LRIG3 is a type-I single-pass membrane protein with an extracellular region containing 15 leucine-rich repeats and three immunoglobulin-like domains, followed by a long cytoplasmic tail. At the plasma membrane it associates with the LRIG/ERBB regulatory system: LRIG3 opposes LRIG1-mediated negative regulation and stabilizes ERBB receptors, although ERBB association does not explain every LRIG3-dependent developmental role. Mouse Lrig3 restricts Ntn1 expression to pattern the lateral semicircular canal, and Xenopus Lrig3 contextually modulates WNT and FGF signaling during neural-crest formation. In glioblastoma models, full-length and soluble LRIG3 suppress growth, invasion and angiogenesis through MET-PI3K-AKT-associated effects; glioma-derived soluble LRIG3 also binds NETO2 on tumor-associated macrophages and limits M2-like polarization. These tumor and nonhuman developmental contexts do not establish a single universal LRIG3 pathway. Two curated isoforms differ at the N terminus, but their functions have not been compared directly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference places LRIG3 activity at the plasma membrane, consistent with its signal peptide and single-pass type-I membrane topology. Reason: Plasma membrane is a defining location for full-length LRIG3 and is independently consistent with the UniProt membrane record and membrane-context ErbB/LRIG1 experiments. The broad PANTHER source set does not supply LRIG3-specific receptor activity, but it does support the conserved membrane topology. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0034476 MGI:MGI:107935 MGI:MGI:1333744 MGI:MGI:1915522 MGI:MGI:2177651 MGI:MGI:2389177 MGI:MGI:2389180 MGI:MGI:2442479 MGI:MGI:3608416 PANTHER:PTN001224703 RGD:1560707 RGD:1585921 RGD:727797 UniProtKB:O15455 UniProtKB:P07359 UniProtKB:Q14392 UniProtKB:Q86UE6 UniProtKB:Q86UN2 UniProtKB:Q86UN3 UniProtKB:Q8TF66 UniProtKB:Q96FE5 UniProtKB:Q96JA1 UniProtKB:Q99467 WB:WBGene00020649 |
| GO:0038023 signaling receptor activity | IBA GO_REF:0000033 | REMOVE | Summary: A broad PANTHER IBA assigns autonomous signaling receptor activity from a mixed LRR membrane-protein family node. Reason: Signaling receptor activity requires receiving a signal and transmitting it to initiate a cellular response. LRIG3 is supported instead as a membrane-associated regulator that binds and modulates ErbB receptors. The IBA source set contains bona fide receptors such as TLR3, RTN4RL1, RTN4RL2, and CD180, so their receptor role must not be transferred across this family boundary to LRIG3. LRIG1 and LRIG2 functions likewise do not establish LRIG3 as an autonomous receptor. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG ROLE CONFLATION Sources checked: FB:FBgn0034476 PANTHER:PTN002809265 RGD:727797 UniProtKB:O15455 · TLR3 SUPPORTS SOURCE BUT NOT TARGET UniProtKB:Q86UN2 · RTN4RL1 SUPPORTS SOURCE BUT NOT TARGET UniProtKB:Q86UN3 · RTN4RL2 SUPPORTS SOURCE BUT NOT TARGET UniProtKB:Q99467 · CD180 SUPPORTS SOURCE BUT NOT TARGET |
| GO:0007605 sensory perception of sound | IBA GO_REF:0000033 | REMOVE | Summary: This auditory-process IBA is propagated from mouse Lrig1 and Lrig2 sources, not from the mouse Lrig3 ortholog. Reason: MGI:107935 is mouse Lrig1 and MGI:2443718 is mouse Lrig2, as verified in the current MGI records; the ordered leaf-source set contains no mouse Lrig3 ortholog. The PANTHER ancestral node is therefore supported here only by Lrig1/ Lrig2 auditory annotations above the paralog split. LRIG3 instead has direct mouse evidence for lateral semicircular-canal morphogenesis, which does not by itself establish sensory perception of sound. The target assertion is therefore an over-propagated paralog transfer rather than evidence for human LRIG3 auditory function. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: MGI:MGI:107935 · mouse Lrig1 SUPPORTS SOURCE BUT NOT TARGET MGI:MGI:2443718 · mouse Lrig2 SUPPORTS SOURCE BUT NOT TARGET PANTHER:PTN009094493 · LRIG auditory-function ancestral node SUPPORTS SOURCE BUT NOT TARGET |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping places LRIG3 at the plasma membrane. Reason: Plasma-membrane localization is appropriate for the full-length signal-peptide- containing, single-pass type-I protein and for its membrane-context interactions with ErbB receptors and LRIG1. This duplicate of the IBA location is independently coherent and may be retained. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0039 · UniProt cell membrane location SUPPORTS TRANSFER |
| GO:0030659 cytoplasmic vesicle membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping assigns LRIG3 to cytoplasmic vesicle membranes, reflecting an intracellular membrane pool. Reason: UniProt reports cytoplasmic-vesicle localization when LRIG3 is coexpressed with ERBB4. This is coherent for a trafficking single-pass membrane protein but is a contextual location, inferred by similarity, rather than LRIG3's defining plasma-membrane site. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB-SubCell:SL-0089 · UniProt cytoplasmic vesicle membrane location SUPPORTS TRANSFER |
| GO:0005515 protein binding | IPI PMID:23723069 Leucine-rich repeat and immunoglobulin domain-containing pro... | MODIFY | Summary: Targeted co-immunoprecipitation shows LRIG3 in a stable complex with LRIG1, while functional experiments show that LRIG3 opposes LRIG1 and stabilizes ErbB receptors. Reason: Generic protein binding loses the experimentally demonstrated function. The paper supports LRIG3 as a signaling-receptor regulator: it associates with LRIG1 through the ectodomains, restricts LRIG1 negative action, and increases ErbB receptor stability. GO:0030545 captures receptor modulation without claiming that LRIG3 is itself a receptor or that it enzymatically activates receptors. This activity is distinct from the negative receptor regulation characteristic of LRIG1 and from LRIG2's context-dependent behavior. Proposed replacements: signaling receptor regulator activity Supporting Evidence: PMID:23723069 Lrig3 opposes Lrig1 negative regulatory |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Proteome-scale affinity-purification mass spectrometry recovered an LRIG3-LRIG1 association in a cell-line-specific human interaction network. Reason: The high-throughput AP-MS observation corroborates physical association with LRIG1 but does not by itself define a molecular activity or physiological consequence. Generic protein binding is therefore retained only as an over-annotation; the targeted PMID:23723069 experiments, not this screen, justify the more informative signaling receptor regulator activity. Supporting Evidence: PMID:33961781 mass spectrometry, we have created two proteome-scale |
| GO:0005576 extracellular region | HDA PMID:22664934 Comparison of tear protein levels in breast cancer patients ... | KEEP AS NON CORE | Summary: High-throughput proteomics detected LRIG3 in human lacrimal-gland secretion (tear fluid), supporting this explicitly tissue-fluid-qualified extracellular location. Reason: The experimental HDA annotation and its part-of lacrimal-secretion extension are retained with curator deference. Detection in tear fluid does not establish that full-length LRIG3 is constitutively soluble or classically secreted; it could reflect an extracellular fragment, vesicle, or cellular material from this single-pass membrane protein. The location is therefore contextual and non-core. |
| GO:0048752 semicircular canal morphogenesis | ISO PMID:19004851 Cross-repressive interactions between Lrig3 and netrin 1 sha... | NEW | Summary: Mouse Lrig3 is required for lateral semicircular-canal morphogenesis through cross-repressive patterning with Ntn1. Reason: Q6P1C6 is the reviewed mouse Lrig3 ortholog, and genetic loss plus Ntn1-dosage rescue directly establish the process in mouse. ISO captures the conserved LRIG3 developmental role while retaining the species boundary and without converting it into a human hearing-perception annotation. Supporting Evidence: PMID:19004851 Lrig3 is necessary |
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Download this section (compressed HTML)Q: Which endogenous ERBB or other receptor complexes contain LRIG3 in normal human tissues, and how does LRIG3 oppose LRIG1 within those complexes?
Q: Is the Lrig3-Ntn1 boundary mechanism conserved in human otic development, and what signal connects membrane LRIG3 to NTN1 transcription?
Q: Which protease generates soluble LRIG3 in vivo, and is NETO2 a physiological target outside the glioma microenvironment?
Q: Do the two curated LRIG3 isoforms differ in membrane delivery, receptor regulation, developmental rescue, or ectodomain release?
Experiment: Endogenously tag LRIG3 in normal human epithelial and neural models; combine quantitative interactomics with receptor phosphorylation, surface turnover, and LRIG1 epistasis after acute LRIG3 depletion and rescue.
Experiment: Generate LRIG3-null human otic organoids and perform spatial transcriptomics, NTN1 imaging, basement-membrane analysis, and isoform-specific rescue during canal-like epithelial morphogenesis.
Experiment: Map soluble-LRIG3 termini by N-terminomics in patient-derived glioma and normal neural cultures, perturb candidate proteases including ADAM17, and test NETO2-dependent macrophage responses with cleavage-resistant rescue constructs.
Experiment: Compare the two curated LRIG3 isoforms using matched genomic knock-in constructs and measure maturation, plasma-membrane residence, vesicle localization, LRIG1/ERBB association, and ectodomain release.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The endogenous human receptor partners, binding interfaces, and direction of LRIG3-mediated receptor regulation remain incompletely defined.
OPEN BIOLOGY MF_DARK
What is known: Human-cell evidence supports LRIG1 cross-talk and ERBB stabilization, but does not establish a universal receptor set, obligate complex, or catalytic mechanism.
Significance: Resolving this mechanism is necessary to distinguish normal receptor regulation from tumor-cell-specific signaling behavior.
What would resolve it: Quantify endogenous LRIG3 complexes and receptor abundance, activation, trafficking, and degradation after LRIG3 perturbation and domain-resolved rescue.
Provenance (the field's own admissions):
Gap: The extent to which the mouse Lrig3-Ntn1 inner-ear mechanism is conserved in human otic development is unknown.
OPEN BIOLOGY BP_DARK
What is known: Mouse genetics strongly establishes lateral-canal morphogenesis, but no direct human developmental assay or LRIG3 disease mechanism is available.
Significance: Human conservation would connect the strongest normal developmental phenotype to LRIG3 biology without over-transferring auditory phenotypes of LRIG1/2.
What would resolve it: Test LRIG3 loss and rescue in human otic organoids with spatial NTN1, basement-membrane remodeling, and epithelial-fusion readouts.
Provenance (the field's own admissions):
Gap: The physiological source, protease, and normal target tissues of soluble LRIG3 are unresolved.
OPEN BIOLOGY BP_DARK
What is known: Soluble LRIG3 and NETO2-dependent macrophage effects are demonstrated in glioma systems; ADAM17 abundance correlates with release but direct cleavage is not established.
Significance: Establishing release and target-cell specificity is essential before treating the glioma-derived ectodomain as a normal intercellular signal.
What would resolve it: Map endogenous LRIG3 cleavage sites and protease dependence, then compare soluble LRIG3 abundance and NETO2-dependent responses across normal and tumor tissues.
Provenance (the field's own admissions):
Gap: The localization and functions of the two curated LRIG3 isoforms have not been compared.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Isoform 2 replaces the canonical N-terminal 79 residues, but sequence difference alone does not establish altered topology, stability, trafficking, or function.
Significance: Isoform-specific processing could alter the extracellular architecture underlying receptor association or shedding.
What would resolve it: Express isoforms at matched endogenous levels and compare maturation, surface delivery, LRIG1/ERBB association, cleavage, and functional rescue.
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