{"gene":"TMEM67","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":2006,"finding":"TMEM67 encodes meckelin, a 995-amino acid seven-transmembrane receptor protein; positional cloning and mutation identification established it as the MKS3 gene product expressed in fetal brain, liver, and kidney.","method":"Positional cloning, direct sequencing, expression analysis","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 1-2 — original positional cloning with mutation identification, highly cited foundational paper","pmids":["16415887"],"is_preprint":false},{"year":2009,"finding":"MKS1 and MKS3 proteins are required for ciliary structure and function, including regulation of cilia length and number; loss of MKS3 in the wpk rat causes functional defects of the connecting cilium in the eye (lack of outer segment formation), very short sperm flagella, and longer renal cilia with centrosome over-duplication; stable shRNA knockdown of Mks3 in IMCD3 cells induced multi-ciliated and multi-centrosomal phenotypes.","method":"Animal model analysis (wpk rat), shRNA knockdown in IMCD3 cells, immunofluorescence, electron microscopy","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (in vivo model, cell knockdown, structural imaging), moderate-strong evidence","pmids":["19515853"],"is_preprint":false},{"year":2009,"finding":"MKS3/TMEM67 protein MKS-3 in C. elegans localizes to the distal end of dendrites and cilium base (not the cilium itself) of ciliated sensory neurons; mks-3 mutants show elongated cilia and abnormal cilia-mediated chemoreception; genetic epistasis shows mks-3 functions in a pathway with other mks genes, and mks-1/mks-3 genetically interact with a separate nphp-1/nphp-4 pathway to influence cilia positioning and formation.","method":"C. elegans genetics, localization studies, behavioral assays, genetic epistasis","journal":"Journal of the American Society of Nephrology","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with multiple mutants, localization, functional readouts in an ortholog","pmids":["20150540"],"is_preprint":false},{"year":2009,"finding":"MKS3/TMEM67 is a membrane glycoprotein predominantly localized to the endoplasmic reticulum; its ER lumenal domain interacts with misfolded surfactant protein C (SP-C) and associated chaperones, while its transmembrane/cytosolic domain interacts with cytosolic p97; knockdown of MKS3 inhibits ERAD-mediated degradation of mutant SP-C, placing MKS3 as a bridge between ER lumenal quality control and cytosolic degradation machinery.","method":"Co-immunoprecipitation, subcellular fractionation, domain deletion constructs, siRNA knockdown, Western blotting","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP, domain mapping, functional knockdown with defined biochemical readout","pmids":["19815549"],"is_preprint":false},{"year":2013,"finding":"In the Tmem67 null (bpck) mouse, canonical Wnt signaling is upregulated in cyst linings and isolated fibroblasts, but not in retina or cochlea; zebrafish tmem67 morphants show convergent extension defects similar to PCP mutants, but analysis of classical vertebrate PCP readouts did not support global loss of planar polarity; defective cilia loading rather than global loss of ciliogenesis or basal body docking underlies dysfunctional cilia in MKS3 tissues.","method":"Tmem67 null mouse analysis, zebrafish morpholino knockdown, Wnt reporter assays, immunofluorescence, stereociliary bundle analysis","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods in two model organisms with defined pathway readouts","pmids":["23393159"],"is_preprint":false},{"year":2013,"finding":"Overexpression of TMEM67 in HEK293 cells activates ERK and JNK signaling pathways; pharmacological inhibition of ERK or JNK suppresses this activation; in bpck mice (Tmem67 loss-of-function), activation of ERK, JNK, and 4E-BP1 phosphorylation is elevated in cystic kidneys, linking TMEM67 to JNK/ERK-dependent pathways in polycystic kidney disease.","method":"Overexpression in HEK293 cells, pharmacological inhibition, Western blotting, animal model (bpck mouse)","journal":"Cell biology international","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, overexpression and inhibitor studies without direct mechanistic reconstitution","pmids":["23456819"],"is_preprint":false},{"year":2015,"finding":"TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 upon Wnt5a stimulation; TMEM67 colocalizes and physically interacts with ROR2 at the ciliary transition zone; the extracellular N-terminal domain of TMEM67 preferentially binds Wnt5a in vitro; loss of TMEM67 abolishes epithelial branching morphogenesis response to Wnt5a in cultured embryonic lungs; RhoA activation rescues pulmonary hypoplasia phenotypes downstream of the Wnt5a-TMEM67-ROR2 axis.","method":"Co-immunoprecipitation, in vitro binding assay, co-localization, Tmem67 knockout mouse, embryonic lung culture, rescue by RhoA activation","journal":"Disease models & mechanisms","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro binding, Co-IP, KO mouse with defined pathway placement and functional rescue, multiple orthogonal methods","pmids":["26035863"],"is_preprint":false},{"year":2019,"finding":"In the Tmem67 knockout mouse cerebellum, loss of TMEM67 leads to aberrantly high canonical Wnt/β-catenin signaling, increased expression of Hoxb5, and HOXB5 occupancy at the β-catenin promoter is increased; increased canonical Wnt signaling following loss of TMEM67 is directly dependent on HOXB5; Tmem67 mutant cerebellum also shows disrupted ciliogenesis and reduced responsiveness to Shh signaling.","method":"Tmem67 knockout mouse, transcriptome profiling, chromatin immunoprecipitation (ChIP), Wnt reporter assays, immunohistochemistry","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 — ChIP, transcriptomics, KO mouse with multiple orthogonal readouts in a single study","pmids":["30931988"],"is_preprint":false},{"year":2019,"finding":"TMEM67 is required for regulation of choroid plexus epithelial cell fluid and electrolyte homeostasis; homozygous Wpk (TMEM67 point mutation) rats develop severe ventriculomegaly and increased Na+, K+, and Cl- in CSF; heterozygotes develop slowly progressing hydrocephalus; aquaporin-1 and claudin-1 remain normally polarized in all genotypes, suggesting a selective permeability effect.","method":"Wpk rat model, MRI, CSF ion analysis, immunofluorescence for tight junction and water channel markers","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — animal model with physiological readouts, but mechanism is incompletely defined","pmids":["30705305"],"is_preprint":false},{"year":2017,"finding":"Wnt signaling (but not Hedgehog signaling) is suppressed in tmem67 zebrafish morphants; wild-type human TMEM67 RNA rescues phenotypes of tmem67 morphants whereas two COACH syndrome-associated mutant RNAs do not; the frameshift mutation p.Tyr920ThrfsX40 accelerates turnover of the TMEM67 protein.","method":"Zebrafish morpholino knockdown, mRNA rescue assay, Western blotting (protein stability)","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — morpholino knockdown with mRNA rescue and pathway readout, single lab","pmids":["28860541"],"is_preprint":false},{"year":2021,"finding":"TMEM67 and TMEM237 are unique components of the photoreceptor outer segment plasma membrane, identified by protein correlation profiling mass spectrometry; TMEM67 is present at this specialized ciliary membrane compartment in vertebrate photoreceptors.","method":"Label-free quantitative mass spectrometry, protein correlation profiling, membrane fractionation","journal":"Molecular & cellular proteomics","confidence":"Medium","confidence_rationale":"Tier 2 — quantitative proteomics with validated markers, but functional consequence not directly tested","pmids":["33933680"],"is_preprint":false},{"year":2021,"finding":"Adult zebrafish tmem67 mutants exhibit hyperactive mTOR signaling; mTOR inhibition (by hypomorphic mtor or rapamycin) ameliorates renal cysts and rescues ciliary abnormalities in adult mutants, placing TMEM67 upstream of mTOR in a pathway relevant to cystogenesis and cilia length regulation.","method":"TALEN-generated zebrafish tmem67 mutants, rapamycin treatment, mtor hypomorphic strain, 3D kidney imaging, ciliary analysis","journal":"Journal of the American Society of Nephrology","confidence":"Medium","confidence_rationale":"Tier 2 — genetic and pharmacological epistasis in zebrafish model, single lab","pmids":["33574160"],"is_preprint":false},{"year":2022,"finding":"TMEM67 is required for the gating function of the ciliary transition zone: TMEM67-KO in hTERT-RPE1 cells leads to impaired ciliogenesis, elongated cilia, and perturbed ciliary localization of membrane-associated proteins ARL13B and INPP5E, but does not affect recruitment of TZ proteins CEP290, RPGRIP1L, and NPHP5; TMEM67 localizes not only to the transition zone but extends into the cilium; ciliopathy-associated TMEM67 mutants can restore ARL13B/INPP5E localization but not aberrant cilium elongation.","method":"CRISPR/Cas9 KO in hTERT-RPE1 cells, immunofluorescence, exogenous mutant expression, confocal microscopy","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined subcellular and functional phenotypes, mutant rescue experiments, multiple orthogonal readouts","pmids":["36334440"],"is_preprint":false},{"year":2022,"finding":"TMEM67 variants associated with mild cholestasis phenotype show significantly decreased protein levels; however, the interaction between these TMEM67 variants and MKS1 remains unaffected, indicating that MKS1-TMEM67 complex formation is preserved despite reduced TMEM67 abundance.","method":"In vitro expression studies, Western blotting, co-immunoprecipitation","journal":"Journal of cellular physiology","confidence":"Low","confidence_rationale":"Tier 3 — single lab, co-IP without full mechanistic follow-up","pmids":["35621037"],"is_preprint":false},{"year":2025,"finding":"TMEM67 is cleaved in its extracellular domain by the metalloproteinase ADAMTS9; this cleavage generates two functional forms: a C-terminal portion localizing to the ciliary transition zone that regulates ciliogenesis, and a non-cleaved full-length form that mediates non-canonical Wnt signaling; a non-cleavable TMEM67 mouse model develops severe ciliopathies phenocopying Tmem67-/- mice but transduces normal Wnt signaling, demonstrating that the two functions are structurally separable; three patient variants within the cleavage motif disrupt cilia structure and function in mammalian cells and C. elegans.","method":"Biochemical cleavage assay, non-cleavable TMEM67 knock-in mouse model, C. elegans patient variant characterization, mammalian cell culture, Wnt signaling assays, ciliary localization studies","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — reconstitution of cleavage, mouse knock-in model, C. elegans genetics, multiple orthogonal approaches in single study","pmids":["40436881"],"is_preprint":false},{"year":2025,"finding":"FUT8-mediated core fucosylation (N-linked glycosylation) of TMEM67 stabilizes the protein by impeding its degradation via the autophagy pathway, ensuring proper localization of TMEM67 to the ciliary transition zone to promote cilium formation; FUT8 physically interacts with TMEM67; Fut8-deficient mice exhibit ciliary defects in kidney, brain, and trachea.","method":"Mass spectrometry-based proteomic analysis, Co-immunoprecipitation, Fut8 knockout mouse, autophagy inhibition assays, immunofluorescence","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — MS identification of PTM, Co-IP, KO mouse with multi-organ phenotype, mechanistic autophagy pathway link","pmids":["40728580"],"is_preprint":false},{"year":2024,"finding":"Two functional forms of TMEM67 generated by ADAMTS9-mediated proteolytic cleavage mediate Wnt signaling and ciliogenesis separately; this was first reported as a preprint before the peer-reviewed publication.","method":"Biochemical cleavage assay, cell culture, C. elegans genetics, non-cleavable mouse model","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 — same findings as peer-reviewed paper (PMID:40436881); preprint version; not adding new discoveries","pmids":["39282264"],"is_preprint":true}],"current_model":"TMEM67 (meckelin) is a seven-transmembrane ciliary transition zone protein whose extracellular domain is cleaved by ADAMTS9 to generate two functional forms: a C-terminal fragment that localizes to the transition zone and regulates ciliogenesis/TZ gating (controlling entry of ARL13B and INPP5E into cilia), and an uncleaved form that acts as a receptor for Wnt5a, phosphorylating ROR2 to mediate non-canonical Wnt signaling; additionally, TMEM67 is core-fucosylated by FUT8, which stabilizes it against autophagic degradation, and it also localizes to the ER where its lumenal domain bridges misfolded cargo to the cytosolic p97 degradation machinery, while loss-of-function activates mTOR and JNK/ERK pathways and dysregulates canonical Wnt/β-catenin signaling via HOXB5 in the cerebellum."},"narrative":{"teleology":[{"year":2006,"claim":"Positional cloning identified TMEM67 as the MKS3 gene, establishing that mutations in a novel seven-transmembrane protein cause Meckel syndrome and linking it to ciliopathy pathogenesis.","evidence":"Positional cloning and mutation identification in MKS families with expression analysis in fetal tissues","pmids":["16415887"],"confidence":"High","gaps":["Subcellular localization not determined","No functional data on cilia or signaling at this stage","Ligand or pathway involvement unknown"]},{"year":2009,"claim":"Studies in rat, mouse, and C. elegans models demonstrated that TMEM67/MKS-3 is required for ciliary structure and function, localizes to the cilium base/transition zone, and operates in a genetic module with other MKS proteins parallel to the NPHP pathway.","evidence":"wpk rat phenotyping (eye, kidney, sperm), IMCD3 shRNA knockdown, C. elegans genetic epistasis and localization","pmids":["19515853","20150540"],"confidence":"High","gaps":["Mechanism by which TMEM67 controls cilia length and centrosome number not resolved","Whether TMEM67 is a structural or regulatory component of the TZ unclear"]},{"year":2009,"claim":"TMEM67 was found to localize predominantly to the ER, where it bridges misfolded lumenal cargo (mutant SP-C) to cytosolic p97, establishing an unexpected role in ERAD distinct from its ciliary function.","evidence":"Co-immunoprecipitation with domain deletions, subcellular fractionation, siRNA knockdown blocking ERAD of mutant SP-C in cell culture","pmids":["19815549"],"confidence":"High","gaps":["Whether the ER pool and TZ pool represent the same biosynthetic route or distinct functional populations is unknown","Range of ERAD substrates beyond SP-C not defined"]},{"year":2013,"claim":"Tmem67-null mice revealed that loss of TMEM67 upregulates canonical Wnt/β-catenin signaling in cystic tissues and activates JNK/ERK pathways, while zebrafish morphants showed convergent extension defects, placing TMEM67 as a regulator of Wnt and MAPK signaling rather than solely a structural ciliary protein.","evidence":"Tmem67 bpck mouse Wnt reporter assays, HEK293 overexpression with MAPK inhibitors, zebrafish morpholino knockdown","pmids":["23393159","23456819"],"confidence":"High","gaps":["Direct molecular mechanism linking TMEM67 to canonical Wnt suppression unresolved","JNK/ERK activation mechanism (direct vs. indirect through cilia loss) unclear"]},{"year":2015,"claim":"TMEM67 was identified as a receptor for Wnt5a that physically interacts with ROR2 to enable non-canonical Wnt signaling and epithelial branching morphogenesis, resolving how TMEM67 engages the Wnt pathway at the molecular level.","evidence":"In vitro Wnt5a binding to TMEM67 N-terminal domain, Co-IP with ROR2, Tmem67 KO embryonic lung culture rescued by RhoA activation","pmids":["26035863"],"confidence":"High","gaps":["Structural basis of Wnt5a–TMEM67 interaction unresolved","Whether TMEM67 acts as a classical co-receptor or independent receptor not distinguished"]},{"year":2019,"claim":"In the cerebellum, loss of TMEM67 was shown to activate canonical Wnt signaling through increased HOXB5 occupancy at the β-catenin promoter, providing a transcription-factor-level mechanism for Wnt dysregulation and linking it to disrupted Shh responsiveness.","evidence":"Tmem67 KO mouse cerebellum transcriptomics and ChIP for HOXB5 at β-catenin promoter","pmids":["30931988"],"confidence":"High","gaps":["How TMEM67 loss leads to HOXB5 upregulation is not defined","Whether this HOXB5 mechanism operates outside the cerebellum is unknown"]},{"year":2021,"claim":"Hyperactive mTOR signaling was identified as a pathogenic effector downstream of TMEM67 loss, with genetic and pharmacological mTOR inhibition rescuing cystogenesis and ciliary defects in adult zebrafish, opening a potential therapeutic axis.","evidence":"TALEN-generated tmem67 zebrafish mutants, rapamycin treatment and mtor hypomorphic epistasis, 3D kidney imaging","pmids":["33574160"],"confidence":"Medium","gaps":["Whether mTOR hyperactivation is cilia-dependent or a direct TMEM67 effect is unresolved","Not validated in mammalian models"]},{"year":2022,"claim":"CRISPR knockout in human cells established that TMEM67 is required for transition zone gating of ARL13B and INPP5E into cilia but is dispensable for recruitment of other TZ components (CEP290, RPGRIP1L, NPHP5), and revealed that ciliopathy-associated mutants can restore gating but not cilia length control, separating these functions.","evidence":"CRISPR/Cas9 KO in hTERT-RPE1 cells with immunofluorescence and mutant rescue","pmids":["36334440"],"confidence":"High","gaps":["Molecular basis by which TMEM67 enforces the diffusion barrier is unknown","Structural arrangement of TMEM67 within the TZ Y-link not resolved"]},{"year":2025,"claim":"ADAMTS9-mediated extracellular cleavage of TMEM67 was shown to generate two structurally and functionally separable forms — a cleaved TZ-localized fragment for ciliogenesis and a full-length form for Wnt signaling — resolving how one protein executes dual functions; patient variants in the cleavage motif disrupt only ciliary function.","evidence":"Biochemical cleavage assay, non-cleavable TMEM67 knock-in mouse phenocopying ciliopathy but with normal Wnt signaling, patient variant analysis in mammalian cells and C. elegans","pmids":["40436881"],"confidence":"High","gaps":["Identity of the TMEM67 cleavage fragment released into the extracellular space and whether it has signaling activity is unknown","Regulation of ADAMTS9-mediated cleavage timing and tissue specificity not defined"]},{"year":2025,"claim":"FUT8-mediated core fucosylation was identified as a post-translational mechanism that stabilizes TMEM67 by preventing its autophagic degradation, ensuring proper TZ localization and ciliogenesis across multiple organs.","evidence":"Mass spectrometry identification of core fucosylation, Co-IP of FUT8 with TMEM67, Fut8 KO mouse ciliary defects in kidney/brain/trachea, autophagy inhibition rescue","pmids":["40728580"],"confidence":"High","gaps":["Which specific glycosylation sites on TMEM67 are critical is not fully mapped","Whether fucosylation status affects ADAMTS9 cleavage efficiency is untested"]},{"year":null,"claim":"Key unresolved questions include the structural basis of TMEM67 within the transition zone diffusion barrier, how its ER-localized ERAD function relates to its ciliary role, whether mTOR hyperactivation upon TMEM67 loss is a direct or cilia-dependent effect, and the identity and fate of the released N-terminal cleavage product.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structural model of TMEM67 at the TZ","Relationship between ER pool and TZ pool mechanistically undefined","Full spectrum of ERAD substrates unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[6,14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,7,12]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[2,10,12,14]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[3]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,6,10]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,6,7,14]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,2,12,14,15]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3,15]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,9]}],"complexes":["MKS/B9 transition zone complex"],"partners":["ROR2","ADAMTS9","FUT8","MKS1","VCP","NPHP1"],"other_free_text":[]},"mechanistic_narrative":"TMEM67 (meckelin) is a seven-transmembrane glycoprotein that functions as a ciliary transition zone component and Wnt signaling receptor, with its dual roles structurally separated by ADAMTS9-mediated extracellular cleavage: the cleaved C-terminal fragment localizes to the transition zone to regulate ciliogenesis and ciliary gate function controlling entry of ARL13B and INPP5E, while the uncleaved full-length form acts as a Wnt5a co-receptor that promotes ROR2 phosphorylation and non-canonical Wnt signaling [PMID:40436881, PMID:26035863, PMID:36334440]. Loss of TMEM67 causes Meckel syndrome (MKS3) and related ciliopathies, with mutant tissues exhibiting aberrant canonical Wnt/β-catenin signaling driven by HOXB5, hyperactive mTOR signaling, cystogenesis, and disrupted Hedgehog responsiveness in the cerebellum [PMID:16415887, PMID:30931988, PMID:33574160, PMID:23393159]. TMEM67 protein stability at the transition zone depends on FUT8-mediated core fucosylation, which protects it from autophagic degradation [PMID:40728580]. TMEM67 also localizes to the endoplasmic reticulum, where its lumenal domain bridges misfolded substrates to the cytosolic p97 AAA-ATPase for ERAD-mediated degradation [PMID:19815549]."},"prefetch_data":{"uniprot":{"accession":"Q5HYA8","full_name":"Meckelin","aliases":["Meckel syndrome type 3 protein","Transmembrane protein 67"],"length_aa":995,"mass_kda":111.7,"function":"Required for ciliary structure and function. Part of the tectonic-like complex which is required for tissue-specific ciliogenesis and may regulate ciliary membrane composition (By similarity). Involved in centrosome migration to the apical cell surface during early ciliogenesis. Involved in the regulation of cilia length and appropriate number through the control of centrosome duplication. Is a key regulator of stereociliary bundle orientation (By similarity). Required for epithelial cell branching morphology. Essential for endoplasmic reticulum-associated degradation (ERAD) of surfactant protein C (SFTPC). Involved in the negative regulation of canonical Wnt signaling, and activation of the non-canonical cascade stimulated by WNT5A (PubMed:26035863). In non-canonical Wnt signaling, it may act as ROR2 coreceptor (By similarity)","subcellular_location":"Cell membrane; Endoplasmic reticulum membrane; Cell projection, cilium; Cytoplasm, cytoskeleton, cilium basal body","url":"https://www.uniprot.org/uniprotkb/Q5HYA8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMEM67","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CANX","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TMEM67","total_profiled":1310},"omim":[{"mim_id":"617778","title":"THIOREDOXIN DOMAIN-CONTAINING PROTEIN 15; TXNDC15","url":"https://www.omim.org/entry/617778"},{"mim_id":"615586","title":"CENTROSOMAL PROTEIN, 19-KD; CEP19","url":"https://www.omim.org/entry/615586"},{"mim_id":"614423","title":"TRANSMEMBRANE PROTEIN 237; TMEM237","url":"https://www.omim.org/entry/614423"},{"mim_id":"614144","title":"B9 DOMAIN-CONTAINING PROTEIN 1; B9D1","url":"https://www.omim.org/entry/614144"},{"mim_id":"613550","title":"NEPHRONOPHTHISIS 11; NPHP11","url":"https://www.omim.org/entry/613550"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"heart muscle","ntpm":20.8}],"url":"https://www.proteinatlas.org/search/TMEM67"},"hgnc":{"alias_symbol":["MGC26979","JBTS6","NPHP11"],"prev_symbol":["MKS3"]},"alphafold":{"accession":"Q5HYA8","domains":[{"cath_id":"-","chopping":"47-170","consensus_level":"medium","plddt":75.0135,"start":47,"end":170}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5HYA8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5HYA8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5HYA8-F1-predicted_aligned_error_v6.png","plddt_mean":84.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMEM67","jax_strain_url":"https://www.jax.org/strain/search?query=TMEM67"},"sequence":{"accession":"Q5HYA8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5HYA8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5HYA8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5HYA8"}},"corpus_meta":[{"pmid":"16415887","id":"PMC_16415887","title":"The transmembrane protein meckelin (MKS3) is mutated in Meckel-Gruber syndrome and the wpk rat.","date":"2006","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16415887","citation_count":219,"is_preprint":false},{"pmid":"17160906","id":"PMC_17160906","title":"The Meckel-Gruber syndrome gene, MKS3, is mutated in Joubert syndrome.","date":"2006","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17160906","citation_count":188,"is_preprint":false},{"pmid":"19574260","id":"PMC_19574260","title":"Mutations in 3 genes (MKS3, CC2D2A and RPGRIP1L) cause COACH syndrome (Joubert syndrome with congenital hepatic fibrosis).","date":"2009","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19574260","citation_count":111,"is_preprint":false},{"pmid":"19508969","id":"PMC_19508969","title":"Hypomorphic mutations in meckelin (MKS3/TMEM67) cause nephronophthisis with liver fibrosis (NPHP11).","date":"2009","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19508969","citation_count":105,"is_preprint":false},{"pmid":"19515853","id":"PMC_19515853","title":"Ciliary and centrosomal defects associated with mutation and depletion of the Meckel syndrome genes MKS1 and MKS3.","date":"2009","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19515853","citation_count":100,"is_preprint":false},{"pmid":"19058225","id":"PMC_19058225","title":"MKS3/TMEM67 mutations are a major cause of COACH Syndrome, a Joubert Syndrome related disorder with liver involvement.","date":"2009","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/19058225","citation_count":79,"is_preprint":false},{"pmid":"20232449","id":"PMC_20232449","title":"Novel TMEM67 mutations and genotype-phenotype correlates in meckelin-related ciliopathies.","date":"2010","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/20232449","citation_count":73,"is_preprint":false},{"pmid":"17397051","id":"PMC_17397051","title":"Spectrum of MKS1 and MKS3 mutations in Meckel syndrome: a genotype-phenotype correlation. Mutation in brief #960. Online.","date":"2007","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/17397051","citation_count":72,"is_preprint":false},{"pmid":"17377820","id":"PMC_17377820","title":"Molecular diagnostics of Meckel-Gruber syndrome highlights phenotypic differences between MKS1 and MKS3.","date":"2007","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17377820","citation_count":58,"is_preprint":false},{"pmid":"20150540","id":"PMC_20150540","title":"Normal ciliogenesis requires synergy between the cystic kidney disease genes MKS-3 and NPHP-4.","date":"2010","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/20150540","citation_count":53,"is_preprint":false},{"pmid":"23393159","id":"PMC_23393159","title":"The Meckel syndrome protein meckelin (TMEM67) is a key regulator of cilia function but is not required for tissue planar polarity.","date":"2013","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23393159","citation_count":48,"is_preprint":false},{"pmid":"26035863","id":"PMC_26035863","title":"The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway.","date":"2015","source":"Disease models & mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/26035863","citation_count":38,"is_preprint":false},{"pmid":"12384791","id":"PMC_12384791","title":"A novel locus for Meckel-Gruber syndrome, MKS3, maps to chromosome 8q24.","date":"2002","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12384791","citation_count":33,"is_preprint":false},{"pmid":"30705305","id":"PMC_30705305","title":"Hydrocephalus in a rat model of Meckel Gruber syndrome with a TMEM67 mutation.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30705305","citation_count":25,"is_preprint":false},{"pmid":"19540516","id":"PMC_19540516","title":"MKS3-related ciliopathy with features of autosomal recessive polycystic kidney disease, nephronophthisis, and Joubert Syndrome.","date":"2009","source":"The Journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/19540516","citation_count":25,"is_preprint":false},{"pmid":"30931988","id":"PMC_30931988","title":"The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30931988","citation_count":19,"is_preprint":false},{"pmid":"28860541","id":"PMC_28860541","title":"Functional validation of novel MKS3/TMEM67 mutations in COACH syndrome.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28860541","citation_count":14,"is_preprint":false},{"pmid":"33933680","id":"PMC_33933680","title":"TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane.","date":"2021","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/33933680","citation_count":14,"is_preprint":false},{"pmid":"29891882","id":"PMC_29891882","title":"Biallelic variants in the ciliary gene TMEM67 cause RHYNS syndrome.","date":"2018","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/29891882","citation_count":13,"is_preprint":false},{"pmid":"28487520","id":"PMC_28487520","title":"An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28487520","citation_count":13,"is_preprint":false},{"pmid":"33574160","id":"PMC_33574160","title":"mtor Haploinsufficiency Ameliorates Renal Cysts and Cilia Abnormality in Adult Zebrafish tmem67 Mutants.","date":"2021","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/33574160","citation_count":12,"is_preprint":false},{"pmid":"36334440","id":"PMC_36334440","title":"TMEM67 is required for the gating function of the transition zone that controls entry of membrane-associated proteins ARL13B and INPP5E into primary cilia.","date":"2022","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/36334440","citation_count":11,"is_preprint":false},{"pmid":"19815549","id":"PMC_19815549","title":"Meckel-Gruber syndrome protein MKS3 is required for endoplasmic reticulum-associated degradation of surfactant protein C.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19815549","citation_count":9,"is_preprint":false},{"pmid":"28719906","id":"PMC_28719906","title":"A Common Ancestral Asn242Ser Mutation in TMEM67 Identified in Multiple Iranian Families with Joubert Syndrome.","date":"2017","source":"Public health genomics","url":"https://pubmed.ncbi.nlm.nih.gov/28719906","citation_count":8,"is_preprint":false},{"pmid":"32000717","id":"PMC_32000717","title":"Novel compound heterozygous TMEM67 variants in a Vietnamese family with Joubert syndrome: a case report.","date":"2020","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32000717","citation_count":8,"is_preprint":false},{"pmid":"24039893","id":"PMC_24039893","title":"Preimplantation genetic diagnosis for a Chinese family with autosomal recessive Meckel-Gruber syndrome type 3 (MKS3).","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24039893","citation_count":6,"is_preprint":false},{"pmid":"23456819","id":"PMC_23456819","title":"Evidence that TMEM67 causes polycystic kidney disease through activation of JNK/ERK-dependent pathways.","date":"2013","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/23456819","citation_count":5,"is_preprint":false},{"pmid":"36221156","id":"PMC_36221156","title":"Upgrading an intronic TMEM67 variant of unknown significance to likely pathogenic through RNA studies and community data sharing.","date":"2022","source":"Prenatal diagnosis","url":"https://pubmed.ncbi.nlm.nih.gov/36221156","citation_count":5,"is_preprint":false},{"pmid":"34356094","id":"PMC_34356094","title":"Prenatal Versus Postnatal Diagnosis of Meckel-Gruber and Joubert Syndrome in Patients with TMEM67 Mutations.","date":"2021","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/34356094","citation_count":5,"is_preprint":false},{"pmid":"26191240","id":"PMC_26191240","title":"A missense mutation in TMEM67 causes Meckel-Gruber syndrome type 3 (MKS3): a family from China.","date":"2015","source":"International journal of clinical and experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/26191240","citation_count":3,"is_preprint":false},{"pmid":"35621037","id":"PMC_35621037","title":"Association of novel TMEM67 variants with mild phenotypes of high gamma-glutamyl transpeptidase cholestasis and congenital hepatic fibrosis.","date":"2022","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/35621037","citation_count":3,"is_preprint":false},{"pmid":"40436881","id":"PMC_40436881","title":"Cleavage of the Meckel-Gruber syndrome protein TMEM67 by ADAMTS9 uncouples Wnt signaling and ciliogenesis.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40436881","citation_count":2,"is_preprint":false},{"pmid":"40728580","id":"PMC_40728580","title":"FUT8-mediated core fucosylation stabilizes TMEM67 to promote ciliogenesis.","date":"2025","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/40728580","citation_count":2,"is_preprint":false},{"pmid":"38844949","id":"PMC_38844949","title":"Two novel TMEM67 variations in a Chinese family with recurrent pregnancy loss: a case report.","date":"2024","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/38844949","citation_count":2,"is_preprint":false},{"pmid":"28726664","id":"PMC_28726664","title":"EXPANDED PHENOTYPE OF TMEM67 GENE MUTATION (CASE REPORT).","date":"2017","source":"Georgian medical news","url":"https://pubmed.ncbi.nlm.nih.gov/28726664","citation_count":1,"is_preprint":false},{"pmid":"37910852","id":"PMC_37910852","title":"A case of Joubert syndrome caused by novel compound heterozygous variants in the TMEM67 gene.","date":"2023","source":"The Journal of international medical research","url":"https://pubmed.ncbi.nlm.nih.gov/37910852","citation_count":1,"is_preprint":false},{"pmid":"38311563","id":"PMC_38311563","title":"[Genetic analysis of a fetus with Meckel syndrome due to variants of TMEM67 gene].","date":"2024","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38311563","citation_count":1,"is_preprint":false},{"pmid":"39027323","id":"PMC_39027323","title":"Novel ocular observations in a child with Joubert syndrome type 6 due to pathogenic variant in TMEM67 gene.","date":"2024","source":"American journal of ophthalmology case reports","url":"https://pubmed.ncbi.nlm.nih.gov/39027323","citation_count":1,"is_preprint":false},{"pmid":"39849212","id":"PMC_39849212","title":"Compound heterozygous TMEM67 biallelic variants including a novel frameshift mutation in two Filipino adolescent siblings with Joubert syndrome.","date":"2025","source":"Journal of neural transmission (Vienna, Austria : 1996)","url":"https://pubmed.ncbi.nlm.nih.gov/39849212","citation_count":0,"is_preprint":false},{"pmid":"39282264","id":"PMC_39282264","title":"Two functional forms of the Meckel-Gruber syndrome protein TMEM67 generated by proteolytic cleavage by ADAMTS9 mediate Wnt signaling and ciliogenesis.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39282264","citation_count":0,"is_preprint":false},{"pmid":"37730223","id":"PMC_37730223","title":"[Analysis of a Chinese pedigree affected with Meckel syndrome due to variants of TMEM67 gene].","date":"2023","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37730223","citation_count":0,"is_preprint":false},{"pmid":"41465080","id":"PMC_41465080","title":"Unexpected Diagnosis of Fahr's Disease in a Patient with Severe Obesity and a Heterozygotic Variant in the TMEM67 Gene.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/41465080","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":21975,"output_tokens":4364,"usd":0.065693},"stage2":{"model":"claude-opus-4-6","input_tokens":7809,"output_tokens":3020,"usd":0.171818},"total_usd":0.237511,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"TMEM67 encodes meckelin, a 995-amino acid seven-transmembrane receptor protein; positional cloning and mutation identification established it as the MKS3 gene product expressed in fetal brain, liver, and kidney.\",\n      \"method\": \"Positional cloning, direct sequencing, expression analysis\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — original positional cloning with mutation identification, highly cited foundational paper\",\n      \"pmids\": [\"16415887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MKS1 and MKS3 proteins are required for ciliary structure and function, including regulation of cilia length and number; loss of MKS3 in the wpk rat causes functional defects of the connecting cilium in the eye (lack of outer segment formation), very short sperm flagella, and longer renal cilia with centrosome over-duplication; stable shRNA knockdown of Mks3 in IMCD3 cells induced multi-ciliated and multi-centrosomal phenotypes.\",\n      \"method\": \"Animal model analysis (wpk rat), shRNA knockdown in IMCD3 cells, immunofluorescence, electron microscopy\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (in vivo model, cell knockdown, structural imaging), moderate-strong evidence\",\n      \"pmids\": [\"19515853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MKS3/TMEM67 protein MKS-3 in C. elegans localizes to the distal end of dendrites and cilium base (not the cilium itself) of ciliated sensory neurons; mks-3 mutants show elongated cilia and abnormal cilia-mediated chemoreception; genetic epistasis shows mks-3 functions in a pathway with other mks genes, and mks-1/mks-3 genetically interact with a separate nphp-1/nphp-4 pathway to influence cilia positioning and formation.\",\n      \"method\": \"C. elegans genetics, localization studies, behavioral assays, genetic epistasis\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with multiple mutants, localization, functional readouts in an ortholog\",\n      \"pmids\": [\"20150540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MKS3/TMEM67 is a membrane glycoprotein predominantly localized to the endoplasmic reticulum; its ER lumenal domain interacts with misfolded surfactant protein C (SP-C) and associated chaperones, while its transmembrane/cytosolic domain interacts with cytosolic p97; knockdown of MKS3 inhibits ERAD-mediated degradation of mutant SP-C, placing MKS3 as a bridge between ER lumenal quality control and cytosolic degradation machinery.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation, domain deletion constructs, siRNA knockdown, Western blotting\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP, domain mapping, functional knockdown with defined biochemical readout\",\n      \"pmids\": [\"19815549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In the Tmem67 null (bpck) mouse, canonical Wnt signaling is upregulated in cyst linings and isolated fibroblasts, but not in retina or cochlea; zebrafish tmem67 morphants show convergent extension defects similar to PCP mutants, but analysis of classical vertebrate PCP readouts did not support global loss of planar polarity; defective cilia loading rather than global loss of ciliogenesis or basal body docking underlies dysfunctional cilia in MKS3 tissues.\",\n      \"method\": \"Tmem67 null mouse analysis, zebrafish morpholino knockdown, Wnt reporter assays, immunofluorescence, stereociliary bundle analysis\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods in two model organisms with defined pathway readouts\",\n      \"pmids\": [\"23393159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Overexpression of TMEM67 in HEK293 cells activates ERK and JNK signaling pathways; pharmacological inhibition of ERK or JNK suppresses this activation; in bpck mice (Tmem67 loss-of-function), activation of ERK, JNK, and 4E-BP1 phosphorylation is elevated in cystic kidneys, linking TMEM67 to JNK/ERK-dependent pathways in polycystic kidney disease.\",\n      \"method\": \"Overexpression in HEK293 cells, pharmacological inhibition, Western blotting, animal model (bpck mouse)\",\n      \"journal\": \"Cell biology international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, overexpression and inhibitor studies without direct mechanistic reconstitution\",\n      \"pmids\": [\"23456819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 upon Wnt5a stimulation; TMEM67 colocalizes and physically interacts with ROR2 at the ciliary transition zone; the extracellular N-terminal domain of TMEM67 preferentially binds Wnt5a in vitro; loss of TMEM67 abolishes epithelial branching morphogenesis response to Wnt5a in cultured embryonic lungs; RhoA activation rescues pulmonary hypoplasia phenotypes downstream of the Wnt5a-TMEM67-ROR2 axis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assay, co-localization, Tmem67 knockout mouse, embryonic lung culture, rescue by RhoA activation\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro binding, Co-IP, KO mouse with defined pathway placement and functional rescue, multiple orthogonal methods\",\n      \"pmids\": [\"26035863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In the Tmem67 knockout mouse cerebellum, loss of TMEM67 leads to aberrantly high canonical Wnt/β-catenin signaling, increased expression of Hoxb5, and HOXB5 occupancy at the β-catenin promoter is increased; increased canonical Wnt signaling following loss of TMEM67 is directly dependent on HOXB5; Tmem67 mutant cerebellum also shows disrupted ciliogenesis and reduced responsiveness to Shh signaling.\",\n      \"method\": \"Tmem67 knockout mouse, transcriptome profiling, chromatin immunoprecipitation (ChIP), Wnt reporter assays, immunohistochemistry\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, transcriptomics, KO mouse with multiple orthogonal readouts in a single study\",\n      \"pmids\": [\"30931988\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMEM67 is required for regulation of choroid plexus epithelial cell fluid and electrolyte homeostasis; homozygous Wpk (TMEM67 point mutation) rats develop severe ventriculomegaly and increased Na+, K+, and Cl- in CSF; heterozygotes develop slowly progressing hydrocephalus; aquaporin-1 and claudin-1 remain normally polarized in all genotypes, suggesting a selective permeability effect.\",\n      \"method\": \"Wpk rat model, MRI, CSF ion analysis, immunofluorescence for tight junction and water channel markers\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — animal model with physiological readouts, but mechanism is incompletely defined\",\n      \"pmids\": [\"30705305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Wnt signaling (but not Hedgehog signaling) is suppressed in tmem67 zebrafish morphants; wild-type human TMEM67 RNA rescues phenotypes of tmem67 morphants whereas two COACH syndrome-associated mutant RNAs do not; the frameshift mutation p.Tyr920ThrfsX40 accelerates turnover of the TMEM67 protein.\",\n      \"method\": \"Zebrafish morpholino knockdown, mRNA rescue assay, Western blotting (protein stability)\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — morpholino knockdown with mRNA rescue and pathway readout, single lab\",\n      \"pmids\": [\"28860541\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMEM67 and TMEM237 are unique components of the photoreceptor outer segment plasma membrane, identified by protein correlation profiling mass spectrometry; TMEM67 is present at this specialized ciliary membrane compartment in vertebrate photoreceptors.\",\n      \"method\": \"Label-free quantitative mass spectrometry, protein correlation profiling, membrane fractionation\",\n      \"journal\": \"Molecular & cellular proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — quantitative proteomics with validated markers, but functional consequence not directly tested\",\n      \"pmids\": [\"33933680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Adult zebrafish tmem67 mutants exhibit hyperactive mTOR signaling; mTOR inhibition (by hypomorphic mtor or rapamycin) ameliorates renal cysts and rescues ciliary abnormalities in adult mutants, placing TMEM67 upstream of mTOR in a pathway relevant to cystogenesis and cilia length regulation.\",\n      \"method\": \"TALEN-generated zebrafish tmem67 mutants, rapamycin treatment, mtor hypomorphic strain, 3D kidney imaging, ciliary analysis\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic and pharmacological epistasis in zebrafish model, single lab\",\n      \"pmids\": [\"33574160\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM67 is required for the gating function of the ciliary transition zone: TMEM67-KO in hTERT-RPE1 cells leads to impaired ciliogenesis, elongated cilia, and perturbed ciliary localization of membrane-associated proteins ARL13B and INPP5E, but does not affect recruitment of TZ proteins CEP290, RPGRIP1L, and NPHP5; TMEM67 localizes not only to the transition zone but extends into the cilium; ciliopathy-associated TMEM67 mutants can restore ARL13B/INPP5E localization but not aberrant cilium elongation.\",\n      \"method\": \"CRISPR/Cas9 KO in hTERT-RPE1 cells, immunofluorescence, exogenous mutant expression, confocal microscopy\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined subcellular and functional phenotypes, mutant rescue experiments, multiple orthogonal readouts\",\n      \"pmids\": [\"36334440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM67 variants associated with mild cholestasis phenotype show significantly decreased protein levels; however, the interaction between these TMEM67 variants and MKS1 remains unaffected, indicating that MKS1-TMEM67 complex formation is preserved despite reduced TMEM67 abundance.\",\n      \"method\": \"In vitro expression studies, Western blotting, co-immunoprecipitation\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, co-IP without full mechanistic follow-up\",\n      \"pmids\": [\"35621037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TMEM67 is cleaved in its extracellular domain by the metalloproteinase ADAMTS9; this cleavage generates two functional forms: a C-terminal portion localizing to the ciliary transition zone that regulates ciliogenesis, and a non-cleaved full-length form that mediates non-canonical Wnt signaling; a non-cleavable TMEM67 mouse model develops severe ciliopathies phenocopying Tmem67-/- mice but transduces normal Wnt signaling, demonstrating that the two functions are structurally separable; three patient variants within the cleavage motif disrupt cilia structure and function in mammalian cells and C. elegans.\",\n      \"method\": \"Biochemical cleavage assay, non-cleavable TMEM67 knock-in mouse model, C. elegans patient variant characterization, mammalian cell culture, Wnt signaling assays, ciliary localization studies\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution of cleavage, mouse knock-in model, C. elegans genetics, multiple orthogonal approaches in single study\",\n      \"pmids\": [\"40436881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FUT8-mediated core fucosylation (N-linked glycosylation) of TMEM67 stabilizes the protein by impeding its degradation via the autophagy pathway, ensuring proper localization of TMEM67 to the ciliary transition zone to promote cilium formation; FUT8 physically interacts with TMEM67; Fut8-deficient mice exhibit ciliary defects in kidney, brain, and trachea.\",\n      \"method\": \"Mass spectrometry-based proteomic analysis, Co-immunoprecipitation, Fut8 knockout mouse, autophagy inhibition assays, immunofluorescence\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — MS identification of PTM, Co-IP, KO mouse with multi-organ phenotype, mechanistic autophagy pathway link\",\n      \"pmids\": [\"40728580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Two functional forms of TMEM67 generated by ADAMTS9-mediated proteolytic cleavage mediate Wnt signaling and ciliogenesis separately; this was first reported as a preprint before the peer-reviewed publication.\",\n      \"method\": \"Biochemical cleavage assay, cell culture, C. elegans genetics, non-cleavable mouse model\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — same findings as peer-reviewed paper (PMID:40436881); preprint version; not adding new discoveries\",\n      \"pmids\": [\"39282264\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TMEM67 (meckelin) is a seven-transmembrane ciliary transition zone protein whose extracellular domain is cleaved by ADAMTS9 to generate two functional forms: a C-terminal fragment that localizes to the transition zone and regulates ciliogenesis/TZ gating (controlling entry of ARL13B and INPP5E into cilia), and an uncleaved form that acts as a receptor for Wnt5a, phosphorylating ROR2 to mediate non-canonical Wnt signaling; additionally, TMEM67 is core-fucosylated by FUT8, which stabilizes it against autophagic degradation, and it also localizes to the ER where its lumenal domain bridges misfolded cargo to the cytosolic p97 degradation machinery, while loss-of-function activates mTOR and JNK/ERK pathways and dysregulates canonical Wnt/β-catenin signaling via HOXB5 in the cerebellum.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TMEM67 (meckelin) is a seven-transmembrane glycoprotein that functions as a ciliary transition zone component and Wnt signaling receptor, with its dual roles structurally separated by ADAMTS9-mediated extracellular cleavage: the cleaved C-terminal fragment localizes to the transition zone to regulate ciliogenesis and ciliary gate function controlling entry of ARL13B and INPP5E, while the uncleaved full-length form acts as a Wnt5a co-receptor that promotes ROR2 phosphorylation and non-canonical Wnt signaling [PMID:40436881, PMID:26035863, PMID:36334440]. Loss of TMEM67 causes Meckel syndrome (MKS3) and related ciliopathies, with mutant tissues exhibiting aberrant canonical Wnt/β-catenin signaling driven by HOXB5, hyperactive mTOR signaling, cystogenesis, and disrupted Hedgehog responsiveness in the cerebellum [PMID:16415887, PMID:30931988, PMID:33574160, PMID:23393159]. TMEM67 protein stability at the transition zone depends on FUT8-mediated core fucosylation, which protects it from autophagic degradation [PMID:40728580]. TMEM67 also localizes to the endoplasmic reticulum, where its lumenal domain bridges misfolded substrates to the cytosolic p97 AAA-ATPase for ERAD-mediated degradation [PMID:19815549].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Positional cloning identified TMEM67 as the MKS3 gene, establishing that mutations in a novel seven-transmembrane protein cause Meckel syndrome and linking it to ciliopathy pathogenesis.\",\n      \"evidence\": \"Positional cloning and mutation identification in MKS families with expression analysis in fetal tissues\",\n      \"pmids\": [\"16415887\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Subcellular localization not determined\", \"No functional data on cilia or signaling at this stage\", \"Ligand or pathway involvement unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Studies in rat, mouse, and C. elegans models demonstrated that TMEM67/MKS-3 is required for ciliary structure and function, localizes to the cilium base/transition zone, and operates in a genetic module with other MKS proteins parallel to the NPHP pathway.\",\n      \"evidence\": \"wpk rat phenotyping (eye, kidney, sperm), IMCD3 shRNA knockdown, C. elegans genetic epistasis and localization\",\n      \"pmids\": [\"19515853\", \"20150540\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which TMEM67 controls cilia length and centrosome number not resolved\", \"Whether TMEM67 is a structural or regulatory component of the TZ unclear\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"TMEM67 was found to localize predominantly to the ER, where it bridges misfolded lumenal cargo (mutant SP-C) to cytosolic p97, establishing an unexpected role in ERAD distinct from its ciliary function.\",\n      \"evidence\": \"Co-immunoprecipitation with domain deletions, subcellular fractionation, siRNA knockdown blocking ERAD of mutant SP-C in cell culture\",\n      \"pmids\": [\"19815549\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the ER pool and TZ pool represent the same biosynthetic route or distinct functional populations is unknown\", \"Range of ERAD substrates beyond SP-C not defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Tmem67-null mice revealed that loss of TMEM67 upregulates canonical Wnt/β-catenin signaling in cystic tissues and activates JNK/ERK pathways, while zebrafish morphants showed convergent extension defects, placing TMEM67 as a regulator of Wnt and MAPK signaling rather than solely a structural ciliary protein.\",\n      \"evidence\": \"Tmem67 bpck mouse Wnt reporter assays, HEK293 overexpression with MAPK inhibitors, zebrafish morpholino knockdown\",\n      \"pmids\": [\"23393159\", \"23456819\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct molecular mechanism linking TMEM67 to canonical Wnt suppression unresolved\", \"JNK/ERK activation mechanism (direct vs. indirect through cilia loss) unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"TMEM67 was identified as a receptor for Wnt5a that physically interacts with ROR2 to enable non-canonical Wnt signaling and epithelial branching morphogenesis, resolving how TMEM67 engages the Wnt pathway at the molecular level.\",\n      \"evidence\": \"In vitro Wnt5a binding to TMEM67 N-terminal domain, Co-IP with ROR2, Tmem67 KO embryonic lung culture rescued by RhoA activation\",\n      \"pmids\": [\"26035863\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of Wnt5a–TMEM67 interaction unresolved\", \"Whether TMEM67 acts as a classical co-receptor or independent receptor not distinguished\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"In the cerebellum, loss of TMEM67 was shown to activate canonical Wnt signaling through increased HOXB5 occupancy at the β-catenin promoter, providing a transcription-factor-level mechanism for Wnt dysregulation and linking it to disrupted Shh responsiveness.\",\n      \"evidence\": \"Tmem67 KO mouse cerebellum transcriptomics and ChIP for HOXB5 at β-catenin promoter\",\n      \"pmids\": [\"30931988\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TMEM67 loss leads to HOXB5 upregulation is not defined\", \"Whether this HOXB5 mechanism operates outside the cerebellum is unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Hyperactive mTOR signaling was identified as a pathogenic effector downstream of TMEM67 loss, with genetic and pharmacological mTOR inhibition rescuing cystogenesis and ciliary defects in adult zebrafish, opening a potential therapeutic axis.\",\n      \"evidence\": \"TALEN-generated tmem67 zebrafish mutants, rapamycin treatment and mtor hypomorphic epistasis, 3D kidney imaging\",\n      \"pmids\": [\"33574160\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether mTOR hyperactivation is cilia-dependent or a direct TMEM67 effect is unresolved\", \"Not validated in mammalian models\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"CRISPR knockout in human cells established that TMEM67 is required for transition zone gating of ARL13B and INPP5E into cilia but is dispensable for recruitment of other TZ components (CEP290, RPGRIP1L, NPHP5), and revealed that ciliopathy-associated mutants can restore gating but not cilia length control, separating these functions.\",\n      \"evidence\": \"CRISPR/Cas9 KO in hTERT-RPE1 cells with immunofluorescence and mutant rescue\",\n      \"pmids\": [\"36334440\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis by which TMEM67 enforces the diffusion barrier is unknown\", \"Structural arrangement of TMEM67 within the TZ Y-link not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"ADAMTS9-mediated extracellular cleavage of TMEM67 was shown to generate two structurally and functionally separable forms — a cleaved TZ-localized fragment for ciliogenesis and a full-length form for Wnt signaling — resolving how one protein executes dual functions; patient variants in the cleavage motif disrupt only ciliary function.\",\n      \"evidence\": \"Biochemical cleavage assay, non-cleavable TMEM67 knock-in mouse phenocopying ciliopathy but with normal Wnt signaling, patient variant analysis in mammalian cells and C. elegans\",\n      \"pmids\": [\"40436881\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the TMEM67 cleavage fragment released into the extracellular space and whether it has signaling activity is unknown\", \"Regulation of ADAMTS9-mediated cleavage timing and tissue specificity not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"FUT8-mediated core fucosylation was identified as a post-translational mechanism that stabilizes TMEM67 by preventing its autophagic degradation, ensuring proper TZ localization and ciliogenesis across multiple organs.\",\n      \"evidence\": \"Mass spectrometry identification of core fucosylation, Co-IP of FUT8 with TMEM67, Fut8 KO mouse ciliary defects in kidney/brain/trachea, autophagy inhibition rescue\",\n      \"pmids\": [\"40728580\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which specific glycosylation sites on TMEM67 are critical is not fully mapped\", \"Whether fucosylation status affects ADAMTS9 cleavage efficiency is untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of TMEM67 within the transition zone diffusion barrier, how its ER-localized ERAD function relates to its ciliary role, whether mTOR hyperactivation upon TMEM67 loss is a direct or cilia-dependent effect, and the identity and fate of the released N-terminal cleavage product.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structural model of TMEM67 at the TZ\", \"Relationship between ER pool and TZ pool mechanistically undefined\", \"Full spectrum of ERAD substrates unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [6, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 7, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [2, 10, 12, 14]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 6, 10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 6, 7, 14]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 2, 12, 14, 15]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3, 15]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 9]}\n    ],\n    \"complexes\": [\n      \"MKS/B9 transition zone complex\"\n    ],\n    \"partners\": [\n      \"ROR2\",\n      \"ADAMTS9\",\n      \"FUT8\",\n      \"MKS1\",\n      \"VCP\",\n      \"NPHP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}