TMEM67

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0035869 ciliary transition zone	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation placing TMEM67 at the ciliary transition zone, inferred by phylogenetic analysis (PANTHER). TMEM67 is a well-established component of the MKS-JBTS module at the ciliary transition zone. Multiple publications confirm this localization. PMID:22121117 states that meckelin "Localizes at the transition zone, a region between the basal body and the ciliary axoneme." PMID:26595381 directly demonstrated transition zone localization by IDA. PMID:34964473 describes TMEM67/MKS3 as "a transmembrane protein that functions at the ciliary transition zone." This is a core localization for this protein. Reason: Transition zone localization is the best-established and most central subcellular localization for TMEM67. It is supported by extensive experimental evidence (IDA in PMID:26595381, NAS from PMID:22179047) and by the IBA phylogenetic inference. This is a core annotation. Supporting Evidence: PMID:26595381 TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome. PMID:34964473 TMEM67/MKS3 is a transmembrane protein that functions at the ciliary transition zone (TZ), which corresponds to the proximal-most 0.2–1.0 μm of the ciliary axoneme
GO:0060271 cilium assembly	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for cilium assembly, inferred by phylogenetic analysis (PANTHER). TMEM67 is required for ciliogenesis. PMID:17185389 demonstrated that "siRNA-mediated reduction of Mks1 and Mks3 expression in a ciliated epithelial cell-line blocked centriole migration to the apical membrane and consequent formation of the primary cilium." PMID:19515853 showed that "MKS1 and MKS3 functions are required for ciliary structure and function." This is a core biological process for TMEM67. Reason: Cilium assembly is a core function of TMEM67. It is supported by extensive experimental evidence including IMP from PMID:19515853 and knockdown data from PMID:17185389. The IBA annotation is fully consistent with published data. Supporting Evidence: PMID:17185389 siRNA-mediated reduction of Mks1 and Mks3 expression in a ciliated epithelial cell-line blocked centriole migration to the apical membrane and consequent formation of the primary cilium. PMID:19515853 MKS1 and MKS3 functions are required for ciliary structure and function, including a role in regulating length and appropriate number through modulating centrosome duplication.
GO:0005789 endoplasmic reticulum membrane	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation mapping TMEM67 to the ER membrane based on UniProt subcellular location vocabulary. PMID:19815549 (Wang et al. 2009) directly demonstrated that "MKS3 was identified as a membrane glycoprotein predominantly localized to the ER." This IEA is consistent with the IDA annotation from the same paper. However, the ER membrane localization represents a secondary localization; the primary localization is the ciliary transition zone. Reason: ER membrane localization is supported by direct experimental evidence (IDA, PMID:19815549). The IEA correctly captures this localization. While ER is not the primary localization of TMEM67 (the ciliary transition zone is), TMEM67 does reside at the ER membrane where it functions in ERAD. Supporting Evidence: PMID:19815549 MKS3 was identified as a membrane glycoprotein predominantly localized to the ER.
GO:0005886 plasma membrane	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation mapping TMEM67 to the plasma membrane based on UniProt subcellular location vocabulary. PMID:17185389 showed that "meckelin localized both to the primary cilium and to the plasma membrane in ciliated cell-lines and primary cells." The UniProt record states "Cell membrane" as a subcellular location. This is a valid but secondary localization relative to the ciliary transition zone. Reason: Plasma membrane localization is experimentally supported by PMID:17185389, which showed meckelin at both the primary cilium and the plasma membrane. This IEA is correct, though the ciliary transition zone is the more specific and informative localization. Supporting Evidence: PMID:17185389 meckelin localized both to the primary cilium and to the plasma membrane in ciliated cell-lines and primary cells.
GO:0005929 cilium	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation mapping TMEM67 to the cilium based on UniProt subcellular location vocabulary. PMID:17185389 confirmed that meckelin localizes to the primary cilium. The UniProt record lists "Cell projection, cilium" as a subcellular location. This is correct but less specific than the ciliary transition zone (GO:0035869), which is the more precise localization supported by IDA evidence in PMID:26595381. Reason: Cilium localization is correct and supported by experimental evidence. While the ciliary transition zone is more specific, the broader cilium term from an IEA is acceptable as it is not incorrect. It is a parent-like term relative to the more specific transition zone annotation. Supporting Evidence: PMID:17185389 meckelin localized both to the primary cilium and to the plasma membrane in ciliated cell-lines and primary cells.
GO:0030030 cell projection organization	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation mapping TMEM67 to cell projection organization based on UniProtKB/Swiss-Prot keyword mapping. This is a broad term. TMEM67 is indeed involved in organizing the cilium (a cell projection) through its role in ciliogenesis. This annotation is not wrong but is very general compared to the more specific cilium assembly (GO:0060271) annotation. Reason: While very general, this IEA mapping is not incorrect. TMEM67 is involved in cilium organization, which is a form of cell projection organization. The more specific cilium assembly annotation exists separately. For an IEA, this level of generality is acceptable.
GO:0036038 MKS complex	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation placing TMEM67 as part of the MKS complex, based on InterPro domain mapping (IPR019170). TMEM67 is a well-established core component of the MKS-JBTS module at the ciliary transition zone. PMID:22179047 identified this complex and PMID:26035863 describes TMEM67 as "a component of the MKS-JBTS module at the transition zone." PMID:34731008 also discusses TMEM67 as part of the MKS-JBTS module. Reason: MKS complex membership is a core annotation for TMEM67. It is well supported by multiple publications and is also annotated by ISS (GO_REF:0000024). The IEA via InterPro is correct. Supporting Evidence: PMID:26035863 TMEM67 is a component of the MKS-JBTS module at the transition zone. PMID:22179047 Using RNAi screening, proteomics, cell biological and mouse genetics approaches, we have identified a complex of nine proteins, seven of which are disrupted in human ciliopathies.
GO:0060271 cilium assembly	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for cilium assembly based on InterPro domain mapping (IPR019170). This is a duplicate of the IBA annotation for the same GO term. The annotation is correct; TMEM67 is required for ciliogenesis as demonstrated in PMID:17185389 and PMID:19515853. Reason: This IEA is correct and consistent with the IBA and IMP annotations for the same term. Cilium assembly is a core function of TMEM67. Supporting Evidence: PMID:17185389 siRNA-mediated reduction of Mks1 and Mks3 expression in a ciliated epithelial cell-line blocked centriole migration to the apical membrane and consequent formation of the primary cilium.
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	REMOVE	Summary: Protein binding annotation based on a high-throughput yeast two-hybrid (Y2H) interactome mapping study (PMID:32814053, Haenig et al. 2020). The WITH/FROM field indicates UniProtKB:P05067-2 (APP isoform 2, amyloid precursor protein). This study was a large-scale screen focused on neurodegenerative disease proteins. The interaction between TMEM67 and APP has no obvious biological context and may represent a false positive from the high-throughput screen. The IntAct database records 3 experiments for this interaction. The "protein binding" term is uninformative. Reason: The generic "protein binding" annotation does not convey any useful information about TMEM67 function. The interaction with APP from a high-throughput Y2H screen lacks biological context for TMEM67 function. No more specific replacement term is available. The interaction likely reflects overexpression artifacts in the Y2H system rather than a biologically meaningful function of TMEM67.
GO:0035869 ciliary transition zone	NAS PMID:22179047 A ciliopathy complex at the transition zone protects the cil...	ACCEPT	Summary: NAS annotation for ciliary transition zone localization from the ComplexPortal, citing PMID:22179047 (Chih et al. 2011). This paper identified a complex of nine proteins at the transition zone, including TMEM231, B9D1, and CC2D2A, that forms a diffusion barrier essential for normal cilia function. While the paper studied the broader complex (and TMEM67 is part of the MKS module), TMEM67 transition zone localization is well established by other evidence (IDA in PMID:26595381, IBA from GO_REF:0000033). Reason: The transition zone localization of TMEM67 is a core annotation supported by multiple evidence types. This NAS from ComplexPortal is consistent with direct evidence from IDA (PMID:26595381) and IBA (GO_REF:0000033). Supporting Evidence: PMID:22179047 Disruption of the complex in vitro causes a reduction in cilia formation and a loss of signalling receptors from the remaining cilia.
GO:1904491 protein localization to ciliary transition zone	NAS PMID:22179047 A ciliopathy complex at the transition zone protects the cil...	ACCEPT	Summary: NAS annotation for protein localization to the ciliary transition zone from the ComplexPortal, citing PMID:22179047 (Chih et al. 2011). The paper showed that the MKS complex components depend on each other for transition zone localization: "The localizations of TMEM231, B9D1 and CC2D2A at the transition zone are dependent on one another." TMEM67 as a member of this complex participates in the mutual localization and recruitment of transition zone proteins. PMID:26595381 further showed that TMEM107 recruits ciliopathy proteins including MKS module members to transition zone subdomains. Reason: TMEM67 is a core component of the MKS module that participates in the recruitment and localization of proteins to the ciliary transition zone. This biological process annotation is well supported by the mutual dependence of MKS complex members for their transition zone localization. Supporting Evidence: PMID:22179047 The localizations of TMEM231, B9D1 (B9 domain-containing protein 1) and CC2D2A (coiled-coil and C2 domain-containing protein 2A) at the transition zone are dependent on one another and on Sept2. PMID:26595381 nematode TMEM-107 occupies an intermediate layer of the TZ-localized MKS module by organizing recruitment of the ciliopathy proteins MKS-1, TMEM-231 (JBTS20) and JBTS-14 (TMEM237).
GO:0035567 non-canonical Wnt signaling pathway	IMP PMID:34964473 Interpreting ciliopathy-associated missense variants of unce...	ACCEPT	Summary: IMP annotation for non-canonical Wnt signaling pathway, based on PMID:34964473 (Lange et al. 2022). This paper used C. elegans CRISPR knock-in models of TMEM67 patient variants to demonstrate functional effects on cilia-dependent phenotypes. The validation was done using a genetic complementation assay in human TMEM67 knockout hTERT-RPE1 cells that "tests a TMEM67 signalling function." The role of TMEM67 in non-canonical Wnt signaling is most extensively characterized in PMID:26035863 (Abdelhamed et al. 2015), which showed that "TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2." Reason: Non-canonical Wnt signaling is a core function of TMEM67. PMID:26035863 extensively characterized TMEM67 as a receptor in the Wnt5a-TMEM67-ROR2 signaling axis. PMID:34964473 provided additional functional validation. The structural study PMID:34731008 confirmed Wnt5a binding to the extracellular domain of TMEM67. Supporting Evidence: PMID:26035863 We propose that TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2, and normally represses Shh signalling. PMID:26035863 TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2) upon stimulation with Wnt5a-conditioned medium. PMID:34731008 Recently, it has been suggested that Meckelin can function as a receptor of β-catenin–independent signaling that binds to Wnt5a and mediates downstream signaling through receptor tyrosine kinase-like orphan receptor 2 as a coreceptor, thereby controlling basal body positioning and epithelial branching morphogenesis (12).
GO:0005515 protein binding	IPI PMID:26035863 The Meckel-Gruber syndrome protein TMEM67 controls basal bod...	MODIFY	Summary: Protein binding annotation based on PMID:26035863 (Abdelhamed et al. 2015), with WITH/FROM UniProtKB:Q01974 (ROR2). This paper demonstrated that "ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone." The interaction between TMEM67 and ROR2 is functionally significant: TMEM67 acts as a co-receptor with ROR2 in non-canonical Wnt signaling. The generic "protein binding" term does not capture this specific and important functional relationship. Reason: The interaction with ROR2 is a functionally significant co-receptor interaction in the non-canonical Wnt signaling pathway, not merely generic protein binding. A more specific term capturing receptor/co-receptor function in Wnt signaling would be more informative than generic protein binding. Proposed replacements: signaling receptor binding Supporting Evidence: PMID:26035863 ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone. PMID:26035863 TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2) upon stimulation with Wnt5a-conditioned medium.
GO:0005515 protein binding	IPI PMID:34731008 Structure of the human Meckel-Gruber protein Meckelin.	MODIFY	Summary: Protein binding annotation based on PMID:34731008 (Liu et al. 2021), with WITH/FROM UniProtKB:P41221 (WNT5A). This structural study demonstrated the cryo-EM structure of meckelin and confirmed that the extracellular CRD domain binds WNT5A. PMID:26035863 had previously shown that "the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay." This is a critical functional interaction. The generic "protein binding" term does not capture the Wnt ligand binding activity. Reason: The interaction with WNT5A represents a specific Wnt ligand binding activity central to TMEM67 function as a non-canonical Wnt receptor. A more specific molecular function term should be used. Proposed replacements: Wnt-protein binding Supporting Evidence: PMID:34731008 Recently, it has been suggested that Meckelin can function as a receptor of β-catenin–independent signaling that binds to Wnt5a and mediates downstream signaling through receptor tyrosine kinase-like orphan receptor 2 as a coreceptor, thereby controlling basal body positioning and epithelial branching morphogenesis (12). PMID:26035863 the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay.
GO:0005515 protein binding	IPI PMID:35137054 The ciliary transition zone protein TMEM218 synergistically ...	KEEP AS NON CORE	Summary: Protein binding annotation based on PMID:35137054 (Epting et al. 2022), with WITH/FROM UniProtKB:A2RU14 (TMEM218). This paper identified TMEM218 as a major component of the ciliary transition zone module and showed that "Co-immunoprecipitation assays resulted in the physical interaction of TMEM218 with the MKS module member TMEM67/Meckelin." This interaction is relevant to transition zone complex formation. Reason: The interaction with TMEM218 reflects the assembly of the MKS transition zone complex. Generic "protein binding" is uninformative, but no ideal replacement MF term exists. The interaction is already captured by the CC annotation GO:0036038 (MKS complex). Keeping as non-core since the WITH/FROM data documents the specific TMEM218 interaction partner. Supporting Evidence: PMID:35137054 Co-immunoprecipitation assays resulted in the physical interaction of TMEM218 with the MKS module member TMEM67/Meckelin that was significantly reduced by the TMEM218 missense change harboured by one of our patients.
GO:0060271 cilium assembly	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation for cilium assembly, transferred from mouse ortholog (UniProtKB:Q8BR76). This is consistent with the IBA (GO_REF:0000033) and IMP (PMID:19515853) annotations for the same term. Cilium assembly is a well-established core function of TMEM67. Reason: The ISS annotation is consistent with experimental evidence from human and model organisms. Cilium assembly is a core function of TMEM67 supported by multiple evidence types.
GO:0035869 ciliary transition zone	IDA PMID:26595381 TMEM107 recruits ciliopathy proteins to subdomains of the ci...	ACCEPT	Summary: IDA annotation for ciliary transition zone localization from PMID:26595381 (Lambacher et al. 2016). This study used super-resolution microscopy in C. elegans and mammalian cells to characterize MKS module protein localizations within transition zone subdomains. The study showed that "MKS module membrane proteins are immobile and super-resolution microscopy in worms and mammalian cells reveals periodic localizations within the TZ." This provides direct evidence for TMEM67 localization at the transition zone. Reason: Direct experimental evidence (IDA) for the core localization of TMEM67 at the ciliary transition zone. This is the strongest evidence type for this annotation and confirms the transition zone as the primary subcellular localization of TMEM67. Supporting Evidence: PMID:26595381 MKS module membrane proteins are immobile and super-resolution microscopy in worms and mammalian cells reveals periodic localizations within the TZ.
GO:0060170 ciliary membrane	TAS Reactome:R-HSA-5617816	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-5617816 (RAB3IP stimulates nucleotide exchange on RAB8A). TMEM67 is placed at the ciliary membrane in the context of cilium assembly pathways. TMEM67 is a transmembrane protein that spans the ciliary membrane at the transition zone. This annotation is correct but less specific than transition zone. Reason: Ciliary membrane is a valid localization for TMEM67 as a transmembrane protein that spans the ciliary membrane at the transition zone. The Reactome pathway context is appropriate. While the transition zone is more specific, the ciliary membrane annotation is not wrong. Supporting Evidence: PMID:17185389 meckelin localized both to the primary cilium and to the plasma membrane in ciliated cell-lines and primary cells.
GO:0060170 ciliary membrane	TAS Reactome:R-HSA-5626681	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-5626681 (Recruitment of transition zone proteins). TMEM67 placed at the ciliary membrane in the context of transition zone protein recruitment. This is a duplicate of the same GO term with a different Reactome source. Reason: Same as other ciliary membrane annotations. This Reactome pathway context (transition zone protein recruitment) is particularly relevant for TMEM67 as a core transition zone component.
GO:0060170 ciliary membrane	TAS Reactome:R-HSA-5638009	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-5638009 (CEP164 recruits RAB3IP-carrying Golgi-derived vesicles to the basal body). TMEM67 placed at the ciliary membrane in the context of vesicle recruitment to the basal body. This is a third Reactome pathway source for the same GO term. Reason: Same as other ciliary membrane annotations. The annotation is correct as TMEM67 is a transmembrane protein at the ciliary membrane.
GO:0031005 filamin binding	IPI PMID:22121117 A meckelin-filamin A interaction mediates ciliogenesis.	ACCEPT	Summary: IPI annotation for filamin binding, based on PMID:22121117 (Adams et al. 2012) with WITH/FROM UniProtKB:P21333 (FLNA, filamin A). This paper demonstrated that "the cytoplasmic domain of meckelin directly interacts with the actin-binding protein filamin A" and that this interaction mediates ciliogenesis. An in-frame deletion mutation in the meckelin C-terminus "abrogate[d] the meckelin-filamin A interaction." The study showed that "loss of filamin A by siRNA knockdown, in patient cells, and in tissues from Flna null mouse embryos results in cellular phenotypes identical to those caused by meckelin loss, namely basal body positioning and ciliogenesis defects." This is a specific and well-characterized molecular function. Reason: Filamin binding is a well-characterized molecular function of TMEM67 that is directly relevant to its role in ciliogenesis and basal body positioning. Unlike generic "protein binding," this term is specific and informative. The interaction is direct and functionally significant. Supporting Evidence: PMID:22121117 the cytoplasmic domain of meckelin directly interacts with the actin-binding protein filamin A, potentially at the apical cell surface associated with the basal body. PMID:22121117 loss of filamin A by siRNA knockdown, in patient cells, and in tissues from Flna(Dilp2) null mouse embryos results in cellular phenotypes identical to those caused by meckelin loss, namely basal body positioning and ciliogenesis defects.
GO:0036038 MKS complex	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation for MKS complex membership, transferred from mouse ortholog (UniProtKB:Q8BR76). TMEM67 is a well-established component of the MKS complex (tectonic-like/B9 complex) at the transition zone. This is consistent with the IEA annotation from InterPro and supported by multiple publications (PMID:22179047, PMID:26035863, PMID:34731008). Reason: MKS complex membership is a core annotation for TMEM67. The ISS transfer from mouse is well supported by human experimental data and consistent with the IEA from InterPro. Supporting Evidence: PMID:26035863 TMEM67 is a component of the MKS-JBTS module at the transition zone.
GO:0005515 protein binding	IPI PMID:17185389 The Meckel-Gruber Syndrome proteins MKS1 and meckelin intera...	KEEP AS NON CORE	Summary: Protein binding annotation based on PMID:17185389 (Dawe et al. 2007) with WITH/FROM UniProtKB:Q9NXB0 (MKS1). The paper demonstrated by co-immunoprecipitation that "wild-type meckelin and MKS1 interact." This interaction between TMEM67 and MKS1 is relevant to the MKS complex at the transition zone. The generic "protein binding" term is uninformative. Reason: The interaction with MKS1 reflects MKS transition zone complex formation. Generic protein binding does not capture this specific relationship. The interaction is already represented by the MKS complex annotation (GO:0036038). No better MF term is available, so this is kept as non-core since the WITH/FROM data documents the specific MKS1 interaction partner. Supporting Evidence: PMID:17185389 Co-immunoprecipitation experiments show that wild-type meckelin and MKS1 interact and, in three-dimensional tissue culture assays, epithelial branching morphogenesis was severely impaired.
GO:0005515 protein binding	IPI PMID:19815549 Meckel-Gruber syndrome protein MKS3 is required for endoplas...	KEEP AS NON CORE	Summary: Protein binding annotation based on PMID:19815549 (Wang et al. 2009). The GOA file shows three separate protein binding entries for this PMID with different WITH/FROM fields: UniProtKB:P08582, UniProtKB:Q8IXB1 (DNAJC10/ERdj5), and UniProtKB:Q9UBS3 (DNAJB9/ERdj4). This YAML entry represents the interactions of TMEM67 with ERAD-associated proteins. The paper showed that "The ER lumenal domain of MKS3 interacted with a complex that included mutant SP-C and associated chaperones, whereas the region predicted to encode the transmembrane domains of MKS3 interacted with cytosolic p97." These interactions reflect TMEM67 adaptor function in ERAD rather than a generic protein binding activity. Reason: The interactions with ERAD components (DNAJB9, DNAJC10, and related proteins) document TMEM67 participation in ERAD as an adaptor. While "protein binding" is uninformative, the WITH/FROM data provide useful documentation of the ERAD interaction partners. This is a non-core function of TMEM67 (ERAD adaptor) compared to its primary role at the ciliary transition zone. The ERAD pathway biological process annotation (GO:0036503) better captures this role. Supporting Evidence: PMID:19815549 The ER lumenal domain of MKS3 interacted with a complex that included mutant SP-C and associated chaperones, whereas the region predicted to encode the transmembrane domains of MKS3 interacted with cytosolic p97.
GO:0005789 endoplasmic reticulum membrane	IDA PMID:19815549 Meckel-Gruber syndrome protein MKS3 is required for endoplas...	KEEP AS NON CORE	Summary: IDA annotation for ER membrane localization from PMID:19815549 (Wang et al. 2009). The paper identified "MKS3 was identified as a membrane glycoprotein predominantly localized to the ER." Additionally, "Expression of MKS3 was up-regulated by genetic or pharmacological inducers of ER stress." This represents a secondary localization relevant to the ERAD function of TMEM67. Reason: The ER membrane localization is experimentally demonstrated (IDA) and relevant to the ERAD adaptor function of TMEM67. However, the primary localization of TMEM67 is the ciliary transition zone. The ER localization may reflect a fraction of the protein pool involved in ERAD. This is a valid but non-core localization. Supporting Evidence: PMID:19815549 MKS3 was identified as a membrane glycoprotein predominantly localized to the ER. PMID:19815549 Expression of MKS3 was up-regulated by genetic or pharmacological inducers of ER stress.
GO:0005813 centrosome	IDA PMID:17185389 The Meckel-Gruber Syndrome proteins MKS1 and meckelin intera...	ACCEPT	Summary: IDA annotation for centrosome localization from PMID:17185389 (Dawe et al. 2007). The UniProt record lists "Cytoplasm, cytoskeleton, cilium basal body" as a subcellular location. The paper described MKS1 localization to basal bodies and meckelin localization to the cilium and plasma membrane. The centrosome/basal body localization is relevant to TMEM67 role in centrosome migration to the apical cell surface during ciliogenesis. PMID:22121117 also confirmed basal body localization. Reason: Centrosome/basal body localization is relevant to the core function of TMEM67 in centriole migration to the apical membrane during ciliogenesis. The basal body is a modified centrosome, and TMEM67 localization there is consistent with its role in ciliogenesis. Supporting Evidence: PMID:17185389 siRNA-mediated reduction of Mks1 and Mks3 expression in a ciliated epithelial cell-line blocked centriole migration to the apical membrane and consequent formation of the primary cilium. PMID:22121117 the cytoplasmic domain of meckelin directly interacts with the actin-binding protein filamin A, potentially at the apical cell surface associated with the basal body.
GO:0010826 negative regulation of centrosome duplication	IMP PMID:19515853 Ciliary and centrosomal defects associated with mutation and...	ACCEPT	Summary: IMP annotation for negative regulation of centrosome duplication from PMID:19515853 (Tammachote et al. 2009). The paper showed that in wpk (Mks3 mutant) rat renal collecting duct cysts, there was "additional evidence of cells with multiple primary cilia and centrosome over-duplication." Stable shRNA knockdown of Mks3 "induced multi-ciliated and multi-centrosomal phenotypes." The paper concluded that "MKS1 and MKS3 functions are required for ciliary structure and function, including a role in regulating length and appropriate number through modulating centrosome duplication." Reason: The negative regulation of centrosome duplication is well supported by the mutant phenotype data in PMID:19515853, showing centrosome over-duplication in Mks3 mutant and knockdown cells. This is a specific and informative biological process annotation directly relevant to TMEM67 function in ciliogenesis. Supporting Evidence: PMID:19515853 In wpk renal collecting duct cysts, cilia were generally longer than normal, with additional evidence of cells with multiple primary cilia and centrosome over-duplication. PMID:19515853 Stable shRNA knockdown of Mks1 and Mks3 in IMCD3 cells induced multi-ciliated and multi-centrosomal phenotypes. PMID:19515853 MKS1 and MKS3 functions are required for ciliary structure and function, including a role in regulating length and appropriate number through modulating centrosome duplication.
GO:0030659 cytoplasmic vesicle membrane	IDA PMID:19815549 Meckel-Gruber syndrome protein MKS3 is required for endoplas...	KEEP AS NON CORE	Summary: IDA annotation for cytoplasmic vesicle membrane localization from PMID:19815549 (Wang et al. 2009). The paper studied TMEM67 in the context of ERAD and identified it as an ER membrane glycoprotein. The cytoplasmic vesicle membrane localization may reflect ER-derived vesicular structures or experimental observation of TMEM67 in vesicular compartments. This is a minor, secondary localization. Reason: This is a secondary localization observed in the context of the ERAD study. While the IDA evidence supports this localization, it is not a primary or core localization for TMEM67. The main localizations are the ciliary transition zone and ER membrane. Supporting Evidence: PMID:19815549 MKS3 was identified as a membrane glycoprotein predominantly localized to the ER.
GO:0036503 ERAD pathway	IMP PMID:19815549 Meckel-Gruber syndrome protein MKS3 is required for endoplas...	KEEP AS NON CORE	Summary: IMP annotation for ERAD pathway involvement from PMID:19815549 (Wang et al. 2009). The paper demonstrated that "Microarray screens for genes involved in SP-C ER-associated degradation identified MKS3/TMEM67." Further, "knockdown of MKS3 also inhibited degradation of mutant SP-C" and "Deletion of the transmembrane and cytosolic domains abrogated interaction of MKS3 with p97 and resulted in accumulation of mutant SP-C proprotein." TMEM67 functions as an adaptor linking the ER lumenal quality control machinery with the cytosolic degradation apparatus (p97/VCP). Reason: The ERAD pathway involvement is well supported by experimental evidence showing that TMEM67 loss inhibits degradation of misfolded surfactant protein C. However, this is a secondary, non-core function of TMEM67. Its primary roles are at the ciliary transition zone in ciliogenesis and non-canonical Wnt signaling. The ERAD role appears to be specific to misfolded SP-C processing and may not represent a general function. Supporting Evidence: PMID:19815549 Microarray screens for genes involved in SP-C ER-associated degradation identified MKS3/TMEM67, a locus previously linked to the ciliopathy Meckel-Gruber syndrome. PMID:19815549 knockdown of MKS3 also inhibited degradation of mutant SP-C. PMID:19815549 These results support a model in which MKS3 links the ER lumenal quality control machinery with the cytosolic degradation apparatus.
GO:0051082 unfolded protein binding	IPI PMID:19815549 Meckel-Gruber syndrome protein MKS3 is required for endoplas...	MARK AS OVER ANNOTATED	Summary: This annotation to GO:0051082 (unfolded protein binding) is based on PMID:19815549 (Wang et al. 2009), which studied the role of MKS3/TMEM67 in ERAD of misfolded surfactant protein C (SP-C). The WITH/FROM field indicates UniProtKB:P11686 (SFTPC). The paper demonstrated that the ER lumenal domain of MKS3 interacted with a complex that included mutant SP-C and associated chaperones (ERdj4/DNAJB9 and ERdj5/DNAJC10), and that the transmembrane domains of MKS3 interacted with cytosolic p97. However, MKS3 is not a chaperone. The authors concluded that MKS3 functions as an adaptor that links the ER lumenal quality control machinery with the cytosolic degradation apparatus, rather than directly binding unfolded protein in a chaperone-like manner. The interaction with misfolded SP-C appears to be indirect, mediated through association with the chaperone complex. TMEM67 is a multi-pass transmembrane protein of the ciliary transition zone with no known chaperone domains. The term GO:0051082 is now formally obsolete (go-ontology issue 30962) because it conflates passive binding with active chaperone functions. This annotation represents an over-annotation where an adaptor role in ERAD was inappropriately classified as unfolded protein binding. Reason: TMEM67/MKS3 is not a chaperone and does not possess intrinsic unfolded protein binding activity. The evidence in PMID:19815549 shows that MKS3 interacts with a complex containing misfolded SP-C and bona fide ER chaperones, but functions as an adaptor linking the ER lumenal quality control machinery with the cytosolic degradation apparatus (p97), not as a chaperone itself. The annotation to GO:0036503 (ERAD pathway) already appropriately captures the biological process role. The molecular function of TMEM67 in this context is better described as an adaptor or scaffold linking chaperone-substrate complexes to the retrotranslocation machinery, not as direct unfolded protein binding. Furthermore, GO:0051082 is now formally obsolete (go-ontology issue 30962) as it conflates passive binding with active chaperone activity. Supporting Evidence: PMID:19815549 These results support a model in which MKS3 links the ER lumenal quality control machinery with the cytosolic degradation apparatus. PMID:19815549 The ER lumenal domain of MKS3 interacted with a complex that included mutant SP-C and associated chaperones, whereas the region predicted to encode the transmembrane domains of MKS3 interacted with cytosolic p97. PMID:19815549 Deletion of the transmembrane and cytosolic domains abrogated interaction of MKS3 with p97 and resulted in accumulation of mutant SP-C proprotein; knockdown of MKS3 also inhibited degradation of mutant SP-C. PMID:19815549 Microarray screens for genes involved in SP-C ER-associated degradation identified MKS3/TMEM67, a locus previously linked to the ciliopathy Meckel-Gruber syndrome.
GO:0060170 ciliary membrane	IDA PMID:17185389 The Meckel-Gruber Syndrome proteins MKS1 and meckelin intera...	ACCEPT	Summary: IDA annotation for ciliary membrane localization from PMID:17185389 (Dawe et al. 2007). The paper demonstrated that "meckelin localized both to the primary cilium and to the plasma membrane in ciliated cell-lines and primary cells." As a multi-pass transmembrane protein, TMEM67 is embedded in the ciliary membrane at the transition zone region. Reason: Ciliary membrane localization is directly demonstrated by immunofluorescence in PMID:17185389. TMEM67 is a transmembrane protein spanning the ciliary membrane at the transition zone. This is consistent with the transition zone localization and represents a core subcellular localization. Supporting Evidence: PMID:17185389 meckelin localized both to the primary cilium and to the plasma membrane in ciliated cell-lines and primary cells.
GO:0060271 cilium assembly	IMP PMID:19515853 Ciliary and centrosomal defects associated with mutation and...	ACCEPT	Summary: IMP annotation for cilium assembly from PMID:19515853 (Tammachote et al. 2009). The paper showed functional defects in the connecting cilium in the eye of wpk (Mks3 mutant) rats, "lack of formation of the outer segment," and "spermatids with very short flagella." Stable shRNA knockdown of Mks3 "induced multi-ciliated and multi-centrosomal phenotypes." The paper concluded that "MKS1 and MKS3 functions are required for ciliary structure and function." Reason: This IMP annotation provides direct experimental evidence from mutant phenotype analysis supporting the core role of TMEM67 in cilium assembly. The data complement the earlier knockdown studies in PMID:17185389 and the IBA annotation. Supporting Evidence: PMID:19515853 Analysis of the wpk rat model of MKS3 revealed functional defects of the connecting cilium in the eye that resulted in lack of formation of the outer segment, whereas infertile wpk males developed spermatids with very short flagella that did not extend beyond the cell body. PMID:19515853 MKS1 and MKS3 functions are required for ciliary structure and function, including a role in regulating length and appropriate number through modulating centrosome duplication.
GO:0017147 Wnt-protein binding	IPI PMID:26035863 The Meckel-Gruber syndrome protein TMEM67 controls basal bod...	NEW	Summary: NEW annotation. PMID:26035863 demonstrated that the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. PMID:34731008 confirmed this interaction structurally. The existing protein binding annotations with WNT5A (PMID:34731008) and ROR2 (PMID:26035863) should be replaced by this more specific term. Reason: TMEM67 directly binds WNT5A via its extracellular cysteine-rich domain, a core molecular function for this protein. The Wnt-protein binding term is significantly more informative than generic protein binding and captures a key functional attribute of TMEM67 as a non-canonical Wnt receptor. Supporting Evidence: PMID:26035863 the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. PMID:34731008 Recently, it has been suggested that Meckelin can function as a receptor of β-catenin–independent signaling that binds to Wnt5a and mediates downstream signaling through receptor tyrosine kinase-like orphan receptor 2 as a coreceptor, thereby controlling basal body positioning and epithelial branching morphogenesis (12).

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