Folliculin (FLCN) is a cytoplasmic DENN/longin-domain protein that, as a heterodimer with FNIP1 or FNIP2, acts as the GTPase-activating protein for the lysosomal Rag GTPases RagC and RagD. By converting RagC/D to the GDP-bound state in response to amino acids it activates mTORC1 toward its non-canonical substrates TFEB and TFE3, keeping these MiT/TFE transcription factors phosphorylated and in the cytoplasm. Under amino acid starvation FLCN-FNIP sits on the lysosomal membrane within the inactive lysosomal folliculin complex with the Rags and Ragulator. FLCN is also reported at primary cilia, centrosomes and the mitotic spindle, contributes to autophagy and lysosome positioning, and human FLCN has been reported to bind and inhibit lactate dehydrogenase A. Loss of FLCN in mammals causes early embryonic lethality and, in heterozygotes, renal tumours (Birt-Hogg-Dube syndrome in human), driven largely by constitutive nuclear TFEB. The donkey protein belongs to the same PANTHER subfamily as human and mouse folliculin (PTHR31441:SF2), is full length (578 aa, 94.6% identity to human), and conserves the catalytic arginine finger (Arg-164).
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0000122 negative regulation of transcription by RNA polymerase II
IEA GO_REF:0000120
KEEP AS NON CORE
Summary: FLCN represses TFE3/TFEB-driven transcription indirectly, by activating mTORC1 so that these transcription factors are retained in the cytoplasm.
Reason: Human FLCN carries an IMP annotation to this term and the effect is real, but FLCN is a cytoplasmic Rag GAP that acts several steps upstream of transcription; it has no DNA-binding or co-regulator activity. The term is retained as a non-core, indirect consequence of its mTORC1-TFE3/TFEB signalling role (in the mouse BHD model, FLCN loss acts through constitutive TFEB activity). The transfer comes from PANTHER node PTN009120754 in subfamily PTHR31441:SF2, which contains the donkey protein together with the experimentally characterised human and mouse folliculins.
In low-amino acid conditions, the lysosomal folliculin complex (LFC) is formed on the membrane of lysosomes, which inhibits the GTPase-activating activity of FLCN, inactivates mTORC1 and maximizes nuclear translocation of TFEB and TFE3
Summary: FLCN is the GAP for RagC/RagD; the catalytic Arg-164 is conserved in the donkey sequence.
Reason: Human FLCN-FNIP stimulates GTP hydrolysis by RagC/RagD (human IDA), and Arg-164, the residue essential for GAP activity, maps to Arg-164 of the donkey protein, which aligns to human at 94.64% identity over its full length. The donkey protein is in the same PANTHER subfamily (PTHR31441:SF2) as human and mouse folliculin, and the GAP term is carried by PANTHER node PTN009120754. This is the defining molecular activity of FLCN. A more specific Rag-GAP term does not exist in GO; the complex term GO:1990877 captures the RagC/D specificity.
Summary: A nuclear pool of FLCN has been reported for the human protein.
Reason: Human FLCN has IDA support for nuclear localization, but its characterized functions are at the lysosome and in the cytosol. Retained as a secondary location.
Summary: FLCN-FNIP is recruited to the lysosomal membrane, where it forms the lysosomal folliculin complex with the Rags and Ragulator.
Reason: Lysosomal membrane recruitment is central to FLCN's regulation of RagC/D and mTORC1 and is supported by multiple human studies, including the cryo-EM structure of the starved-state lysosomal folliculin complex.
Summary: FLCN-FNIP is cytosolic in nutrient-replete cells and relocates to lysosomes on starvation.
Reason: Cytosol is a well-supported location for human FLCN (several IDA studies) and is consistent with its role as a soluble, lysosome-recruited GAP. The cytosol term is also carried by PANTHER node PTN009120754.
Summary: Human FLCN localizes to primary and motile cilia and has a flow-stress role through primary cilia.
Reason: Ciliary localization is supported for human FLCN and linked to LKB1/AMPK regulation under flow stress, but it is a secondary, context-specific role relative to lysosomal Rag regulation.
Also localizes to motile and non-motile cilia, centrosomes and the mitotic spindle
GO:0009968 negative regulation of signal transduction
IEA GO_REF:0000117
MARK AS OVER ANNOTATED
Summary: Very broad ARBA term; FLCN's principal signalling role is positive regulation of TORC1.
Reason: Human FLCN has scattered single-study or ISS annotations to negative regulation of particular pathways (Rho, ERK, PI3K-AKT), but none is a defining activity, and the generic parent conveys no information while sitting awkwardly beside the well-established positive regulation of TORC1 signalling. The ARBA assertion is not independent evidence; it is retained only as an over-annotation.
Summary: Mouse Flcn has an IMP annotation to positive regulation of TGF-beta receptor signalling; the effect is indirect.
Reason: The TreeGrafter transfer comes from PANTHER node PTN009120754 (subfamily PTHR31441:SF2), which places the donkey protein with mouse Flcn (IMP) and human FLCN (ISS), so the phylogenetic placement is sound. However, neither UniProt record contains curated text describing a TGF-beta signalling role, and the primary experimental paper behind the mouse IMP is not cached and could not be read in this re-review. Any effect is likely indirect (via TFE3/TFEB-dependent transcription) rather than a role within the receptor signalling pathway. The previous KEEP_AS_NON_CORE was based only on the GO line of the mouse record, which restates the annotation rather than supporting it, so this is changed to UNDECIDED until the primary evidence is checked.
Summary: Correct but general; FLCN activates mTORC1 (TORC1) specifically, through its RagC/D GAP activity.
Reason: The claim is true, but the evidence supports the more specific child term positive regulation of TORC1 signaling (GO:1904263), which the gene already carries from the PANTHER node PTN009120754. FLCN acts on the amino acid-Rag-mTORC1 axis, not on mTORC2. Per the refinement rule, the general term is refined to that descendant rather than accepted as is.
Summary: Core process; FLCN-FNIP GAP activity on RagC/D activates mTORC1 toward TFEB/TFE3.
Reason: Human FLCN is experimentally established (IDA) as a positive regulator of TORC1 signalling via its Rag GAP activity, and the donkey protein retains the catalytic arginine and full domain architecture.
the phosphorylation of TFEB-unlike other substrates of mTORC1, such as S6K and 4E-BP1- is strictly dependent on the amino-acid-mediated activation of RagC and RagD GTPases
ISS file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt
NEW
Summary: FLCN acts as a heterodimer with FNIP1 or FNIP2; this complex is the RagC/D GAP.
Reason: The FLCN-FNIP heterodimer is the functional unit of the GAP activity (human IDA), and the donkey GOA record has no complex annotation. The FNIP-interacting C-terminal DENN region is fully present in the donkey protein.
Interacts (via C-terminus) with FNIP1 or FNIP2 (via C-terminus)
Core Functions
As a heterodimer with FNIP1/FNIP2, FLCN is the GTPase-activating protein for RagC/RagD at the lysosome, activating mTORC1 toward TFEB/TFE3 in response to amino acids.
Q: Human FLCN is reported (single study) to bind and uncompetitively inhibit LDHA via a region (human residues 210-220) that is identical in donkey; is LDHA inhibition a conserved, physiological activity of mammalian folliculin, which would justify an enzyme inhibitor activity annotation beyond human?
Q: Is the TGF-beta signalling effect of FLCN loss (mouse IMP) a direct role in the receptor pathway or an indirect consequence of deregulated TFE3/TFEB transcription?
Suggested Experiments
Experiment: Measure RagC/RagD GAP activity of recombinant donkey FLCN-FNIP2 and of an R164A mutant, to confirm that the conserved catalytic arginine supports the same activity as in human.
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Assessment of 5 ProtNLM2 GO predictions for donkey folliculin (A0A8C4MM62), a full-length ortholog of human FLCN (94.64% identity, same PANTHER subfamily PTHR31441:SF2, catalytic Arg-164 conserved) whose core function is RagC/RagD GAP activity with FNIP1/2, driving mTORC1 phosphorylation of TFEB and TFE3. One prediction is correct and absent from the donkey GOA record (enzyme inhibitor activity, from direct LDHA inhibition by human FLCN). Two are incorrect because they restate knockout phenotypes as participation in a process (in utero embryonic development, cell-cell junction assembly), the same grounds on which the human FLCN review marks these terms over-annotated. Two are uncertain because FLCN acts upstream of them only indirectly or through a generic consequence of its specific mTORC1 role (transforming growth factor beta receptor signalling pathway, positive regulation of protein phosphorylation). ProtNLM2 emitted no non-GO function-text or subcellular-location output for this accession in the frozen snapshot.
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
Review rationale: The experimental evidence (Bhd-null mouse cells and a FLCN-null human renal cancer line) shows that FLCN loss reduces TGF-beta-dependent transcription and alters expression of TGF-beta pathway genes, which supports at most regulation of the pathway, not participation in it. FLCN is a cytoplasmic and lysosomal Rag GAP with no reported role as a component of TGF-beta receptor signalling, and the effect is thought to be indirect, via TFE3/TFEB deregulation. The donkey GOA record carries positive regulation of TGF-beta receptor signalling, which the donkey review leaves UNDECIDED and the human review keeps as non-core; regulation of a pathway is not an is_a child of the pathway, so the prediction is not a less precise form of that term. The evidence neither establishes nor refutes direct involvement.
Supporting Evidence:
PMID:21258407: "results instead from reduced Bim transcription associated with a general loss of TGFΞ²-mediated transcription and chromatin modifications"
PMID:20573232: "We identified genes that were differentially expressed in the cell lines with or without wild-type FLCN, many of which are involved in TGF-beta signaling"
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
Review rationale: Human FLCN binds lactate dehydrogenase A directly and acts as an uncompetitive inhibitor (PMID:34381247, human IDA to this term; the human review prefers the more specific child L-lactate dehydrogenase inhibitor activity, GO:0160193, and treats it as non-core). The donkey protein is a full-length ortholog in the same PANTHER subfamily at 94.64% identity, and the term is absent from the donkey GOA record, which carries only GTPase activator activity as MF. The finding comes from a single laboratory and the inhibitory region was not mapped residue by residue, so the transfer rests on orthology.
Supporting Evidence:
PMID:34381247: "we identify the human tumor suppressor folliculin (FLCN) as a binding partner and uncompetitive inhibitor of LDHA"
GO:0001934 positive regulation of protein phosphorylationGO_BP
UNC β Uncertain Review score: 1/2
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
Review rationale: FLCN loss abolishes mTORC1 phosphorylation of TFE3 and TFEB while leaving S6K and 4E-BP1 phosphorylation intact, because FLCN GAP activity on RagC is needed to recruit these substrates to the lysosome. The effect is therefore real but substrate-specific and mediated through mTORC1, and it is already captured more informatively by positive regulation of TORC1 signalling (GO:1904263), which the donkey GOA record carries and the donkey review accepts. GO:1904263 is not a descendant of GO:0001934 (OLS4 ancestry), so the prediction is not simply less precise. Neither human FLCN, FNIP1, RagC nor RagD carries this term or its descendants in GOA, indicating that regulators of this pathway are conventionally annotated to TORC1 signalling rather than to generic protein phosphorylation. The prediction is defensible but uninformative, and cannot be scored as clearly correct or incorrect.
Supporting Evidence:
PMID:35358174: "loss of the mTORC1 regulator folliculin (FLCN) renders mTORC1 specifically incompetent to phosphorylate TFE3"
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
Review rationale: Homozygous Flcn knockout mice die at 5.5-6.5 dpc, which shows that FLCN is necessary for embryonic development, not that it performs a step of it. The human FLCN review marks this term over-annotated on exactly these grounds; the mouse source is a phenotype-based IMP and the lethality is most plausibly a downstream consequence of unrestrained TFE3 activity. FLCN's activity is Rag GAP-mediated control of mTORC1, and no developmental-process mechanism has been shown. The term is absent from the donkey GOA record. The prediction converts a knockout phenotype into process participation, so it is scored as incorrect.
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
Review rationale: The only experimental basis is a knockdown study in mouse renal collecting-duct cells, in which FLCN or p0071 deficiency caused tight junction defects and E-cadherin mislocalization, and FLCN only partially co-localized with p0071 at junctions. This shows that FLCN deficiency perturbs junctions, not that FLCN participates in junction assembly, and the human FLCN review marks the term over-annotated on these grounds. No mechanism linking FLCN Rag GAP activity directly to junction assembly is known. The term is absent from the donkey GOA record.
Supporting Evidence:
PMID:22965878: "Deficiency of folliculin and of p0071 resulted in tight junction defects and mislocalization of E-cadherin in mouse inner medullary collecting duct-3 renal tubular cells."
PMID:22965878: "Folliculin and p0071 partially co-localized at cell junctions and in mitotic cells"