FAM149B1 supports normal primary-cilium length and architecture and the distribution of intraflagellar transport proteins within cilia. It associates with TBC1D32/BROMI and CCRK/CDK20, but its molecular activity and precise cellular location remain unresolved. Loss of FAM149B1 function causes elongated cilia with abnormal tip accumulation of IFT proteins and impaired Hedgehog signaling responses. Biallelic truncating variants cause a Joubert-related ciliopathy. The relative functions of the natural 582- and 528-residue products remain unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:30905400 Bi-allelic Mutations in FAM149B1 Cause Abnormal Primary Cili... | KEEP AS NON CORE | Summary: FAM149B1 associates with TBC1D32/BROMI in controlled cellular co-immunoprecipitation assays. Reason: PMID:30905400 Figure 5 reports co-immunoprecipitation of GFP-tagged FAM149B1 with MYC-DDK-tagged TBC1D32 in human HEK293 cells, with matched IgG controls and input blots. PMID:35609210 Figure 6 and Supplementary Figure S3 independently support tagged cellular association and map BROMI association to the FAM149B1 C-terminal region, with an EGFP-alone control. These are lysate co-association assays, not purified binary binding or a native stoichiometric complex. Retain the supported generic interaction as non-core under the standing campaign exception. Current adaptor and cargo-adaptor definitions were considered, but the experiments do not establish FAM149B1-mediated bridging of defined partners, motor-cargo coupling, or kinase regulation; the proposed cyclin-like CCRK mechanism remains a hypothesis. The 2019 construct sequence is unspecified, while the 2022 human NM_173348.2-derived full-length and engineered fragments do not establish equivalent activity of the natural 528-residue product. |
| GO:0005929 cilium | IEA GO_REF:0000044 | UNDECIDED | Summary: The cilium mapping is traceable, but the physical location of human FAM149B1 remains unresolved. Reason: GO_REF:0000044 correctly maps UniProt subcellular location SL-0066 to GO:0005929. The Q96BN6 record assigns cilium with ECO:0000305 based on PMID:30905400, so this is an inferred location rather than a direct FAM149B1 microscopy result. That original images ciliary markers and IFT proteins in patient fibroblasts; it establishes altered ciliary morphology and protein distribution. In the independent human RPE1 knockout/rescue study, the authors explicitly could not show distinct ciliary localization of FAM149B1 (PMID:35609210, Discussion). This does not demonstrate absence, and GO:0005929 includes cytoplasmic ciliary parts as well as the projecting organelle. A transient, low-abundance or base-associated pool remains possible. Retain the positive curated inference, but leave this exact target-location assertion unresolved rather than infer residence solely from ciliary function or infer universal loss from unsuccessful localization. Neither natural splice product has a separately established location in these assays. Propagation Review Root cause: UNRESOLVED Sources checked: UniProtKB-SubCell:SL-0066 UNRESOLVED The official SL-0066-to-GO:0005929 translation and Q96BN6 CC source are verified. Uncertainty concerns the physical target location behind ECO:0000305/PubMed:30905400, not a missing or erroneous vocabulary mapping. The later human study could not resolve distinct target ciliary localization. |
| GO:0060271 cilium assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Retain the inherited cilium-assembly role, including normal extension and architecture. Reason: The actual PANTHER v19 tree places the exact human 582-residue sequence at PTN002528684 below PTN002842395, and the actual IBD asserts GO:0060271 using experimental descendant UniProtKB:Q96BN6. No NOT assertion occurs on the target path; target self-WITH is valid experimental grounding. PMID:30905400 Figure 3 and Supplementary Figure S1 show normal ciliation frequency but elongated, bulbous cilia with abnormal IFT88/IFT46 tip accumulation in patient fibroblasts. Normal frequency does not exclude defective assembly or extension of the ciliary structure, and UniProt VAR_083866 already records that endpoint. PMID:35609210 Figure 7 independently demonstrates elongated cilia after human RPE1 knockout and restoration of normal length by intact full-length FAM149B1. Neither the 1–179 nor the 180–582 fragment restores length in those assays. Retain the original assembly assertion rather than generalizing to organization solely because cilia are present. The evidence does not establish a FAM149B1 kinase-regulatory mechanism or equivalent activity of the natural 528-residue product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002842395 SUPPORTS TRANSFER The exact human target sequence is a verified descendant of PTN002842395 in the actual v19 tree. The node carries the cilium-assembly IBD with Q96BN6 experimental descendant evidence, and no NOT occurs along the target path. Human morphology and knockout/rescue findings support the inherited assembly role; normal ciliation frequency alone does not establish loss of that role or an ancestral term-scoping error. |
| GO:0060271 cilium assembly | IMP PMID:30905400 Bi-allelic Mutations in FAM149B1 Cause Abnormal Primary Cili... | ACCEPT | Summary: FAM149B1 supports normal cilium assembly and extension, with abnormal length and tip architecture after disruption. Reason: PMID:30905400 Figure 3 and Supplementary Figure S1 show that fibroblasts from the FAM149B1 p.Lys119Ilefs*18 patient retain normal ciliation frequency but have longer cilia and abnormal IFT88/IFT46 accumulation at bulbous tips. Cilium assembly is not restricted to an all-or-none count of cells initiating a cilium; these structural phenotypes do not justify replacing the curator’s assembly assertion by its broader organization parent. Independently, PMID:35609210 Figure 7 and Supplementary Figure S2 show elongated cilia in human RPE1 FAM149B1 knockout cells and restoration of length by intact tagged full-length FAM149B1. Neither engineered 1–179 nor 180–582 fragment restores length, although 1–179 improves IFT88 distribution. The 2019 patient and 2022 knockout/rescue experiments remain distinct. No specific kinase-regulatory activity, direct IFT transport-rate measurement or functional equivalence of the natural 528-residue product is asserted. |
| GO:0061512 protein localization to cilium | IBA GO_REF:0000033 | ACCEPT | Summary: Accept the inherited role in maintaining normal protein distribution within cilia. Reason: The exact human sequence and actual GO:0061512 IBD from PTN002842395 are verified on the saved PANTHER v19 target path, with valid experimental self-WITH evidence and no target-path NOT. The current term includes proteins transported to or maintained in a location within a cilium; it does not require a demonstrated defect in initial ciliary entry. PMID:30905400 shows selective IFT88/IFT46 tip pooling in patient fibroblasts, while IFT122 shaft staining remains comparable to controls. In PMID:35609210, human RPE1 knockout cells accumulate IFT88 and ICK at ciliary tips; full-length FAM149B1-EGFP rescues the IFT88-distribution defect. The engineered 1–179 fragment also improves IFT88 distribution without restoring normal ciliary length, separating this endpoint from length control. These controlled target phenotypes support a contribution to protein localization/maintenance within the cilium. They do not establish an autonomous transport motor, cargo-adaptor activity, direct IFT88 binding, a measured trafficking rate, or physical residence of FAM149B1 in the ciliary compartment. The natural 528-residue product was not tested independently. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002842395 SUPPORTS TRANSFER The actual GO:0061512 IBD and exact human target descent agree. Target experimental self-WITH is legitimate descendant grounding; human patient and independent knockout/rescue data support the maintenance-inclusive term without assigning FAM149B1 an unmeasured motor or kinase activity. |
| GO:0061512 protein localization to cilium | IMP PMID:30905400 Bi-allelic Mutations in FAM149B1 Cause Abnormal Primary Cili... | ACCEPT | Summary: FAM149B1 helps maintain the normal distribution of proteins within cilia. Reason: The current GO:0061512 definition includes transport to, or maintenance at a location within, a cilium. PMID:30905400 Figure 3 and Supplementary Figure S1 show abnormal IFT88/IFT46 tip accumulation in human FAM149B1-mutant fibroblasts, with IFT122 distribution relatively preserved. PMID:35609210 Figure 7 independently shows IFT88 tip accumulation in human RPE1 FAM149B1 knockout cells and rescue by full-length FAM149B1 and the engineered 1–179 fragment; normal cilium length was restored by intact full-length FAM149B1, whereas neither the 1–179 nor the 180–582 fragment restored it in these assays. These perturbation/rescue results support the retained localization process without identifying FAM149B1 as a motor or cargo adaptor. Retrograde turnaround is a mechanistic interpretation, not a time-resolved FAM149B1-knockout transport measurement. The authors could not distinctly demonstrate ciliary localization of FAM149B1 itself, which is a separate claim from its role in IFT-protein distribution. No equivalence of the two natural products is inferred. |
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Download this section (compressed HTML)Q: Which molecular step connects FAM149B1 association with BROMI and CCRK to cilium length and IFT-protein distribution, and do these two outputs require the same interaction or activity?
Q: Where do the natural 582- and 528-residue products act, and do their abundance, localization and contributions to ciliary organization differ across human cell types or cell-cycle states?
Experiment: Compare sequence-verified full-length FAM149B1, separation-of-function mutants and the existing engineered fragments at matched near-endogenous levels in human knockout/rescue cells. Measure live IFT trajectories, tip dwell times, cilium length and IFT88 distribution separately. In parallel, test purified CCRK-dependent ICK phosphorylation with and without FAM149B1 and BROMI, with kinase-inactive, partner-omission and protein-integrity controls. Measure binding separately from kinase output, so cellular association is not treated as a biochemical mechanism.
Hypothesis: Dissociating the molecular and cellular endpoints can distinguish a direct effect on CCRK activity from partner-dependent organization or another mechanism, without presupposing that FAM149B1 is a kinase regulator or transport motor.
Experiment: Establish product-specific transcript and protein measurements in human ciliated cells, then compare the two sequence-verified natural products at matched levels. Use endogenous tagging and independently validated detection with knockout controls to test ciliary base, shaft and other cellular pools over time, preserving the possibility of transient or low-abundance localization. Relate those measurements to separate rescue of length and protein-distribution phenotypes; keep engineered fragments and patient truncations distinct from natural products.
Hypothesis: The natural splice difference may alter localization or partner-dependent function, but equivalent behavior and transient residence are outcomes to test rather than assumptions imposed by the full-length rescue result.
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