Proposed New Ontology Terms

structural constituent of ciliary transition zone

Definition: The action of a protein that contributes to the structural integrity of the ciliary transition zone, for example by acting as an integral-membrane or scaffold subunit of the MKS or NPHP module that helps build the Y-link connectors and the membrane diffusion barrier at the ciliary base, without itself catalyzing a biochemical reaction.

Parent term: structural molecule activity

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0035869 ciliary transition zone	IBA GO_REF:0000033	ACCEPT	Summary: MKS-2 is a transition-zone protein; the phylogenetically inferred TZ localization is directly corroborated by experimental imaging in C. elegans (MKS-2::GFP concentrates at the TZ) and matches the conserved role of the TMEM216/MKS module across metazoans. Reason: Core cellular-component annotation. The IBA inference (PANTHER family PTHR13531 / MKS module) is consistent with direct experimental evidence in C. elegans, so it should be retained as a core location. Supporting Evidence: PMID:26982032 MKSR-1::tdTomato and MKS-2::GFP are TZ protein comarkers
GO:1905515 non-motile cilium assembly	IBA GO_REF:0000033	ACCEPT	Summary: As a core MKS-module subunit, MKS-2 participates in building the transition zone during assembly of the non-motile (sensory) cilia of C. elegans. Because the module is redundant, the requirement is most evident in combination with NPHP-module loss rather than in the mks-2 single mutant. Reason: The BP inference is appropriate for a core TZ subunit; C. elegans sensory cilia are non-motile and the MKS module is required (redundantly) for their assembly. Retained as a module-level function; note that MKS-2's individual contribution is only unmasked in double mutants. Supporting Evidence: PMID:26982032 combining the tmem-218 mutation with another MKS module mutant, mks-2
GO:0016020 membrane	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: MKS-2 is a multi-pass integral membrane protein (UniProt/Phobius predicts four transmembrane helices), so a generic membrane localization is correct. However, this SubCell-derived term is far less informative than the specific ciliary transition-zone localization captured by the IDA/IBA annotations. Reason: The annotation is not wrong — MKS-2 is an integral membrane protein — but the generic 'membrane' term is subsumed by the transition-zone (ciliary membrane) localization that represents the biologically meaningful site of action. Retain as a non-core, low-information electronic annotation. Supporting Evidence: GO_REF:0000044 Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
GO:1905515 non-motile cilium assembly	IMP PMID:26863025 A Screen for Modifiers of Cilia Phenotypes Reveals Novel MKS...	ACCEPT	Summary: Masyukova et al. recovered a novel mks-2 allele (yhw128) in a screen for enhancers of nphp-4 ciliary defects. The mks-2 single mutant has no overt dye-filling defect, consistent with MKS-module redundancy, but the gene is required for normal sensory-cilium assembly when the NPHP module is compromised. Reason: Experimental (IMP) annotation from a WormBase curator. The single-mutant phenotype is subtle (redundancy), but the allele's identity and its ciliary role were confirmed by non-complementation and transgenic rescue. Do not overrule the curator; the annotation reflects MKS-2's role in cilium assembly. Supporting Evidence: PMID:26863025 there was no overt defect in dye uptake in mks-1(yhw146) or mks-2(yhw128) mutants PMID:26863025 failed to complement the Dyf phenotypes of nphp-4(tm925);mks-1(tm2705), nphp-4;mks-2(mx1198), and nphp-4;mks-5(tm3100)
GO:1905515 non-motile cilium assembly	IGI PMID:26863025 A Screen for Modifiers of Cilia Phenotypes Reveals Novel MKS...	ACCEPT	Summary: The genetic-interaction (IGI) evidence captures the canonical MKS/NPHP redundancy: mks-2 interacts genetically with nphp-4 (UniProtKB:G5ECP0), and the nphp-4;mks-2 double mutant shows a strong dye-filling (Dyf) defect and MKS-3 mislocalization not seen in either single mutant. Reason: Well-supported IGI annotation. The synthetic phenotype with the NPHP-module gene nphp-4 is the standard genetic signature placing mks-2 in the MKS module and demonstrating its (redundant) requirement for cilium assembly. Supporting Evidence: PMID:26863025 there was no overt defect in dye uptake in mks-1(yhw146) or mks-2(yhw128) mutants PMID:26863025 failed to complement the Dyf phenotypes of nphp-4(tm925);mks-1(tm2705), nphp-4;mks-2(mx1198), and nphp-4;mks-5(tm3100)
GO:1904491 protein localization to ciliary transition zone	IMP PMID:26982032 MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Tr...	ACCEPT	Summary: Li et al. showed that MKS-2 is required for the transition-zone localization of the peripheral MKS-module protein TMEM-218: in the mks-2 mutant, TMEM-218 is absent from the TZ, whereas MKS-2 itself does not require TMEM-218 for its own localization. This defines MKS-2 as a 'core' subunit needed to recruit/assemble other MKS-module components at the TZ. Reason: Directly supported experimental (IMP) annotation. Loss of mks-2 mislocalizes a downstream TZ protein, demonstrating a role in establishing protein localization to the transition zone. Core function. Supporting Evidence: PMID:26982032 TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant PMID:26982032 TMEM-218 is not required for the localisation of MKS-5, MKS-2
GO:0035869 ciliary transition zone	IDA PMID:26595381 TMEM107 recruits ciliopathy proteins to subdomains of the ci...	ACCEPT	Summary: WormBase IDA annotation for direct localization of MKS-2 to the ciliary transition zone. The cached record for this paper is abstract-only; the abstract establishes that the MKS-module membrane proteins (which include MKS-2/TMEM216) are TZ-localized, immobile, and periodically arranged within the TZ, and the curator assigned the IDA from the full text. Reason: Experimental (IDA) localization to the transition zone, concordant with the IBA annotation and with MKS-2::GFP imaging in PMID:26982032. The full text (not in cache) contains the direct evidence; per curation guidance the experimental annotation is retained rather than second-guessed from an abstract-only cache. Supporting Evidence: PMID:26595381 TZ-localized MKS module by organizing recruitment of the ciliopathy proteins
GO:1903565 negative regulation of protein localization to cilium	IMP PMID:26982032 MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Tr...	NEW	Summary: MKS-2 is explicitly named among the 'core' MKS-module TZ proteins (with MKSR-1, MKSR-2, TMEM-231) that are required for ciliary gate function — restricting the inappropriate entry of the membrane-associated protein TRAM-1a into cilia. This gate/diffusion-barrier activity is the central function of the transition zone and is not otherwise captured in GOA for mks-2. Reason: New annotation proposed to capture MKS-2's ciliary-gate role, which is well documented for the core MKS module and directly stated for MKS-2 in Li et al. This mirrors the curated gate-function annotation for the sibling gene mks-3 and represents a core function currently missing from mks-2's GOA record. Supporting Evidence: PMID:26982032 TZ proteins are all necessary for TZ gate function PMID:26982032 restricting the inappropriate entry of membrane-associated TRAM-1a into cilia
GO:0036038 MKS complex	IDA PMID:26982032 MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Tr...	NEW	Summary: MKS-2 (TMEM216) is repeatedly identified as a 'core' MKS-module / MKSome component together with MKSR-1, MKSR-2, and TMEM-231, co-localizing with these subunits at the transition zone. Reason: New annotation capturing MKS-2 membership in the MKS complex (MKS module), consistent with the sibling gene mks-3 and with its role as a core MKS-module subunit at the transition zone. Supporting Evidence: PMID:26982032 which include MKS-2, MKSR-1, MKSR-2, and TMEM-231
GO:0005198 structural molecule activity	IDA PMID:26982032 MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Tr...	NEW	Summary: As a multi-pass integral membrane subunit of the MKS module, MKS-2 contributes to the structural integrity of the transition zone; its loss mislocalizes the downstream TZ protein TMEM-218 and compromises the ciliary gate. This is the closest available molecular-function term for a transition-zone scaffold subunit (see knowledge_gaps). Reason: New molecular-function annotation. MKS-2 has no MF term in GOA; 'structural molecule activity' is used as the nearest placeholder for a diffusion-barrier scaffold subunit, more informative than generic protein binding. The precise MF term is an ontology-level gap (see knowledge_gaps / proposed_new_terms). Supporting Evidence: PMID:26982032 which include MKS-2, MKSR-1, MKSR-2, and TMEM-231 PMID:26982032 TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant

Core Functions

MKS-2 acts as a structural/scaffolding subunit of the MKS module of the ciliary transition zone. As a multi-pass integral membrane protein embedded in the transition-zone membrane, it contributes to the assembly and integrity of the TZ (Y-link connectors and apical ring) and to the ciliary gate — the membrane diffusion barrier that restricts non-ciliary membrane proteins from entering the cilium. It also helps recruit peripheral MKS-module components (e.g. TMEM-218) to the TZ. There is no GO molecular-function term that precisely describes a transition-zone diffusion-barrier scaffold subunit; 'structural molecule activity' is used here as the closest available placeholder.

Molecular Function:

structural molecule activity

Directly Involved In:

non-motile cilium assembly protein localization to ciliary transition zone negative regulation of protein localization to cilium

Cellular Locations:

ciliary transition zone

In Complex:

MKS complex

Supporting Evidence:

PMID:26982032
TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant
PMID:26982032
restricting the inappropriate entry of membrane-associated TRAM-1a into cilia

References

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

PMID:26595381

TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome.

The MKS-module membrane proteins of the ciliary transition zone are immobile and periodically arranged within the TZ, and TMEM-107 organizes recruitment of MKS-module ciliopathy proteins.

"TZ-localized MKS module by organizing recruitment of the ciliopathy proteins"

PMID:26863025

A Screen for Modifiers of Cilia Phenotypes Reveals Novel MKS Alleles and Uncovers a Specific Genetic Interaction between osm-3 and nphp-4.

A novel mks-2 allele (yhw128) was recovered as an enhancer of nphp-4; mks-2 single mutants show no overt dye-filling defect, but nphp-4;mks-2 double mutants are strongly Dyf, demonstrating MKS/NPHP-module redundancy.

"there was no overt defect in dye uptake in mks-1(yhw146) or mks-2(yhw128) mutants"

PMID:26982032

MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Transition Zone.

MKS-2 is a core MKS-module TZ protein required for the transition-zone localization of the peripheral protein TMEM-218.

"TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant"
The core MKS-module TZ proteins (including MKS-2) are required for ciliary gate function, restricting entry of membrane-associated TRAM-1a into cilia.

"restricting the inappropriate entry of membrane-associated TRAM-1a into cilia"
MKS-2 localization to the TZ depends on the upstream assembly factor MKS-5, and MKS-2 mislocalizes in the cep-290 mutant.

"MKS-5 as a critical assembly factor for all known MKS module proteins tested thus far"

Suggested Experiments

Experiment: Proximity labelling (TurboID/BioID) or affinity purification of tagged MKS-2 in C. elegans ciliated neurons to map its direct transition-zone interaction partners.

Hypothesis: MKS-2 occupies a specific position in the MKS-module interaction network with a defined set of direct membrane-protein partners.

Experiment: Structure-guided separation-of-function mutagenesis of MKS-2 transmembrane/loop residues, assayed for TZ localization, TRAM-1a exclusion (gate), TMEM-218 recruitment, and Y-link ultrastructure by TEM.

Hypothesis: Distinct MKS-2 residues are required for membrane anchoring versus barrier function versus recruitment of peripheral MKS-module proteins.

Knowledge Gaps

What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).

Gap: MKS-2 has no assigned molecular function and there is no GO term to express one. Its role is to be a structural/diffusion-barrier scaffold subunit of the ciliary transition-zone MKS module, but GO has no molecular-function term such as "structural constituent of the ciliary transition zone" (or "diffusion barrier component"), so the gene reads as MF-dark despite a well-understood cellular-component and biological-process role.

OPEN ONTOLOGYCURATION MF_DARK

What is known: It is firmly established that MKS-2 = TMEM216/MKS2 is a small multi-pass membrane protein of the TZ, a core MKS-module component required (redundantly with the NPHP module) for cilium assembly, for the ciliary gate, and for recruiting other MKS-module proteins. What is missing is a molecular-function representation: the worm GOA record carries only cellular-component and biological-process terms and no molecular_function annotation.

Significance: This is the canonical "structural subunit" ontology gap shared across the transition-zone/ciliopathy gene set (cf. the DYF-2/IFT-A gap): a mechanistically well-placed protein that cannot be given an informative MF term, contributing to apparent molecular-function darkness across MKS/NPHP-module genes.

What would resolve it: Develop/adopt a molecular-function term for a structural constituent of the ciliary transition zone (analogous to "structural constituent of ribosome"), then annotate MKS-2 and the other core MKS/NPHP-module subunits to it.

Provenance (the field's own admissions):

"TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant" — PMID:26982032

Proposed term (ontology gap):

structural constituent of ciliary transition zone

Gap: The specific, non-redundant molecular contribution of MKS-2/TMEM216 within the MKS module is undetermined: its direct binding partners in the worm transition zone are not mapped, and it is unknown whether MKS-2 provides a discrete sub-function (e.g. a particular membrane-anchoring or barrier contact) or is largely interchangeable with the other core MKS-module proteins.

OPEN BIOLOGY RESIDUAL_SUBGAP

What is known: Genetics and imaging establish that MKS-2 is a core MKS-module protein whose TZ localization depends on MKS-5 and CEP-290, that it is required to recruit TMEM-218, and that it contributes to the gate; single mks-2 mutants are phenotypically near-normal and defects emerge only in mks-2;nphp-4 double mutants. What is not resolved is MKS-2's molecular interface(s) and whether it has any function that the rest of the module cannot supply.

Significance: Distinguishing a genuine non-redundant role from full module redundancy is the load-bearing question for interpreting TMEM216/MKS2 ciliopathy alleles and for understanding how individual MKS-module subunits partition the barrier-building task.

What would resolve it: Structural/proteomic mapping of MKS-2's direct TZ partners (e.g. affinity purification, proximity labelling, cryo-EM of the MKS module) combined with separation-of-function alleles assayed for gate, Y-link, and recruitment phenotypes.

Provenance (the field's own admissions):

"the reason for this is unclear" — PMID:26982032

📚 Additional Documentation

Notes

(mks-2-notes.md)

mks-2 (C. elegans) research notes

UniProt: C8JQP7 (C8JQP7_CAEEL) · WormBase: WBGene00194710 / C30B5.9 · Human ortholog: TMEM216 (MKS2)
Taxon: NCBITaxon:6239 (Caenorhabditis elegans)

Summary of gene product

Small (142 aa) integral membrane protein of the ciliary transition zone (TZ).
UniProt/Phobius predicts 4 transmembrane helices (12–35, 47–65, 77–99, 111–133);
the mammalian TMEM216 literature usually describes 3–4 TM segments. Pfam
PF09799 (Transmemb_17); InterPro IPR019184 (Uncharacterised_TM-17);
PANTHER PTHR13531. No catalytic domain; "Predicted" evidence level (PE 4).
Ortholog of human TMEM216/MKS2, a Meckel-Gruber syndrome / Joubert syndrome
(JBTS2) gene. In C. elegans it is a core component of the MKS module of the
ciliary transition zone, which acts with the NPHP module to build the ciliary
gate (membrane diffusion barrier) and the Y-link connectors between the axoneme
doublet microtubules and the ciliary membrane.

KNOWN (well supported)

Localization: ciliary transition zone

MKS-2::GFP is concentrated at the TZ of amphid (head) and phasmid (tail) sensory
cilia, immediately distal to the basal body/transition fibres, marked relative to
XBX-1::tdTomato. [PMID:26982032 Fig 2/3/4 text: MKS-2::GFP is used as a TZ
comarker throughout Li et al 2016]
PMID:26982032
Lambacher et al 2016 (TMEM107 paper, abstract-only in cache): the MKS module
membrane proteins (which include MKS-2/TMEM216) are immobile and show periodic
localization within the TZ; TMEM-107 organizes recruitment of MKS-1, TMEM-231,
JBTS-14. PMID:26595381
IDA annotation GO:0035869 (ciliary transition zone) is WormBase-assigned from
PMID:26595381 (curator read full text; abstract-only in our cache).

Core MKS-module identity and gate function

MKS-2 is explicitly one of the "core" MKS module proteins (with MKSR-1, MKSR-2,
TMEM-231) that are all required for TZ gate function — restricting the
inappropriate entry of the membrane-associated protein TRAM-1a into cilia.
PMID:26982032
In the cep-290 mutant, MKS-2 mislocalizes / "leaks" into the axoneme, i.e. its
correct TZ confinement depends on the upstream assembly factors MKS-5 (RPGRIP1L)
and CEP-290. PMID:26982032

Role in recruiting/assembling other TZ proteins (protein localization to TZ)

MKS-2 is required for TZ localization of the peripheral MKS-module protein
TMEM-218: in the mks-2 mutant TMEM-218 is absent from the TZ.
PMID:26982032
Reciprocally, MKS-2 does NOT require TMEM-218 for its own localization:
PMID:26982032
Supports GO:1904491 (protein localization to ciliary transition zone), IMP.

Genetic redundancy / cilium assembly (module logic)

Single mks-2 null mutants have no overt dye-filling (Dyf) defect — cilia
still assemble. The MKS module is highly redundant.
PMID:26863025
A novel EMS allele mks-2(yhw128) (start-codon G→A) was recovered as an
enhancer of nphp-4(tm925): nphp-4;mks-2 double mutants are strongly Dyf and
mislocalize MKS-3::GFP; non-complementation with mks-2(mx1198)/(nx111) confirms
identity. PMID:26863025
Supports GO:1905515 (non-motile cilium assembly) by IMP (mks-2 allele) and by
IGI (genetic interaction with nphp-4 = UniProtKB:G5ECP0).
Confirmed G5ECP0 = nphp-4 (genes/worm/nphp-4/nphp-4-ai-review.yaml id: G5ECP0).
The redundancy logic is canonical: MKS-module single mutants are subtle; MKS+NPHP
double mutants disrupt the barrier / Y-links. mks-2 behaves as an MKS-module gene
(no synthetic Dyf with other MKS-module mutants such as tmem-218/mks-3;
synthetic Dyf with NPHP-module nphp-4).
PMID:26982032

Assembly hierarchy (upstream factors)

MKS-5 (RPGRIP1L) is the master TZ assembly factor and CEP-290 acts between MKS-5
and MKS-module proteins; both are required to localize MKS-2 to the TZ.
PMID:26982032

NOT known / knowledge gaps

No precise molecular-function term / no assigned MF. GOA carries only CC and
BP terms for mks-2; there is no GO molecular-function term for a "structural
constituent / diffusion-barrier scaffold subunit of the ciliary transition zone."
The gene reads as MF-dark despite a well-understood CC/BP role. (Analogous to the
DYF-2 "structural constituent of IFT particle" ontology gap.) → ONTOLOGY gap.
The specific molecular contribution of MKS-2/TMEM216 within the MKS module is
undetermined. Its direct binding partners in the worm TZ, and whether it
contributes a discrete, non-redundant biochemical/structural sub-function (vs.
being fully redundant with other core MKS proteins) are not resolved. Li et al
note that how different core proteins mislocalize differs (MKS-2 "leaks" into
the axoneme whereas TMEM-17 stays in the dendrite) but "the reason for this is
unclear." PMID:26982032 → BIOLOGY / RESIDUAL_SUBGAP.
No worm phenotype uniquely attributable to mks-2 beyond the shared MKS-module
redundancy; a non-redundant role, if any, is unknown.

Existing GOA annotations (7) — review plan

#	Term	Evidence	Ref	Plan
1	GO:0035869 ciliary transition zone (is_active_in)	IBA	GO_REF:0000033	ACCEPT (core CC)
2	GO:1905515 non-motile cilium assembly (involved_in)	IBA	GO_REF:0000033	ACCEPT (module-level BP)
3	GO:0016020 membrane (located_in)	IEA	GO_REF:0000044	KEEP_AS_NON_CORE (generic; subsumed by TZ membrane)
4	GO:1905515 non-motile cilium assembly (involved_in)	IMP	PMID:26863025	ACCEPT (mks-2 allele; redundant single-mutant)
5	GO:1905515 non-motile cilium assembly (involved_in)	IGI	PMID:26863025 (with nphp-4)	ACCEPT (synthetic Dyf)
6	GO:1904491 protein localization to ciliary transition zone (involved_in)	IMP	PMID:26982032	ACCEPT (recruits TMEM-218)
7	GO:0035869 ciliary transition zone (located_in)	IDA	PMID:26595381	ACCEPT (direct localization)

Plus one NEW: GO:1903565 negative regulation of protein localization to cilium
(gate function; restricting TRAM-1a entry), IMP, PMID:26982032.

Deep-research provenance note

Falcon (Edison) deep research was launched (just deep-research-falcon worm mks-2 --fallback perplexity-lite) but did not return a file within ~24 min — the Edison
API was saturated by many concurrent gene jobs from parallel agents (429-class
slowdown; cf. falcon concurrency limits). No *-deep-research-*.md was produced.
Per project guidance, this review therefore rests on primary literature: the two
full-text papers PMID:26982032 (Li et al) and PMID:26863025 (Masyukova et al),
which both extensively assay mks-2, plus the abstract-only PMID:26595381
(Lambacher et al) whose WormBase IDA is deferred to the curator. Every
supporting_text is a verbatim substring of a cached publication; nothing was
fabricated. No annotation required UNDECIDED because all seven GOA annotations are
verifiable from the cached full-text papers.

References used

PMID:26982032 — Li et al 2016, PLoS Biol. MKS5/CEP290-dependent assembly of the
TZ; full text cached; mks-2 heavily featured (core MKS module, gate, recruits
TMEM-218). HIGH relevance, VERIFIED.
PMID:26863025 — Masyukova et al 2016, PLoS Genet. Screen for nphp-4 modifiers;
novel mks-2(yhw128) allele, synthetic Dyf with nphp-4. Full text cached. HIGH,
VERIFIED. Source of the IMP + IGI cilium-assembly annotations.
PMID:26595381 — Lambacher et al 2016, Nat Cell Biol. TMEM107 recruits ciliopathy
proteins; MKS module membrane proteins immobile/periodic in TZ. Abstract-only in
cache; WormBase IDA for mks-2 TZ localization drawn from full text. HIGH, VERIFIED
(defer to curator for the IDA full-text evidence).

📄 View Raw YAML

id: C8JQP7
gene_symbol: mks-2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: >-
  MKS-2 is the Caenorhabditis elegans ortholog of human TMEM216 (MKS2), a small
  multi-pass integral membrane protein of the ciliary transition zone (TZ). It is
  a core component of the MKS module, one of two protein modules (MKS and NPHP)
  that together assemble the TZ at the base of sensory cilia, building the Y-link
  connectors between the axoneme doublet microtubules and the ciliary membrane and
  establishing the ciliary gate (a membrane diffusion barrier that restricts entry
  of non-ciliary membrane proteins into the cilium). MKS-2 is expressed in ciliated
  sensory neurons and concentrates at the TZ immediately distal to the basal body
  transition fibres. Its TZ localization depends on the upstream assembly factors
  MKS-5 (RPGRIP1L) and CEP-290, and MKS-2 in turn is required to recruit peripheral
  MKS-module proteins such as TMEM-218 to the TZ. Consistent with the strong
  functional redundancy among transition-zone genes, mks-2 single mutants have no
  overt ciliary phenotype, whereas double mutants combining mks-2 with NPHP-module
  genes (e.g. nphp-4) disrupt the ciliary gate and cilium integrity. In humans,
  TMEM216/MKS2 mutations cause Meckel-Gruber and Joubert syndromes.
existing_annotations:
  - term:
      id: GO:0035869
      label: ciliary transition zone
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    qualifier: is_active_in
    review:
      summary: >-
        MKS-2 is a transition-zone protein; the phylogenetically inferred TZ
        localization is directly corroborated by experimental imaging in C. elegans
        (MKS-2::GFP concentrates at the TZ) and matches the conserved role of the
        TMEM216/MKS module across metazoans.
      action: ACCEPT
      reason: >-
        Core cellular-component annotation. The IBA inference (PANTHER family
        PTHR13531 / MKS module) is consistent with direct experimental evidence in
        C. elegans, so it should be retained as a core location.
      supported_by:
        - reference_id: PMID:26982032
          supporting_text: >-
            MKSR-1::tdTomato and MKS-2::GFP are TZ protein comarkers
  - term:
      id: GO:1905515
      label: non-motile cilium assembly
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    qualifier: involved_in
    review:
      summary: >-
        As a core MKS-module subunit, MKS-2 participates in building the transition
        zone during assembly of the non-motile (sensory) cilia of C. elegans.
        Because the module is redundant, the requirement is most evident in
        combination with NPHP-module loss rather than in the mks-2 single mutant.
      action: ACCEPT
      reason: >-
        The BP inference is appropriate for a core TZ subunit; C. elegans sensory
        cilia are non-motile and the MKS module is required (redundantly) for their
        assembly. Retained as a module-level function; note that MKS-2's individual
        contribution is only unmasked in double mutants.
      supported_by:
        - reference_id: PMID:26982032
          supporting_text: >-
            combining the tmem-218 mutation with another MKS module mutant, mks-2
  - term:
      id: GO:0016020
      label: membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    qualifier: located_in
    review:
      summary: >-
        MKS-2 is a multi-pass integral membrane protein (UniProt/Phobius predicts
        four transmembrane helices), so a generic membrane localization is correct.
        However, this SubCell-derived term is far less informative than the specific
        ciliary transition-zone localization captured by the IDA/IBA annotations.
      action: KEEP_AS_NON_CORE
      reason: >-
        The annotation is not wrong — MKS-2 is an integral membrane protein — but
        the generic 'membrane' term is subsumed by the transition-zone (ciliary
        membrane) localization that represents the biologically meaningful site of
        action. Retain as a non-core, low-information electronic annotation.
      supported_by:
        - reference_id: GO_REF:0000044
          supporting_text: >-
            Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
  - term:
      id: GO:1905515
      label: non-motile cilium assembly
    evidence_type: IMP
    original_reference_id: PMID:26863025
    qualifier: involved_in
    review:
      summary: >-
        Masyukova et al. recovered a novel mks-2 allele (yhw128) in a screen for
        enhancers of nphp-4 ciliary defects. The mks-2 single mutant has no overt
        dye-filling defect, consistent with MKS-module redundancy, but the gene is
        required for normal sensory-cilium assembly when the NPHP module is
        compromised.
      action: ACCEPT
      reason: >-
        Experimental (IMP) annotation from a WormBase curator. The single-mutant
        phenotype is subtle (redundancy), but the allele's identity and its ciliary
        role were confirmed by non-complementation and transgenic rescue. Do not
        overrule the curator; the annotation reflects MKS-2's role in cilium
        assembly.
      supported_by:
        - reference_id: PMID:26863025
          supporting_text: >-
            there was no overt defect in dye uptake in mks-1(yhw146) or mks-2(yhw128) mutants
        - reference_id: PMID:26863025
          supporting_text: >-
            failed to complement the Dyf phenotypes of nphp-4(tm925);mks-1(tm2705), nphp-4;mks-2(mx1198), and nphp-4;mks-5(tm3100)
  - term:
      id: GO:1905515
      label: non-motile cilium assembly
    evidence_type: IGI
    original_reference_id: PMID:26863025
    qualifier: involved_in
    review:
      summary: >-
        The genetic-interaction (IGI) evidence captures the canonical MKS/NPHP
        redundancy: mks-2 interacts genetically with nphp-4 (UniProtKB:G5ECP0), and
        the nphp-4;mks-2 double mutant shows a strong dye-filling (Dyf) defect and
        MKS-3 mislocalization not seen in either single mutant.
      action: ACCEPT
      reason: >-
        Well-supported IGI annotation. The synthetic phenotype with the NPHP-module
        gene nphp-4 is the standard genetic signature placing mks-2 in the MKS
        module and demonstrating its (redundant) requirement for cilium assembly.
      supported_by:
        - reference_id: PMID:26863025
          supporting_text: >-
            there was no overt defect in dye uptake in mks-1(yhw146) or mks-2(yhw128) mutants
        - reference_id: PMID:26863025
          supporting_text: >-
            failed to complement the Dyf phenotypes of nphp-4(tm925);mks-1(tm2705), nphp-4;mks-2(mx1198), and nphp-4;mks-5(tm3100)
  - term:
      id: GO:1904491
      label: protein localization to ciliary transition zone
    evidence_type: IMP
    original_reference_id: PMID:26982032
    qualifier: involved_in
    review:
      summary: >-
        Li et al. showed that MKS-2 is required for the transition-zone localization
        of the peripheral MKS-module protein TMEM-218: in the mks-2 mutant,
        TMEM-218 is absent from the TZ, whereas MKS-2 itself does not require
        TMEM-218 for its own localization. This defines MKS-2 as a 'core' subunit
        needed to recruit/assemble other MKS-module components at the TZ.
      action: ACCEPT
      reason: >-
        Directly supported experimental (IMP) annotation. Loss of mks-2 mislocalizes
        a downstream TZ protein, demonstrating a role in establishing protein
        localization to the transition zone. Core function.
      supported_by:
        - reference_id: PMID:26982032
          supporting_text: >-
            TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant
        - reference_id: PMID:26982032
          supporting_text: >-
            TMEM-218 is not required for the localisation of MKS-5, MKS-2
  - term:
      id: GO:0035869
      label: ciliary transition zone
    evidence_type: IDA
    original_reference_id: PMID:26595381
    qualifier: located_in
    review:
      summary: >-
        WormBase IDA annotation for direct localization of MKS-2 to the ciliary
        transition zone. The cached record for this paper is abstract-only; the
        abstract establishes that the MKS-module membrane proteins (which include
        MKS-2/TMEM216) are TZ-localized, immobile, and periodically arranged within
        the TZ, and the curator assigned the IDA from the full text.
      action: ACCEPT
      reason: >-
        Experimental (IDA) localization to the transition zone, concordant with the
        IBA annotation and with MKS-2::GFP imaging in PMID:26982032. The full text
        (not in cache) contains the direct evidence; per curation guidance the
        experimental annotation is retained rather than second-guessed from an
        abstract-only cache.
      supported_by:
        - reference_id: PMID:26595381
          supporting_text: >-
            TZ-localized MKS module by organizing recruitment of the ciliopathy proteins
  - term:
      id: GO:1903565
      label: negative regulation of protein localization to cilium
    evidence_type: IMP
    original_reference_id: PMID:26982032
    qualifier: involved_in
    review:
      summary: >-
        MKS-2 is explicitly named among the 'core' MKS-module TZ proteins (with
        MKSR-1, MKSR-2, TMEM-231) that are required for ciliary gate function —
        restricting the inappropriate entry of the membrane-associated protein
        TRAM-1a into cilia. This gate/diffusion-barrier activity is the central
        function of the transition zone and is not otherwise captured in GOA for
        mks-2.
      action: NEW
      reason: >-
        New annotation proposed to capture MKS-2's ciliary-gate role, which is well
        documented for the core MKS module and directly stated for MKS-2 in Li et
        al. This mirrors the curated gate-function annotation for the sibling gene
        mks-3 and represents a core function currently missing from mks-2's GOA
        record.
      supported_by:
        - reference_id: PMID:26982032
          supporting_text: >-
            TZ proteins are all necessary for TZ gate function
        - reference_id: PMID:26982032
          supporting_text: >-
            restricting the inappropriate entry of membrane-associated TRAM-1a into cilia
  - term:
      id: GO:0036038
      label: MKS complex
    evidence_type: IDA
    original_reference_id: PMID:26982032
    qualifier: part_of
    review:
      summary: >-
        MKS-2 (TMEM216) is repeatedly identified as a 'core' MKS-module / MKSome
        component together with MKSR-1, MKSR-2, and TMEM-231, co-localizing with
        these subunits at the transition zone.
      action: NEW
      reason: >-
        New annotation capturing MKS-2 membership in the MKS complex (MKS module),
        consistent with the sibling gene mks-3 and with its role as a core
        MKS-module subunit at the transition zone.
      supported_by:
        - reference_id: PMID:26982032
          supporting_text: >-
            which include MKS-2, MKSR-1, MKSR-2, and TMEM-231
  - term:
      id: GO:0005198
      label: structural molecule activity
    evidence_type: IDA
    original_reference_id: PMID:26982032
    qualifier: enables
    review:
      summary: >-
        As a multi-pass integral membrane subunit of the MKS module, MKS-2
        contributes to the structural integrity of the transition zone; its loss
        mislocalizes the downstream TZ protein TMEM-218 and compromises the ciliary
        gate. This is the closest available molecular-function term for a
        transition-zone scaffold subunit (see knowledge_gaps).
      action: NEW
      reason: >-
        New molecular-function annotation. MKS-2 has no MF term in GOA; 'structural
        molecule activity' is used as the nearest placeholder for a diffusion-barrier
        scaffold subunit, more informative than generic protein binding. The precise
        MF term is an ontology-level gap (see knowledge_gaps / proposed_new_terms).
      supported_by:
        - reference_id: PMID:26982032
          supporting_text: >-
            which include MKS-2, MKSR-1, MKSR-2, and TMEM-231
        - reference_id: PMID:26982032
          supporting_text: >-
            TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant
references:
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
      vocabulary mapping, accompanied by conservative changes to GO terms applied by
      UniProt
    findings: []
  - id: PMID:26595381
    title: TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition
      zone and causes Joubert syndrome.
    findings:
      - statement: >-
          The MKS-module membrane proteins of the ciliary transition zone are
          immobile and periodically arranged within the TZ, and TMEM-107 organizes
          recruitment of MKS-module ciliopathy proteins.
        supporting_text: >-
          TZ-localized MKS module by organizing recruitment of the ciliopathy proteins
    reference_review:
      relevance: HIGH
      correctness: VERIFIED
      review_notes: >-
        PubMed-verified (Lambacher et al 2016, Nat Cell Biol). Cached record is
        abstract-only; the abstract supports the MKS module TZ localization and
        barrier context. The WormBase IDA for MKS-2 TZ localization draws on the
        full text; deferring to the curator for that experimental evidence.
  - id: PMID:26863025
    title: A Screen for Modifiers of Cilia Phenotypes Reveals Novel MKS Alleles and
      Uncovers a Specific Genetic Interaction between osm-3 and nphp-4.
    findings:
      - statement: >-
          A novel mks-2 allele (yhw128) was recovered as an enhancer of nphp-4;
          mks-2 single mutants show no overt dye-filling defect, but nphp-4;mks-2
          double mutants are strongly Dyf, demonstrating MKS/NPHP-module redundancy.
        supporting_text: >-
          there was no overt defect in dye uptake in mks-1(yhw146) or mks-2(yhw128) mutants
    reference_review:
      relevance: HIGH
      correctness: VERIFIED
      review_notes: >-
        PubMed-verified (Masyukova et al 2016, PLoS Genet); full text cached.
        Source of the IMP and IGI non-motile-cilium-assembly annotations for mks-2;
        allele identity confirmed by non-complementation and transgenic rescue.
  - id: PMID:26982032
    title: MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Transition Zone.
    findings:
      - statement: >-
          MKS-2 is a core MKS-module TZ protein required for the transition-zone
          localization of the peripheral protein TMEM-218.
        supporting_text: >-
          TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant
      - statement: >-
          The core MKS-module TZ proteins (including MKS-2) are required for ciliary
          gate function, restricting entry of membrane-associated TRAM-1a into cilia.
        supporting_text: >-
          restricting the inappropriate entry of membrane-associated TRAM-1a into cilia
      - statement: >-
          MKS-2 localization to the TZ depends on the upstream assembly factor
          MKS-5, and MKS-2 mislocalizes in the cep-290 mutant.
        supporting_text: >-
          MKS-5 as a critical assembly factor for all known MKS module proteins tested thus far
    reference_review:
      relevance: HIGH
      correctness: VERIFIED
      review_notes: >-
        PubMed-verified (Li et al 2016, PLoS Biol); full text cached and mks-2 is
        extensively assayed as a core MKS-module comarker. Supports the protein
        localization to TZ (IMP), the ciliary-gate NEW annotation, and the assembly
        hierarchy.
core_functions:
  - description: >-
      MKS-2 acts as a structural/scaffolding subunit of the MKS module of the
      ciliary transition zone. As a multi-pass integral membrane protein embedded in
      the transition-zone membrane, it contributes to the assembly and integrity of
      the TZ (Y-link connectors and apical ring) and to the ciliary gate — the
      membrane diffusion barrier that restricts non-ciliary membrane proteins from
      entering the cilium. It also helps recruit peripheral MKS-module components
      (e.g. TMEM-218) to the TZ. There is no GO molecular-function term that
      precisely describes a transition-zone diffusion-barrier scaffold subunit;
      'structural molecule activity' is used here as the closest available placeholder.
    molecular_function:
      id: GO:0005198
      label: structural molecule activity
    in_complex:
      id: GO:0036038
      label: MKS complex
    locations:
      - id: GO:0035869
        label: ciliary transition zone
    directly_involved_in:
      - id: GO:1905515
        label: non-motile cilium assembly
      - id: GO:1904491
        label: protein localization to ciliary transition zone
      - id: GO:1903565
        label: negative regulation of protein localization to cilium
    supported_by:
      - reference_id: PMID:26982032
        supporting_text: >-
          TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant
      - reference_id: PMID:26982032
        supporting_text: >-
          restricting the inappropriate entry of membrane-associated TRAM-1a into cilia
knowledge_gaps:
  - gap_statement: >-
      MKS-2 has no assigned molecular function and there is no GO term to express
      one. Its role is to be a structural/diffusion-barrier scaffold subunit of the
      ciliary transition-zone MKS module, but GO has no molecular-function term such
      as "structural constituent of the ciliary transition zone" (or "diffusion
      barrier component"), so the gene reads as MF-dark despite a well-understood
      cellular-component and biological-process role.
    boundary: >-
      It is firmly established that MKS-2 = TMEM216/MKS2 is a small multi-pass
      membrane protein of the TZ, a core MKS-module component required (redundantly
      with the NPHP module) for cilium assembly, for the ciliary gate, and for
      recruiting other MKS-module proteins. What is missing is a molecular-function
      representation: the worm GOA record carries only cellular-component and
      biological-process terms and no molecular_function annotation.
    gap_kind:
      - ONTOLOGY
      - CURATION
    dark_aspect: MF_DARK
    status: OPEN
    significance: >-
      This is the canonical "structural subunit" ontology gap shared across the
      transition-zone/ciliopathy gene set (cf. the DYF-2/IFT-A gap): a mechanistically
      well-placed protein that cannot be given an informative MF term, contributing to
      apparent molecular-function darkness across MKS/NPHP-module genes.
    resolution: >-
      Develop/adopt a molecular-function term for a structural constituent of the
      ciliary transition zone (analogous to "structural constituent of ribosome"),
      then annotate MKS-2 and the other core MKS/NPHP-module subunits to it.
    provenance:
      - reference_id: PMID:26982032
        supporting_text: >-
          TMEM-218 is no longer present at the TZ in the mks-2 MKS module mutant
        reference_section_type: RESULTS
    proposed_terms:
      - proposed_name: structural constituent of ciliary transition zone
        proposed_definition: >-
          The action of a protein that contributes to the structural integrity of the
          ciliary transition zone, for example by acting as an integral-membrane or
          scaffold subunit of the MKS or NPHP module that helps build the Y-link
          connectors and the membrane diffusion barrier at the ciliary base, without
          itself catalyzing a biochemical reaction.
        proposed_parent:
          id: GO:0005198
          label: structural molecule activity
  - gap_statement: >-
      The specific, non-redundant molecular contribution of MKS-2/TMEM216 within the
      MKS module is undetermined: its direct binding partners in the worm transition
      zone are not mapped, and it is unknown whether MKS-2 provides a discrete
      sub-function (e.g. a particular membrane-anchoring or barrier contact) or is
      largely interchangeable with the other core MKS-module proteins.
    boundary: >-
      Genetics and imaging establish that MKS-2 is a core MKS-module protein whose TZ
      localization depends on MKS-5 and CEP-290, that it is required to recruit
      TMEM-218, and that it contributes to the gate; single mks-2 mutants are
      phenotypically near-normal and defects emerge only in mks-2;nphp-4 double
      mutants. What is not resolved is MKS-2's molecular interface(s) and whether it
      has any function that the rest of the module cannot supply.
    gap_kind:
      - BIOLOGY
    dark_aspect: RESIDUAL_SUBGAP
    status: OPEN
    significance: >-
      Distinguishing a genuine non-redundant role from full module redundancy is the
      load-bearing question for interpreting TMEM216/MKS2 ciliopathy alleles and for
      understanding how individual MKS-module subunits partition the barrier-building
      task.
    resolution: >-
      Structural/proteomic mapping of MKS-2's direct TZ partners (e.g. affinity
      purification, proximity labelling, cryo-EM of the MKS module) combined with
      separation-of-function alleles assayed for gate, Y-link, and recruitment
      phenotypes.
    provenance:
      - reference_id: PMID:26982032
        supporting_text: >-
          the reason for this is unclear
        reference_section_type: RESULTS
proposed_new_terms:
  - proposed_name: structural constituent of ciliary transition zone
    proposed_definition: >-
      The action of a protein that contributes to the structural integrity of the
      ciliary transition zone, for example by acting as an integral-membrane or
      scaffold subunit of the MKS or NPHP module that helps build the Y-link
      connectors and the membrane diffusion barrier at the ciliary base, without
      itself catalyzing a biochemical reaction.
    proposed_parent:
      id: GO:0005198
      label: structural molecule activity
suggested_questions:
  - question: >-
      Does MKS-2/TMEM216 make direct physical contacts with specific MKS-module
      partners (e.g. MKSR-1/MKSR-2, TMEM-231, MKS-5) that define a discrete
      sub-architecture of the transition zone?
    experts: []
  - question: >-
      Does MKS-2 have any non-redundant function unmasked only in specific cell types
      or under stress, or is it fully interchangeable with the other core MKS-module
      subunits?
    experts: []
suggested_experiments:
  - description: >-
      Proximity labelling (TurboID/BioID) or affinity purification of tagged MKS-2 in
      C. elegans ciliated neurons to map its direct transition-zone interaction
      partners.
    hypothesis: >-
      MKS-2 occupies a specific position in the MKS-module interaction network with a
      defined set of direct membrane-protein partners.
  - description: >-
      Structure-guided separation-of-function mutagenesis of MKS-2 transmembrane/loop
      residues, assayed for TZ localization, TRAM-1a exclusion (gate), TMEM-218
      recruitment, and Y-link ultrastructure by TEM.
    hypothesis: >-
      Distinct MKS-2 residues are required for membrane anchoring versus barrier
      function versus recruitment of peripheral MKS-module proteins.
tags:
  - caeel-ciliopathy

mks-2

Gene Description