Affinage

TMEM216

Transmembrane protein 216 · UniProt Q9P0N5

Length
145 aa
Mass
16.5 kDa
Annotated
2026-04-28
43 papers in source corpus 9 papers cited in narrative 11 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TMEM216 is a transmembrane protein that localizes to the ciliary transition zone, where it functions as a core component of the MKS/JBTS multi-protein complex to regulate ciliogenesis, ciliary membrane composition, vesicular trafficking to cilia, and ciliary shedding (PMID:20512146, PMID:21725307, PMID:22282472, PMID:32163404). Within this complex, TMEM216 interacts with Meckelin/TMEM67, Mks1, Cep290, B9d1, Tctn1/2, and Cc2d2a, and is co-regulated and functionally interdependent with TMEM138 for vesicle delivery to primary cilia (PMID:21725307, PMID:22282472). At the signaling level, TMEM216 competes with SUFU for binding to GLI2/GLI3, preventing GLI processing into repressor forms and thereby activating Hedgehog signaling; its loss also causes RhoA and Dishevelled hyperactivation (PMID:38261656, PMID:20512146). Loss-of-function mutations cause Joubert and Meckel syndromes, and non-coding promoter variants reducing TMEM216 expression cause non-syndromic retinitis pigmentosa through photoreceptor-restricted ciliogenesis defects (PMID:20512146, PMID:39191256).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2010 High

    Establishing TMEM216 as a ciliary base protein required for ciliogenesis resolved the question of where and how this uncharacterized transmembrane protein acts, revealing that its loss blocks centrosomal docking and hyperactivates RhoA/Dishevelled signaling.

    Evidence Immunofluorescence localization, fibroblast knockdown, RhoA/Dishevelled activity assays, and zebrafish morpholino knockdown with gastrulation phenotypes

    PMID:20512146

    Open questions at the time
    • Mechanism by which TMEM216 restrains RhoA activity not defined
    • Whether TMEM216-Meckelin interaction is direct or bridged by other TZ proteins not resolved
    • No structural information on TMEM216
  2. 2011 High

    Defining TMEM216 as a subunit of the broader MKS transition zone complex (with Mks1, Tmem67, Cep290, B9d1, Tctn1/2, Cc2d2a) answered whether ciliopathy gene products operate in a shared molecular machine at a specific ciliary subcompartment.

    Evidence Reciprocal co-immunoprecipitation, co-localization at the transition zone, and genetic loss-of-function with ciliary membrane protein readouts

    PMID:21725307

    Open questions at the time
    • Stoichiometry and architecture of the complex not determined
    • Which direct binary interactions TMEM216 makes within the complex remain unclear
  3. 2012 High

    Demonstrating that TMEM216 and TMEM138 share a cis-regulatory element and are functionally interdependent for vesicular transport to cilia revealed a co-regulatory mechanism coupling gene expression with ciliary trafficking function.

    Evidence Evolutionary genomic analysis, reporter gene assay for shared regulatory element, vesicular transport functional assays

    PMID:22282472

    Open questions at the time
    • Whether TMEM216 and TMEM138 physically interact or act in parallel vesicle pools not resolved
    • Vesicle identity and cargo specificity not defined
  4. 2020 Medium

    Showing that TMEM216 depletion causes constitutive ciliary shedding in Paramecium extended its transition zone role beyond ciliogenesis to active maintenance of cilium-cell body attachment.

    Evidence RNAi knockdown in Paramecium with live imaging and electron microscopy of transition zone ultrastructure

    PMID:32163404

    Open questions at the time
    • Whether shedding phenotype is conserved in vertebrate systems not tested
    • Molecular mechanism linking TZ disruption to shedding not identified
  5. 2020 High

    CRISPR knockout of tmem216 in zebrafish demonstrated its specific requirement for photoreceptor outer segment protein trafficking and disc morphogenesis, explaining the retinal degeneration seen in TMEM216 ciliopathies.

    Evidence Zebrafish CRISPR/Cas9 KO, immunofluorescence of rhodopsin/GNAT2/red opsin localization, electron microscopy, TUNEL assay

    PMID:32687549

    Open questions at the time
    • Whether TMEM216 directly gates specific outer segment cargo at the TZ not determined
    • Temporal requirement for TMEM216 in photoreceptor maintenance versus development not separated
  6. 2021 Medium

    Epistasis analysis in C. elegans placed MKS-2/TMEM216 in very close functional association with the B9 complex, refining its position within the modular TZ architecture.

    Evidence C. elegans gene editing, quantitative cilium/TZ structure assays, epistasis analysis with B9D2 alleles

    PMID:33234550

    Open questions at the time
    • Whether TMEM216–B9D2 interaction is direct not established
    • Single-lab study in one model organism
  7. 2022 Medium

    Comprehensive phenotyping of zebrafish tmem216 CRISPR mutants showed that phenotypic variability from a single genotype mirrors the spectrum of human TMEM216-associated syndromes, establishing a genotype–phenotype framework.

    Evidence CRISPR/Cas9 knockout zebrafish, systematic phenotypic analysis across TZ mutant panel

    PMID:36533556

    Open questions at the time
    • Modifiers that drive phenotypic variability not identified
    • Single comparative study
  8. 2024 High

    Identifying TMEM216 as a competitor of SUFU for GLI2/GLI3 binding resolved a long-standing question of how this structural TZ protein influences Hedgehog signaling, providing a direct molecular mechanism.

    Evidence Co-immunoprecipitation, competition binding assays, nuclear/cytoplasmic fractionation, Tmem216-deficient mouse model with Hh target gene readouts

    PMID:38261656

    Open questions at the time
    • Whether TMEM216–GLI interaction occurs at the TZ or elsewhere not resolved
    • Relative contribution of SUFU competition versus ciliogenesis defect to Hh phenotype not separated
    • No structural basis for the competition mechanism
  9. 2024 Medium

    Non-coding variants upstream of TMEM216 were shown to reduce promoter activity and cause non-syndromic retinitis pigmentosa, establishing that partial TMEM216 loss preferentially affects photoreceptors.

    Evidence Luciferase reporter assay, allele-specific Nanopore sequencing, qPCR in patient leukocytes and genome-edited RPE1 cells

    PMID:39191256

    Open questions at the time
    • Threshold of TMEM216 expression required for different tissues not quantified
    • Single study; independent replication pending

Open questions

Synthesis pass · forward-looking unresolved questions
  • The structural basis of TMEM216 within the transition zone complex, the identity of vesicular cargoes it controls, and how it integrates ciliary gate function with Hedgehog signal transduction remain unresolved.
  • No high-resolution structure of TMEM216 or its complexes
  • Vesicle cargo specificity and sorting mechanism unknown
  • Whether RhoA hyperactivation and GLI regulation represent independent or linked functions not tested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0098772 molecular function regulator activity 1
Localization
GO:0005929 cilium 5
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 4 R-HSA-162582 Signal Transduction 2 R-HSA-5653656 Vesicle-mediated transport 1
Partners
B9D1CC2D2ACEP290GLI2GLI3SUFUTMEM138TMEM67
Complex memberships
MKS/JBTS transition zone complex

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2010 TMEM216 localizes to the base of primary cilia, and loss of TMEM216 in mutant fibroblasts or after knockdown causes defective ciliogenesis and centrosomal docking, with concomitant hyperactivation of RhoA and Dishevelled. Immunofluorescence localization, knockdown in fibroblasts, RhoA/Dishevelled activity assays Nature genetics High 20512146
2010 TMEM216 forms a protein complex with Meckelin (TMEM67), a protein encoded by another gene mutated in Joubert and Meckel syndromes. Co-immunoprecipitation / pulldown Nature genetics Medium 20512146
2010 Disruption of tmem216 expression in zebrafish caused gastrulation defects consistent with ciliary dysfunction, placing TMEM216 in the ciliary morphogenesis pathway. Morpholino knockdown in zebrafish with gastrulation phenotype readout Nature genetics High 20512146
2011 TMEM216 is a component of a transition zone complex that includes Mks1, Tmem67, Cep290, B9d1, Tctn2, Cc2d2a, and Tctn1; components co-localize at the transition zone between the basal body and ciliary axoneme and are required for ciliary membrane composition and ciliogenesis. Co-immunoprecipitation, immunofluorescence co-localization, genetic loss-of-function with ciliary membrane protein readouts Nature genetics High 21725307
2012 TMEM216 and TMEM138 are arranged in a head-to-tail gene cluster joined by chromosomal rearrangement, share a conserved cis-regulatory element, and are coordinately expressed; their coordinated expression is important for their interdependent cellular role in vesicular transport to primary cilia. Genomic/evolutionary analysis, reporter gene assay for shared regulatory element, functional cell biology assays of vesicular transport Science High 22282472
2020 Depletion of MKS2/TMEM216 in Paramecium induces constitutive deciliation of some cilia, demonstrating that TMEM216 at the transition zone controls ciliary shedding. RNAi knockdown in Paramecium, live imaging, electron microscopy of transition zone ultrastructure PLoS biology Medium 32163404
2020 Loss of TMEM216 in zebrafish leads to shortened photoreceptor ciliary axoneme, mislocalization of outer segment proteins (rhodopsin, GNAT2, red opsin) to the inner segment and cell bodies, abnormal outer segment disc morphology, and photoreceptor degeneration. CRISPR/Cas9 knockout in zebrafish, immunofluorescence, TUNEL assay, electron microscopy Investigative ophthalmology & visual science High 32687549
2021 In C. elegans, MKS-2/TMEM216 functions within the MKS module at the ciliary transition zone; alleles of B9D2 reveal a very close functional association between the B9 complex and MKS-2/TMEM216, and loss of MKS-2/TMEM216 disrupts transition zone organization. C. elegans gene editing (knock-in alleles), quantitative assays of cilium/TZ structure and function, epistasis analysis Disease models & mechanisms Medium 33234550
2024 TMEM216 interacts with SUFU (a negative regulator of Hedgehog signaling) and with GLI2/GLI3 transcription factors; TMEM216 competes with SUFU for binding to GLI2/GLI3, thereby inhibiting cleavage of GLI2/GLI3 into repressor forms, resulting in nuclear accumulation of full-length GLI2 and decreased nuclear localization of cleaved GLI3, thus activating Hedgehog signaling. Co-immunoprecipitation, competition binding assays, nuclear/cytoplasmic fractionation, Tmem216-deficient mouse model with Hh target gene readouts, cell-based KO assays Science signaling High 38261656
2024 Non-coding variants 69 bp upstream of TMEM216 reduce promoter activity (shown by luciferase reporter assay) and lower TMEM216 transcript levels, causing photoreceptor-restricted ciliogenesis defects and non-syndromic retinitis pigmentosa. Luciferase reporter assay, Nanopore sequencing of allele-specific expression, qPCR in patient leukocytes and genome-edited hTERT-RPE1 cells American journal of human genetics Medium 39191256
2022 Zebrafish tmem216 mutants generated by CRISPR/Cas9 display ciliary transition zone-associated phenotypes consistent with tissue-specific functions of TZ proteins, and phenotypic variability within progeny of a single tmem216 mutant mirrors the multiple disease syndromes associated with TMEM216 mutations in humans. CRISPR/Cas9 knockout zebrafish, comprehensive phenotypic analysis of TZ mutants Disease models & mechanisms Medium 36533556

Source papers

Stage 0 corpus · 43 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2011 A transition zone complex regulates mammalian ciliogenesis and ciliary membrane composition. Nature genetics 522 21725307
2010 Mutations in TMEM216 perturb ciliogenesis and cause Joubert, Meckel and related syndromes. Nature genetics 227 20512146
2006 The transmembrane protein meckelin (MKS3) is mutated in Meckel-Gruber syndrome and the wpk rat. Nature genetics 219 16415887
2007 Pleiotropic effects of CEP290 (NPHP6) mutations extend to Meckel syndrome. American journal of human genetics 215 17564974
2011 TMEM237 is mutated in individuals with a Joubert syndrome related disorder and expands the role of the TMEM family at the ciliary transition zone. American journal of human genetics 165 22152675
1984 Superkiller mutations in Saccharomyces cerevisiae suppress exclusion of M2 double-stranded RNA by L-A-HN and confer cold sensitivity in the presence of M and L-A-HN. Molecular and cellular biology 122 6371496
2010 Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy. Journal of medical genetics 112 21068128
2011 Engineering of bacterial methyl ketone synthesis for biofuels. Applied and environmental microbiology 91 22038610
2008 C2cd3 is required for cilia formation and Hedgehog signaling in mouse. Development (Cambridge, England) 85 19004860
2009 Joubert syndrome 2 (JBTS2) in Ashkenazi Jews is associated with a TMEM216 mutation. American journal of human genetics 82 20036350
2003 Linkage analysis in families with Joubert syndrome plus oculo-renal involvement identifies the CORS2 locus on chromosome 11p12-q13.3. American journal of human genetics 74 12917796
2007 Spectrum of MKS1 and MKS3 mutations in Meckel syndrome: a genotype-phenotype correlation. Mutation in brief #960. Online. Human mutation 72 17397051
2012 Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (New York, N.Y.) 71 22282472
2003 Description, nomenclature, and mapping of a novel cerebello-renal syndrome with the molar tooth malformation. American journal of human genetics 68 12908130
2011 B9D1 is revealed as a novel Meckel syndrome (MKS) gene by targeted exon-enriched next-generation sequencing and deletion analysis. Human molecular genetics 67 21493627
2005 Distinguishing the four genetic causes of Jouberts syndrome-related disorders. Annals of neurology 66 15786477
2013 C5orf42 is the major gene responsible for OFD syndrome type VI. Human genetics 63 24178751
1998 A gene for Meckel syndrome maps to chromosome 11q13. American journal of human genetics 62 9758620
2013 Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome. American journal of human genetics 46 23972372
2009 Multiple biochemical and morphological factors underlie the production of methylketones in tomato trichomes. Plant physiology 46 19801397
2012 Founder mutations and genotype-phenotype correlations in Meckel-Gruber syndrome and associated ciliopathies. Cilia 43 23351400
2010 Molecular genetics and pathogenic mechanisms for the severe ciliopathies: insights into neurodevelopment and pathogenesis of neural tube defects. Molecular neurobiology 42 21110233
2007 Meckel syndrome: genetics, perinatal findings, and differential diagnosis. Taiwanese journal of obstetrics & gynecology 42 17389183
2002 A novel locus for Meckel-Gruber syndrome, MKS3, maps to chromosome 8q24. Human genetics 33 12384791
2020 MKS-NPHP module proteins control ciliary shedding at the transition zone. PLoS biology 31 32163404
2021 Interpreting the pathogenicity of Joubert syndrome missense variants in Caenorhabditis elegans. Disease models & mechanisms 27 33234550
2022 Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants. Disease models & mechanisms 17 36533556
2016 A Screen for Modifiers of Cilia Phenotypes Reveals Novel MKS Alleles and Uncovers a Specific Genetic Interaction between osm-3 and nphp-4. PLoS genetics 16 26863025
2017 (Pro)renin receptor (ATP6AP2) depletion arrests As4.1 cells in the G0/G1 phase thereby increasing formation of primary cilia. Journal of cellular and molecular medicine 12 28215051
2020 TMEM216 Deletion Causes Mislocalization of Cone Opsin and Rhodopsin and Photoreceptor Degeneration in Zebrafish. Investigative ophthalmology & visual science 9 32687549
2023 Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome. Journal of medical genetics 8 36788019
2024 TMEM216 promotes primary ciliogenesis and Hedgehog signaling through the SUFU-GLI2/GLI3 axis. Science signaling 7 38261656
2024 Substitution of a single non-coding nucleotide upstream of TMEM216 causes non-syndromic retinitis pigmentosa and is associated with reduced TMEM216 expression. American journal of human genetics 7 39191256
2018 Determination of candidate genes involved in schizophrenia using the whole-exome sequencing. Bratislavske lekarske listy 7 30226068
2019 Characterization of Solanum melongena Thioesterases Related to Tomato Methylketone Synthase 2. Genes 6 31323901
2004 Comparative physical maps of the human and mouse Meckel syndrome critical regions. Mammalian genome : official journal of the International Mammalian Genome Society 6 15112103
2024 Exploration of lncRNA/circRNA-miRNA-mRNA network in patients with chronic atrophic gastritis in Tibetan plateau areas based on DNBSEQ-G99 RNA sequencing. Scientific reports 4 38649401
2012 Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216. Molecular biology and evolution 4 22936720
2019 Identification and Functional Characterization of a Soybean (Glycine max) Thioesterase that Acts on Intermediates of Fatty Acid Biosynthesis. Plants (Basel, Switzerland) 3 31597241
2018 Thumb duplication: molecular analysis of different clinical types. European journal of orthopaedic surgery & traumatology : orthopedie traumatologie 3 30498907
2025 Identification of a Sinorhizobium meliloti YbgC-like thioesterase that contributes to the production of the infochemical 2-tridecanone. The Biochemical journal 1 40938124
2024 Novel PIBF1 Pathogenic Variant in Three Siblings with Joubert Syndrome Type 33. Molecular syndromology 1 41230208
2025 Renal insufficiency caused by TMEM216 gene mutation: Case Report. Frontiers in medicine 0 40365501