Human TMEM216: functional annotation and evidence review Falcon Edison Scientific Literature 40 citations 2 artifacts 2026-10-03T22:25:04.786082

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Human TMEM216: functional annotation and evidence review

Identity and principal function

The target is human TMEM216, UniProt Q9P0N5, encoding transmembrane protein 216 (also called HSPC244). Its supplied UniProt annotation identifies the Uncharacterised_TM-17/Transmemb_17 domain (InterPro IPR019184; Pfam PF09799). The domain name does not identify the gene as TMEM17. Likewise, adjacent TMEM138 is a separate, nonhomologous gene: a primary genetic study distinguished its three-pass protein from four-pass TMEM216 and showed that the two have different cellular distributions despite coordinated expression. These distinctions are essential because experiments on other similarly named proteins do not establish TMEM216 function. (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 1-3, lee2012evolutionarilyassembledcisregulatory pages 6-9)

Best-supported primary annotation: TMEM216 is a small, predicted four-pass membrane protein that helps establish the primary cilium at its base. It participates in periciliary vesicle trafficking and is associated with the basal-body/transition-zone network that organizes ciliary assembly and membrane compartmentalization. It is not established as an enzyme, an ion transporter, or a transporter with a defined substrate; the domain annotation predicts membrane topology, not catalytic or substrate specificity. Its contribution to a selective ciliary gate is well motivated by its protein associations, but direct TMEM216-specific cargo-selectivity evidence is more limited than the evidence for its role in cilium formation and vesicle delivery. (lee2012evolutionarilyassembledcisregulatory pages 3-4, shoaib2020biochemicalandgeneticc pages 205-208, shoaib2020biochemicalandgenetica pages 64-68, moran2024transportandbarrier pages 14-15)

The evidence and its limits are summarized below.

Topic TMEM216-specific finding Experimental basis / source Evidence level and limitation
Identity and topology Target is human TMEM216 / HSPC244, UniProt Q9P0N5, annotated with Uncharacterised_TM-17 / PF09799 (Transmemb_17) and predicted to be a four-pass membrane protein. “Transmemb_17” is a domain-family name—not the gene TMEM17. Lee et al. independently described TMEM216 as tetraspan and distinct from adjacent, nonhomologous TMEM138. User-supplied UniProt record; Lee et al., Science (24 February 2012), DOI (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 1-3, lee2012evolutionarilyassembledcisregulatory pages 6-9) High for identity and predicted topology; PF09799 is sequence annotation, not proof of a transporter, receptor, or catalytic activity.
Cellular localization Endogenous TMEM216 localized primarily to basal bodies and to adjacent vesicles around the ciliary base in IMCD3 cells. Immuno-EM and live imaging additionally placed it on Golgi/post-Golgi vesicles along microtubules, with net vesicular movement toward the centrosome. Immunofluorescence, immuno-EM, time-lapse imaging and FRAP; Lee et al. 2012, DOI (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 6-9, lee2012evolutionarilyassembledcisregulatory media ad67491e) High for basal-body/periciliary-vesicle localization in the tested cells. “Transition-zone protein” is supported by the wider interaction network, but Lee’s strongest direct image places TMEM216 primarily at the basal body.
Requirement for ciliogenesis Fibroblasts carrying TMEM216 p.R73L failed ciliogenesis after 48 h serum starvation; cilia under 1 μm were scored, with 40–50 cells analyzed and ANOVA/Bonferroni testing. Patient fibroblasts; Lee et al. 2012, DOI (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 6-9, lee2012evolutionarilyassembledcisregulatory media ad67491e) Moderate–high disease-linked cellular evidence. The short-cilium phenotype in the same figure belongs to TMEM138 p.A126T, whereas failure of ciliogenesis belongs to TMEM216 p.R73L; they must not be conflated.
Vesicle delivery and TRAPPII TMEM216 and TMEM138 mark distinct, tethered vesicle pools. TMEM216 knockdown disrupted TMEM138 and CEP290 trafficking, whereas TMEM138 depletion did not notably alter TMEM216 movement. TRAPPC9/TRAPPII knockdown separated the vesicle pools, and myc-TRAPPC9 largely rescued tethering (n = 90–110). siRNA, live-cell imaging and rescue; Lee et al. 2012, DOI (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 4-6, lee2012evolutionarilyassembledcisregulatory pages 6-9) High for an upstream periciliary trafficking role. This is not equivalent to demonstrating that TMEM216 itself transports a molecular substrate across the ciliary membrane.
TCTN1/MKS-complex association and gate inference TMEM216 co-immunoprecipitated with TCTN1 but was absent from the corresponding mass-spectrometry set, consistent with a peripheral or sub-stoichiometric association with the MKS/Tectonic transition-zone complex. The complex-level model supports ciliary membrane gating. Garcia-Gonzalo et al., Nature Genetics (July 2011), DOI (shoaib2020biochemicalandgeneticc pages 205-208, shoaib2020biochemicalandgeneticb pages 205-208) Moderate for biochemical association; indirect for TMEM216-specific gate activity. Cargo-localization effects involving ARL13B, AC3, SMO and PKD2 were demonstrated principally through perturbation of TCTN1 or other complex members, not a TMEM216-specific cargo-selectivity assay.
RhoA–actin and basal-body docking Loss of TMEM216 in human fibroblasts or knockdown in zebrafish was reported to cause RhoA hyperactivation, hypothesized to disturb apical actin remodeling and thereby inhibit normal basal-body docking. Kalot et al., Frontiers in Nephrology (5 January 2024), DOI, summarizing Valente et al. 2010 (kalot2024primaryciliaand pages 11-12) Moderate because the 2024 source is a review of earlier experiments. The actin-to-docking causal chain is explicitly a mechanistic interpretation; do not substitute TMEM237- or TMEM67-specific RhoA assays as direct TMEM216 evidence.
Functional relationship with TMEM237 Human TMEM216 mRNA significantly rescued zebrafish tmem237 morphant phenotypes, and TMEM237 mRNA rescued tmem216 suppression phenotypes comparably to TMEM216 mRNA. Reciprocal mRNA/morpholino rescue; Huang et al., American Journal of Human Genetics (9 December 2011), DOI (huang2011tmem237ismutated pages 8-9, huang2011tmem237ismutated pages 9-11) Moderate evidence of functional complementation in vivo. Reciprocal rescue does not by itself establish direct physical binding. RhoA and actin-stress-fiber experiments in that paper primarily tested TMEM237, not TMEM216.
Hedgehog signaling development (2024) A 2024 report concluded that TMEM216 promotes primary ciliogenesis and Hedgehog signaling through the SUFU–GLI2/GLI3 axis. Wang et al., Science Signaling 17(820):eabo0465 (January 2024), DOI; identified through secondary citation because the original full text was unavailable (sun2025renalinsufficiencycaused pages 2-4) Promising but incompletely verified here. Treat pathway direction as reported, but do not infer direct TMEM216–SUFU binding or numerical effect sizes without checking the primary article.
Noncoding retinal disease development (2024) A homozygous single-nucleotide substitution upstream of TMEM216 was reported to cause nonsyndromic retinitis pigmentosa and to be associated with reduced TMEM216 expression. Malka et al., American Journal of Human Genetics 111:2012–2030 (September 2024), DOI; primary text unavailable in this search Clinically important but indirectly assessed here. The result supports dosage-sensitive retinal function, not a newly demonstrated biochemical activity or proof that every upstream TMEM216 variant is pathogenic.
Predominantly renal presentation (2025) A 21-year-old man with proteinuria from age 15, bilateral renal cysts and progression to ESRD carried compound-heterozygous c.253C>T (p.R85*) and c.143T>C (p.L48P) variants. p.R85* met pathogenic criteria; p.L48P remained a VUS without functional validation. Whole-exome sequencing and Sanger segregation; Sun et al., Frontiers in Medicine (29 April 2025), DOI (sun2025renalinsufficiencycaused pages 4-5, sun2025renalinsufficiencycaused pages 1-2, sun2025renalinsufficiencycaused pages 5-7) Low–moderate genotype–phenotype evidence because this is one case and one allele remains a VUS. It expands the possible phenotype but does not prove isolated TMEM216 nephropathy or establish a treatment.

Table: A source-graded matrix separating direct human TMEM216 evidence from complex-level inference, experiments on neighboring transition-zone proteins, and recent findings whose primary texts were unavailable.

Where TMEM216 acts and how it supports ciliogenesis

The basal body is the mother-centriole-derived structure at the base of a cilium; the adjoining transition zone lies between the basal body and ciliary axoneme and helps establish the cilium as a distinct membrane compartment. In mouse IMCD3 cells, antibody staining placed endogenous TMEM216 primarily at basal bodies, with additional adjacent vesicles near the ciliary base. Immunoelectron microscopy also detected TMEM216 on Golgi/post-Golgi vesicles along microtubules. Thus, “transition-zone-associated” is an appropriate network description, but it should not obscure the particularly strong direct evidence for basal-body and periciliary-vesicle localization. Lee and colleagues’ cropped localization and mutant-cell panels provide visual evidence for that distinction. (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 6-9, lee2012evolutionarilyassembledcisregulatory media ad78b7ce)

In live-cell imaging, TMEM216-positive vesicles showed net movement toward the centrosome and traveled alongside a distinct, tethered population marked by TMEM138. Depleting TMEM216 disrupted movement of TMEM138-associated vesicles and the ciliary protein CEP290; depleting TMEM138 did not comparably disrupt TMEM216-vesicle movement. Knockdown of TRAPPC9, a TRAPPII tethering-complex subunit, separated the vesicle populations, and TRAPPC9 re-expression largely restored tethering. This supports an asymmetric, TMEM216-dependent delivery/tethering role upstream of cilium assembly. It does not show that TMEM216 itself carries cargo through a membrane pore or directly binds every protein in the affected vesicles. (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 4-6, lee2012evolutionarilyassembledcisregulatory pages 6-9)

The cellular consequence is experimentally clear. After 48 hours of serum starvation, fibroblasts carrying TMEM216 p.R73L showed failed ciliogenesis in Lee and colleagues’ assay, which scored cilia shorter than 1 μm; the figure reports 40–50 cells for its comparison. The short-cilium mutant shown alongside it was TMEM138 p.A126T, not TMEM216. TMEM216 depletion also impaired ciliogenesis in IMCD3 cells. In zebrafish, tmem216 knockdown produced cilia-associated developmental phenotypes, including curved tails, cardiac edema and hydrocephalus; Lee and colleagues scored more than 50 embryos per condition for the illustrated comparison. These are functional tests, not simply localization-based predictions. (lee2012evolutionarilyassembledcisregulatory pages 3-4, lee2012evolutionarilyassembledcisregulatory pages 4-6, lee2012evolutionarilyassembledcisregulatory pages 6-9, lee2012evolutionarilyassembledcisregulatory media ad67491e)

TMEM216 also belongs functionally to the Meckel/Joubert-associated transition-zone network. In the Tectonic-complex study, TMEM216 associated with TCTN1 by co-immunoprecipitation but was not identified in the corresponding mass-spectrometry analysis; it was therefore considered a possible peripheral or sub-stoichiometric associate, not an established stoichiometric core subunit. The wider TCTN1 complex includes other ciliopathy proteins and controls ciliary assembly and membrane composition, but the published cargo-localization perturbations emphasized TCTN1 and other components. Their effects on ARL13B, adenylyl cyclase 3, Smoothened or PKD2 should not automatically be assigned to TMEM216 loss. Garcia-Gonzalo et al., Nature Genetics, published July 2011: doi:10.1038/ng.891. (shoaib2020biochemicalandgeneticc pages 205-208, shoaib2020biochemicalandgeneticb pages 205-208)

A second line of evidence connects TMEM216 to TMEM237 and transition-zone assembly. Huang and colleagues found reciprocal functional rescue: human TMEM216 expression improved zebrafish tmem237 knockdown phenotypes, while TMEM237 improved tmem216 suppression phenotypes. Their C. elegans experiments likewise implicated the TMEM216 ortholog in a transition-zone interaction network. Functional rescue supports overlapping activity, not proof of direct protein binding. Notably, the prominent RhoA, actin-stress-fiber and Wnt assays in this paper tested TMEM237-deficient cells; those measurements are not TMEM216-loss effect sizes. Huang et al., American Journal of Human Genetics, published 9 December 2011: doi:10.1016/j.ajhg.2011.11.005. (huang2011tmem237ismutated pages 1-2, huang2011tmem237ismutated pages 8-9, huang2011tmem237ismutated pages 9-11)

Signaling pathways: established effects versus mechanism inferred

RhoA–actin and basal-body docking. A 2024 review reports that TMEM216 loss in human fibroblasts or knockdown in zebrafish causes RhoA hyperactivation. The proposed explanation is that abnormal RhoA-dependent actin organization impedes centrosome/basal-body movement or docking at the apical membrane, thereby inhibiting ciliogenesis. This is a biologically coherent explanation of the docking defect, but the full causal sequence for TMEM216 is presented as a hypothesis rather than a demonstrated direct TMEM216–RhoA biochemical interaction. Kalot et al., Frontiers in Nephrology, published January 2024: doi:10.3389/fneph.2023.1331847. (kalot2024primaryciliaand pages 11-12, shoaib2020biochemicalandgeneticc pages 64-68)

Hedgehog signaling. Cilia are sites of Hedgehog signal transduction, so loss of cilia or disruption of their organization can alter pathway output. A 2024 primary paper specifically reports that TMEM216 promotes ciliogenesis and Hedgehog signaling through the SUFU–GLI2/GLI3 axis: Wang et al., Science Signaling 17(820):eabo0465, doi:10.1126/scisignal.abo0465. The original paper’s full experimental text was not retrievable in this review; the TMEM216–SUFU–GLI finding is therefore noted as reported in the literature, without claiming a verified direct physical interaction, an exact signaling effect size or independence from the ciliogenesis defect. (sun2025renalinsufficiencycaused pages 2-4, moran2024transportandbarrier pages 14-15)

These pathways should not be collapsed into a single established molecular reaction. The most concrete TMEM216-specific mechanistic result remains vesicle delivery/tethering toward the ciliary base. Current expert discussion treats vesicular transport, transition-zone barriers and intraflagellar transport as interconnected but incompletely resolved processes; membership in a transition-zone complex alone does not identify which cargo TMEM216 selects or whether its principal action is at the mature gate. Moran et al., Nature Reviews Nephrology 20:83–100, published online October 2023 for the 2024 volume: doi:10.1038/s41581-023-00773-2. (lee2012evolutionarilyassembledcisregulatory pages 3-4, moran2024transportandbarrier pages 14-15)

Human relevance and research applications

Established disease association. Biallelic TMEM216 disruption is implicated in the Joubert–Meckel ciliopathy spectrum. The biological link is unusually direct: disease-associated cells fail to assemble normal cilia, and the implicated cellular machinery is positioned at the ciliary base. Neurological, renal and retinal findings vary across this spectrum; phenotype alone should not be treated as a readout of a particular TMEM216 molecular activity. Lee et al., Science 335:966–969, published 24 February 2012: doi:10.1126/science.1213506. For clinical-spectrum context, see Van De Weghe et al., Annual Review of Genomics and Human Genetics 23:301–329, 2022: doi:10.1146/annurev-genom-121321-093528. (lee2012evolutionarilyassembledcisregulatory pages 1-3, shoaib2020biochemicalandgeneticc pages 64-68)

Recent retinal genetics. Malka et al. reported in American Journal of Human Genetics 111:2012–2030, September 2024, that a single noncoding nucleotide substitution upstream of TMEM216 causes nonsyndromic retinitis pigmentosa and is associated with reduced TMEM216 expression: doi:10.1016/j.ajhg.2024.07.020. This is important for variant interpretation because coding-only searches can miss regulatory mechanisms. The primary article was unavailable for detailed examination here, so an exact patient count, expression change or experimentally resolved photoreceptor mechanism cannot be independently supplied. The finding should not be mistaken for the separate experimental work on photoreceptor TMEM138. (lee2012evolutionarilyassembledcisregulatory pages 1-3, lee2012evolutionarilyassembledcisregulatory pages 6-9)

A recent renal case—and a necessary caution. A report published 29 April 2025 describes one man with proteinuria beginning at 15 years, bilateral kidney cysts and progression to end-stage renal disease by 21 years. Exome sequencing and parental Sanger testing found TMEM216 c.253C>T (p.R85*) inherited from his father and c.143T>C (p.L48P) from his mother. The authors classified p.R85* as pathogenic, but p.L48P remained a variant of uncertain significance without functional validation. Accordingly, this is a clinically useful candidate diagnosis and illustrates the value of segregation testing in unexplained early-onset kidney disease; one case does not prove a distinct, isolated TMEM216 kidney disorder. Sun et al., Frontiers in Medicine 12:1579732: doi:10.3389/fmed.2025.1579732. (sun2025renalinsufficiencycaused pages 4-5, sun2025renalinsufficiencycaused pages 1-2, sun2025renalinsufficiencycaused pages 5-7)

Practical interpretation. TMEM216 is relevant to ciliopathy genetic testing, including evaluation of potentially causal noncoding variation, and to research assays measuring ciliogenesis, basal-body positioning, periciliary trafficking and pathway responses. The evidence reviewed here does not establish a TMEM216-targeted treatment. In particular, proposed actin-pathway interventions or therapies studied for other ciliopathy genes must not be presented as validated TMEM216-specific clinical applications. (kalot2024primaryciliaand pages 11-12, sun2025renalinsufficiencycaused pages 4-5, moran2024transportandbarrier pages 14-15)

Overall assessment: human TMEM216 is best annotated as a cilium-assembly and basal-body/transition-zone-associated membrane factor, with direct evidence for TMEM216-dependent periciliary vesicle trafficking. RhoA–actin dysregulation and Hedgehog abnormalities explain or extend its developmental impact, while its precise direct binding partners, mature-gate cargo specificity and any biochemical substrate remain unresolved. (lee2012evolutionarilyassembledcisregulatory pages 3-4, kalot2024primaryciliaand pages 11-12, shoaib2020biochemicalandgeneticc pages 205-208, moran2024transportandbarrier pages 14-15)

References

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Artifacts

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