular zinc homeostasis. It forms homodimers and heterodimers with ZNT-family transporters (ZNT1–4), and conserved aspartate residues (D124/D128) and E286 are critical for zinc transport activity (PMID:27917477, PMID:31697912, PMID:36204728). TMEM163 physically interacts with TRPML1 to modulate intracellular zinc levels and with P2X receptors to regulate ATP-gated channel properties relevant to pain signaling, and its trafficking to lysosome-related organelles depends on an N-terminal dileucine motif recognized sequentially by AP-3 and BLOC-1 (PMID:25130899, PMID:32492420, PMID:41985787). Missense variants in TMEM163 cause hypomyelinating leukodystrophy through impaired zinc efflux and oligodendrocyte dysfunction, as demonstrated by patient-derived mutant analysis and zebrafish rescue experiments (PMID:35953447, PMID:35455965).

1. 2007 High

   Establishing that TMEM163 (SV31) is an integral membrane protein of synaptic vesicles resolved its subcellular identity and positioned it as a candidate vesicular transporter or signaling component.

   Evidence Subcellular fractionation, immunocytochemistry, and immunoelectron microscopy in brain tissue and heterologous expression systems

   PMID:17623043

   Open questions at the time

   • No transport function demonstrated
   • Ligand or substrate unknown
   • No knockout or knockdown phenotype assessed
2. 2011 High

   Demonstrating that TMEM163 selectively binds Zn²⁺ and Ni²⁺ — but not other divalent cations — identified it as a zinc-binding protein and implied a role in zinc homeostasis.

   Evidence Recombinant protein metal-binding assays, FluoZin-3 live-cell imaging, sucrose density gradient fractionation in PC12 cells

   PMID:21668449

   Open questions at the time

   • Binding demonstrated but active transport not yet shown
   • Physiological relevance of Ni²⁺ binding unclear
3. 2014 High

   Identifying TRPML1 as a physical interactor revealed that TMEM163 operates within a protein network governing lysosomal/endosomal zinc flux, and TMEM163 knockdown increasing intracellular zinc provided the first loss-of-function evidence for zinc efflux activity.

   Evidence Yeast two-hybrid, reciprocal co-IP, mass spectrometry, N-terminal deletion mutagenesis, fluorescent zinc assays in HEK-293 cells

   PMID:25130899

   Open questions at the time

   • Direction and mechanism of transport not defined
   • TRPML1 interaction domain on TRPML1 side not mapped
4. 2016 High

   Reconstitution in proteoliposomes proved TMEM163 is a bona fide proton-coupled zinc transporter (Km ~44 µM), and nanodisc experiments established that dimerization enhances Zn²⁺ binding, placing it functionally within the CDF/SLC30 family.

   Evidence Cell-free synthesis, nanodisc reconstitution, native mass spectrometry, proteoliposome transport assay with FluoZin-1, site-directed mutagenesis

   PMID:27917477

   Open questions at the time

   • Transport stoichiometry (Zn²⁺:H⁺) not determined
   • No structural model at atomic resolution
5. 2019 High

   Identification of D124, D128, and E286 as essential residues for zinc efflux in human cells, combined with the finding that TMEM163 knockdown in pancreatic β-cells dysregulates insulin storage, defined the molecular determinants of transport and a physiological role in insulin-secreting cells.

   Evidence Site-directed mutagenesis with radionuclide (⁶⁵Zn) and dual fluorescent dye efflux assays; siRNA knockdown in MIN6 cells with insulin content/secretion measurements

   PMID:31697912 PMID:31813547

   Open questions at the time

   • In vivo β-cell phenotype in knockout animals not assessed
   • Whether E286K is a natural variant with clinical consequence was not established at this time
6. 2020 High

   A genome-wide functional screen uncovered TMEM163 as a modulator of P2X receptor channel properties, expanding its role beyond zinc transport to regulation of purinergic signaling and ATP-evoked pain behavior.

   Evidence Genome-wide ORF screen, electrophysiology, and in vivo behavioral pain assays in mice

   PMID:32492420

   Open questions at the time

   • Mechanism of P2X modulation (direct binding vs. zinc-dependent) not resolved
   • Which P2X subunit(s) are the primary physiological targets in vivo unclear
7. 2022 High

   Discovery that TMEM163 heterodimerizes with ZNT1–4 established it as an integral member of the ZNT transporter network, and identification of causative missense variants in hypomyelinating leukodystrophy — validated by zebrafish rescue — linked TMEM163 loss-of-function to a human Mendelian disease affecting myelination.

   Evidence Co-IP and zinc flux assays for ZNT interactions; patient variant functional assays in HeLa and oligodendroglial lines; zebrafish morphant model with human mRNA rescue

   PMID:35455965 PMID:35953447 PMID:36204728

   Open questions at the time

   • Structural basis for ZNT heterodimerization unknown
   • Why oligodendrocytes are selectively vulnerable to TMEM163 mutations not explained
   • Genotype–phenotype correlation across different leukodystrophy variants incomplete
8. 2024 Medium

   Demonstrating that TMEM163 loads vesicular zinc in DRG neurons and that age-related upregulation of TMEM163 causes excessive spinal zinc release and chronic itch via disinhibition of NPY⁺ interneurons established a circuit-level role for TMEM163-dependent zinc signaling in somatosensory pathology.

   Evidence In vivo mouse aging model, zinc imaging, spinal cord electrophysiology, zinc chelation rescue

   PMID:39602426

   Open questions at the time

   • Causal relationship tested only pharmacologically, not with conditional TMEM163 knockout
   • Generalizability beyond aged-mouse itch model not shown
9. 2025 Medium

   Cooperative zinc efflux by ZnT3–TMEM163 complexes in hippocampal neurons, and their ischemia-induced internalization with consequent extracellular zinc overload, extended the functional relevance of TMEM163 heterodimers to excitotoxic neuronal injury.

   Evidence Co-IP, surface biotinylation, siRNA/overexpression, FluoZin-3 zinc imaging, TUNEL and MTT assays in oxygen-glucose deprivation model

   PMID:41504061

   Open questions at the time

   • Mechanism of ischemia-triggered internalization not determined
   • In vivo stroke model validation lacking
   • Single-lab finding without independent replication
10. 2026 High

    Mapping the LEDRGL69L70 dileucine motif as the AP-3/BLOC-1 recognition site, and showing competitive sequential binding of these complexes, resolved the trafficking mechanism by which TMEM163 reaches lysosome-related organelles such as platelet dense granules.

    Evidence Dileucine mutagenesis, co-IP with AP and BLOC complexes, confocal localization, MEG-01 knockout lines

    PMID:41985787

    Open questions at the time

    • Whether the same sorting motif governs TMEM163 targeting in neurons not tested
    • Structural basis of AP-3 vs. BLOC-1 competitive binding not resolved

• No high-resolution structure of TMEM163 exists, the Zn²⁺:H⁺ transport stoichiometry is undefined, the mechanism by which TMEM163 modulates P2X receptor gating (direct binding versus zinc-mediated) is unresolved, and the selective vulnerability of oligodendrocytes to TMEM163 mutations remains unexplained.
• No atomic-resolution structure
• Transport stoichiometry undetermined
• P2X modulation mechanism unresolved
• Oligodendrocyte-selective pathology mechanism unknown