Affinage

ELMOD3

ELMO domain-containing protein 3 · UniProt Q96FG2

Length
381 aa
Mass
43.0 kDa
Annotated
2026-06-09
10 papers in source corpus 7 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ELMOD3 is an ELMO-domain-containing GTPase-activating protein (GAP) that links ARF-family GTPase regulation to actin-cytoskeleton dynamics and membrane trafficking, with a prominent role in cochlear hair-cell stereocilia (PMID:24039609, PMID:31628468). Recombinant ELMOD3 has GAP activity toward Arl2 in vitro, an activity that depends on the integrity of the ELMO domain and is abolished by the deafness-associated p.Leu265Ser substitution (PMID:24039609). In cells, ELMOD3 associates closely with the actin cytoskeleton at the plasma membrane and within actin-based microvilli, and disease-associated ELMO-domain mutations disrupt this localization and destabilize the protein (PMID:24039609, PMID:29713870). Genetically, loss of Elmod3 in mice produces progressive hearing loss with stereocilia shortening, fusion, and degeneration accompanied by reduced cochlear F-actin, directly tying ELMOD3 to stereocilia actin maintenance (PMID:31628468). ELMOD3 also governs membrane trafficking: its deletion impairs primary ciliogenesis and causes ciliary cargo to accumulate at the Golgi, defects rescued by activating ARL3 or ARL16 mutants that place ELMOD3 upstream of these GTPases in Golgi-to-cilia transport (PMID:34818063). Beyond GTPase regulation, the ELMO domain binds β-catenin to promote β-catenin levels and Wnt target-gene expression while modulating E-cadherin, RAF/MEK/ERK signaling, and F-actin organization in gastric cancer cells (PMID:39621020).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2013 High

    Established the core biochemical identity of ELMOD3 as an ARF-family GAP and tied its catalytic competence to a human deafness mutation, defining the molecular basis of disease.

    Evidence In vitro GAP assay with recombinant GST-ELMOD3 against Arl2 plus p.Leu265Ser site-directed mutagenesis

    PMID:24039609

    Open questions at the time
    • Activity shown only against Arl2 in vitro; physiological substrate spectrum in cells not defined here
    • No structural basis for how Leu265 supports catalysis
    • Did not test whether GAP activity is required for the stereocilia phenotype
  2. 2013 Medium

    Connected the biochemical GAP to a cytoskeletal context by showing ELMOD3 localizes with actin in epithelial cells and in inner-ear stereocilia, implicating it in hair-cell actin structures.

    Evidence Fluorescence and super-resolution imaging of ELMOD3 fusions in MDCK/LLC-PK1-CL4 cells and immunostaining of rodent inner ear

    PMID:24039609

    Open questions at the time
    • Co-localization does not establish direct actin binding
    • No fractionation or FRAP to confirm stable association
    • Mechanism linking GAP activity to actin localization unresolved
  3. 2018 Medium

    Demonstrated that ELMO-domain residues control ELMOD3 protein stability and localization, explaining how a missense mutation can be pathogenic without necessarily abolishing catalysis.

    Evidence Western blot half-life/stability assay and immunofluorescence comparing WT vs. p.His171Arg ELMOD3

    PMID:29713870

    Open questions at the time
    • Degradation pathway (proteasomal vs. lysosomal) not identified
    • Single lab, cell-line based
    • Link between instability and hearing phenotype inferred, not tested in vivo
  4. 2019 High

    Provided in vivo proof that ELMOD3 is required for stereocilia integrity and F-actin maintenance, moving from biochemistry to a defined organ-level mechanism for deafness.

    Evidence CRISPR/Cas9 Elmod3 knockout mice with ABR testing, scanning electron microscopy, and F-actin immunostaining

    PMID:31628468

    Open questions at the time
    • Does not show whether the F-actin loss is a direct or indirect consequence of lost GAP activity
    • No identification of the relevant GTPase substrate in hair cells
    • Molecular link between ELMOD3 and actin assembly machinery undefined
  5. 2021 High

    Defined a trafficking function by placing ELMOD3 upstream of ARL3 and ARL16 in Golgi-to-cilia transport, expanding its role beyond actin to ciliary cargo delivery.

    Evidence Elmod3-deletion MEFs with ciliogenesis assays, ciliary-marker immunofluorescence, and epistasis rescue using constitutively active ARL3/ARL16

    PMID:34818063

    Open questions at the time
    • Does not establish whether ELMOD3 acts as a direct GAP on ARL3/ARL16
    • Specific ciliary cargoes affected only partially characterized
    • Relationship between ciliary trafficking and stereocilia phenotype unclear
  6. 2023 Medium

    Extended the trafficking role to apical vesicle transport by defining an ELMOD3→Rab1A→Flotillin2 cascade required for lumen formation, broadening the GTPase partners linked to ELMOD3.

    Evidence Co-immunoprecipitation, loss-of-function, localization imaging, and epistasis in Ciona notochord

    PMID:36918025

    Open questions at the time
    • Demonstrated in Ciona, not mammalian cells
    • Direct GAP activity on Rab1A not tested
    • Conservation of the cascade in vertebrate epithelia unverified
  7. 2024 Medium

    Identified a signaling function in which the ELMO domain binds β-catenin to promote Wnt output and reorganize F-actin, linking ELMOD3 to cancer-relevant pathways.

    Evidence Co-immunoprecipitation (ELMO domain–β-catenin), ELMOD3 knockout in gastric cancer cells, pathway western blots, F-actin staining, and xenograft model

    PMID:39621020

    Open questions at the time
    • Whether β-catenin binding depends on or competes with GAP activity is unknown
    • Single cancer cell context; generality unproven
    • Direct vs. indirect effects on RAF/MEK/ERK not separated
  8. 2025 Low

    Reinforced that conserved ELMO-domain residues are required for ELMOD3 stability and actin association by characterizing an additional destabilizing mutation.

    Evidence Protein stability assay, F-actin co-localization imaging, and molecular modeling of WT vs. p.Gly214Ser (preprint)

    PMID:bio_10.1101_2025.02.11.25321773

    Open questions at the time
    • Preprint, single functional assay per endpoint
    • Steric-clash prediction is computational and unvalidated structurally
    • Not confirmed in an in vivo or independent system

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved which GTPase substrate(s) ELMOD3 acts on within hair cells to maintain stereocilia F-actin, and how its GAP activity, actin association, trafficking, and β-catenin functions are mechanistically integrated.
  • No demonstration of direct GAP activity on ARL3/ARL16/Rab1A in cells
  • No structural model of the ELMO domain bound to a GTPase or β-catenin
  • Causal chain from GAP activity to F-actin maintenance not established

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008092 cytoskeletal protein binding 2 GO:0098772 molecular function regulator activity 2 GO:0060090 molecular adaptor activity 1
Localization
GO:0005856 cytoskeleton 2 GO:0005794 Golgi apparatus 1 GO:0005886 plasma membrane 1 GO:0005929 cilium 1
Pathway
R-HSA-5653656 Vesicle-mediated transport 2 R-HSA-162582 Signal Transduction 1 R-HSA-9709957 Sensory Perception 1
Partners
ARL16ARL2ARL3CTNNB1FLOT2RAB1A

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2013 Recombinant human GST-ELMOD3 exhibits GTPase-activating protein (GAP) activity against the Arl2 GTPase in vitro; this activity is completely abolished by the deafness-associated p.Leu265Ser mutation in the ELMO domain. In vitro GAP assay with recombinant GST-ELMOD3 and site-directed mutagenesis (p.Leu265Ser) PLoS genetics High 24039609
2013 Fluorescently tagged ELMOD3 co-localizes with the actin cytoskeleton in MDCK cells and actin-based microvilli of LLC-PK1-CL4 epithelial cells; the p.Leu265Ser mutation impairs this co-localization. Super-resolution imaging confirmed close association of ELMOD3 with actin at the plasma membrane. Fluorescence microscopy, super-resolution imaging, ELMOD3-fluorescent fusion protein expression in epithelial cell lines, mutagenesis PLoS genetics Medium 24039609
2013 In rodents, ELMOD3 is expressed in the sensory epithelia of the inner ear and localizes prominently in the stereocilia of cochlear hair cells. Immunofluorescence/immunohistochemistry in rodent inner ear tissue sections PLoS genetics Medium 24039609
2018 The ELMOD3 p.His171Arg (c.512A>G) mutation causes abnormal subcellular localization of ELMOD3 protein and accelerates its degradation (shorter protein half-life), demonstrating that this ELMO-domain residue is required for normal protein stability and localization. Western blot (protein level and stability assay), immunofluorescence staining in cell lines expressing WT vs. mutant ELMOD3 Human genetics Medium 29713870
2019 Elmod3 knockout mice (CRISPR/Cas9) develop progressive hearing loss with shortening and fusion of inner hair cell stereocilia and degeneration of outer hair cell stereocilia, accompanied by markedly reduced F-actin in cochlear hair cells, establishing a direct role for ELMOD3 in actin cytoskeleton dynamics in stereocilia. CRISPR/Cas9 knockout mouse model, auditory brainstem response (ABR) testing, scanning electron microscopy of stereocilia, F-actin immunostaining Human molecular genetics High 31628468
2021 Deletion of Elmod3 in mouse embryonic fibroblasts impairs primary cilia formation, causes loss of a subset of ciliary proteins from cilia, and leads to accumulation of ciliary proteins at the Golgi, indicating a role for ELMOD3 in trafficking from the Golgi to cilia. These phenotypes are rescued by expression of activating mutants of ARL3 or ARL16, placing ELMOD3 upstream of ARL3/ARL16 in this pathway. Elmod3-deletion MEF lines, ciliogenesis assays, immunofluorescence for ciliary markers, epistasis rescue with constitutively active ARL3/ARL16 mutants Molecular biology of the cell High 34818063
2023 In Ciona notochord, ELMOD3 physically interacts with Rab1A (a GTPase regulating vesicle trafficking) and with the lipid-raft protein Flotillin2, and regulates Flotillin2 subcellular localization; loss of ELMOD3 blocks notochord lumen formation, phenocopied by loss of Rab1A or Flotillin2, defining an ELMOD3→Rab1A→Flotillin2 cascade for apical vesicle trafficking. Co-immunoprecipitation/interaction assays, loss-of-function experiments in Ciona, subcellular localization imaging, epistasis analysis Open biology Medium 36918025
2024 The ELMO domain of ELMOD3 directly interacts with β-catenin (demonstrated by co-immunoprecipitation), and ELMOD3 promotes β-catenin protein levels and downstream target gene expression; knockout of ELMOD3 in gastric cancer cells decreases β-catenin signaling, elevates E-cadherin, suppresses the RAF/MEK/ERK pathway, and disrupts F-actin cytoskeleton formation. Co-immunoprecipitation (ELMO domain–β-catenin), ELMOD3 knockout in gastric cancer cell lines, western blot for pathway components, F-actin staining, xenograft tumor model FASEB journal Medium 39621020
2025 The ELMOD3 p.Gly214Ser mutation disrupts F-actin co-localization and accelerates protein degradation compared to wild-type, confirming that Gly214 is required for normal ELMOD3 stability and actin-cytoskeletal association; molecular modeling predicts steric clashes with adjacent residues Ala160 and Cys162. Protein stability assay, immunofluorescence co-localization with F-actin, molecular modeling/structural analysis in cells expressing WT vs. mutant ELMOD3 bioRxiv (preprint)preprint Low bio_10.1101_2025.02.11.25321773

Source papers

Stage 0 corpus · 10 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2013 An alteration in ELMOD3, an Arl2 GTPase-activating protein, is associated with hearing impairment in humans. PLoS genetics 39 24039609
2018 ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Human genetics 18 29713870
2019 Elmod3 knockout leads to progressive hearing loss and abnormalities in cochlear hair cell stereocilia. Human molecular genetics 14 31628468
2019 ELMOD3-SH2D6 gene fusion as a possible co-star actor in autism spectrum disorder scenario. Journal of cellular and molecular medicine 12 31800155
2021 The ARF GAPs ELMOD1 and ELMOD3 act at the Golgi and cilia to regulate ciliogenesis and ciliary protein traffic. Molecular biology of the cell 11 34818063
2018 Homozygous 2p11.2 deletion supports the implication of ELMOD3 in hearing loss and reveals the potential association of CAPG with ASD/ID etiology. Journal of applied genetics 11 30284680
2023 ELMOD3-Rab1A-Flotillin2 cascade regulates lumen formation via vesicle trafficking in Ciona notochord. Open biology 7 36918025
2023 Gene regulation analysis of patient-derived iPSCs and its CRISPR-corrected control provides a new tool for studying perturbations of ELMOD3 c.512A>G mutation during the development of inherited hearing loss. PloS one 5 37708136
2025 Case Report: A novel ELMOD3-ALK and EML4-ALK double-fusion responses to neoadjuvant alectinib in a lung adenocarcinoma patient. Frontiers in pharmacology 1 40297141
2024 Depletion of ELMOD3 inhibits the growth and migration of gastric cancer cells by disrupting the β-catenin signaling and the F-actin cytoskeleton. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 0 39621020

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