CFAP410 (C21ORF2/LRRC76) is a leucine-rich-repeat-containing protein that associates with NEK1 and is required for primary-cilium formation and function. It localizes to ciliary basal bodies and photoreceptor ciliary structures and also has a cytoplasmic pool. Loss or pathogenic variants impair ciliogenesis, with associated intraflagellar-transport and Hedgehog-signaling defects in human cellular models. CFAP410 also supports homologous-recombination repair of DNA double-strand breaks through a mechanism linked to NEK1; a catalytic activity of CFAP410 itself has not been established. Biallelic variants cause retinal ciliopathies with variable skeletal involvement, and some variants are associated with amyotrophic lateral sclerosis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001750 photoreceptor outer segment | IDA PMID:27548899 Identification of Novel Mutations in the LRR-Cap Domain of C... | UNDECIDED | Summary: The specific photoreceptor outer-segment localization remains unresolved. Reason: The Suga full text was not accessible, and its abstract identifies photoreceptor cilia without resolving the outer-segment compartment. Independent connecting-cilium localization does not establish outer-segment localization: the GO terms are distinct. PMID:26974433 reports human CFAP410-EGFP restricted to cilia rather than surrounding outer-segment structures in mouse photoreceptors, but this construct and cellular context cannot by themselves refute the original Suga observation. Neither the IDA nor its electronic subcellular-location mapping has independently verified support for this precise compartment; retain UNDECIDED pending the original images and methods rather than assume acceptance or remap from an abstract. Supporting Evidence: PMID:27548899 the protein localized to the photoreceptor cilia in the adult retina. PMID:26294103 Immunohistochemical studies in human, pig and mouse retinas localised C21orf2 protein to the ciliary structures of the photoreceptor cell (the daughter basal body, the centriole adjacent to the basal body, and the connecting cilium). |
| GO:0001750 photoreceptor outer segment | IEA GO_REF:0000044 | UNDECIDED | Summary: The specific photoreceptor outer-segment localization remains unresolved. Reason: The Suga full text was not accessible, and its abstract identifies photoreceptor cilia without resolving the outer-segment compartment. Independent connecting-cilium localization does not establish outer-segment localization: the GO terms are distinct. PMID:26974433 reports human CFAP410-EGFP restricted to cilia rather than surrounding outer-segment structures in mouse photoreceptors, but this construct and cellular context cannot by themselves refute the original Suga observation. Neither the IDA nor its electronic subcellular-location mapping has independently verified support for this precise compartment; retain UNDECIDED pending the original images and methods rather than assume acceptance or remap from an abstract. Supporting Evidence: PMID:27548899 the protein localized to the photoreceptor cilia in the adult retina. PMID:26294103 Immunohistochemical studies in human, pig and mouse retinas localised C21orf2 protein to the ciliary structures of the photoreceptor cell (the daughter basal body, the centriole adjacent to the basal body, and the connecting cilium). |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | REMOVE | Summary: A high-throughput interaction with ATOX1 is recorded by this IPI annotation. Reason: Generic protein binding provides no informative molecular function for CFAP410. Remove this uninformative term without disputing the interaction detected in the systematic interactome study. The ATOX1 interaction alone does not establish copper transfer, copper binding, or a specific adapter activity. Supporting Evidence: PMID:25416956 By systematically screening half of the interactome space with minimal inspection bias, we more than doubled the number of high-quality binary PPIs available from the literature. |
| GO:0005515 protein binding | IPI PMID:26167768 An siRNA-based functional genomics screen for the identifica... | MODIFY | Summary: CFAP410 associates with the serine/threonine kinase NEK1, a functionally relevant partner in ciliogenesis and homologous recombination. Reason: Replace generic protein binding with protein serine/threonine kinase binding to capture the experimentally identified partner class. Co-immunoprecipitation and mutation-sensitive association support binding within the complex, without establishing that CFAP410 independently activates NEK1 catalysis or that the association is necessarily direct (PMIDs:26167768,26290490,37188479). Proposed replacements: protein serine/threonine kinase binding Supporting Evidence: PMID:26167768 Importantly, both the p.Arg73Pro and p.Leu224Pro mutations in C21orf2 abolished the interaction with NEK1 |
| GO:0005515 protein binding | IPI PMID:26290490 The NEK1 interactor, C21ORF2, is required for efficient DNA ... | MODIFY | Summary: CFAP410 associates with the serine/threonine kinase NEK1, a functionally relevant partner in ciliogenesis and homologous recombination. Reason: Replace generic protein binding with protein serine/threonine kinase binding to capture the experimentally identified partner class. Co-immunoprecipitation and mutation-sensitive association support binding within the complex, without establishing that CFAP410 independently activates NEK1 catalysis or that the association is necessarily direct (PMIDs:26167768,26290490,37188479). Proposed replacements: protein serine/threonine kinase binding Supporting Evidence: PMID:26290490 The fact that C21ORF2 interacts with NEK1 biochemically predicts that they interact functionally as well. PMID:26290490 Knockdown of both C21ORF2 and NEK1 resulted in defective HR repair, as shown by significantly decreased percentages of GFP-positive (HR-repaired) cells |
| GO:0005737 cytoplasm | IDA PMID:21834987 Identification and characterization of a set of conserved an... | REMOVE | Summary: Remove the unsupported Bai2011 cytoplasm IDA; independent evidence retains cytoplasmic localization. Reason: The complete Bai2011 text, Figure 8 and supplements show that its localization experiment tested ARC, FAM40A, FAM40B, FMNL3 and ZRANB1, not CFAP410. Its CFAP410 knockdown phenotype does not support an IDA localization assertion. Apply the same evidence-specific decision as for the plasma-membrane row. The separate PMID:26290490 cytoplasm IDA remains ACCEPT; removing this unsupported assertion does not deny the biological localization. Preserve the original source fields and record this evidence-support defect on the annotation, without classifying the paper itself as MISCITED. Supporting Evidence: PMID:26290490 C21ORF2 was observed to be localized to the cytoplasm in these cells PMID:21834987 To investigate how overexpression of selected PMMs affected cell morphology and cytoskeletal organisation and to determine their localization, cDNAs for ARC, FAM40A, FAM40B, FMNL3 and ZRANB1 were cloned downstream of GFP and transfected into PC3 cells (Figure 8A). |
| GO:0005737 cytoplasm | IDA PMID:26290490 The NEK1 interactor, C21ORF2, is required for efficient DNA ... | ACCEPT | Summary: CFAP410 has an experimentally observed cytoplasmic pool. Reason: Cytoplasmic localization is directly documented for HA-tagged CFAP410 in HeLa cells in PMID:26290490 and is consistent with its basal-body localization. Retain this independently supported cytoplasm IDA alongside the more informative ciliary locations; the unsupported Bai2011 IDA is removed separately. Supporting Evidence: PMID:26290490 C21ORF2 was observed to be localized to the cytoplasm in these cells |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: CFAP410 has an experimentally observed cytoplasmic pool. Reason: Cytoplasmic localization is directly documented for HA-tagged CFAP410 in HeLa cells in PMID:26290490 and is consistent with its basal-body localization. Retain this broader location alongside the more informative ciliary locations. For the PMID:21834987 row, independent localization evidence corroborates the term; the accessible screening paper does not independently resolve its precise localization experiment. Supporting Evidence: PMID:26290490 C21ORF2 was observed to be localized to the cytoplasm in these cells |
| GO:0005739 mitochondrion | IDA PMID:9325172 Immunochemical characterization of a novel mitochondrially l... | KEEP AS NON CORE | Summary: An early immunochemical study reported mitochondrial CFAP410 localization. Reason: PMID:9325172 explicitly reports antibody staining and co-localization with a mitochondrial dye in human cells; the available abstract does not establish an isoform-specific mitochondrial pool. Retain this historical localization as non-core. In a distinct context, human CFAP410 (NM_004928.2) fused to EGFP and expressed in mouse photoreceptors localized to connecting cilia and showed a distribution complementary to a mitochondrial marker (PMID:26974433, Figure 6O–Q). This argues against universal mitochondrial localization, not against the original human-cell observation. Variant-induced respiratory defects do not themselves demonstrate mitochondrial residence or an intrinsic mitochondrial enzymatic function. Supporting Evidence: PMID:9325172 Immunofluorescence studies and co-staining with a mitochondrial-specific dye suggest the subcellular localization of the protein to mitochondria. PMID:26974433 We stained mitochondria by Kusabira-Orange fused with mitochondria localizing signal and found that subcellular distribution of the C21orf2-EGFP fusion protein was complementary to that of mitochondria (Fig 6O–6Q). |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: An early immunochemical study reported mitochondrial CFAP410 localization. Reason: PMID:9325172 explicitly reports antibody staining and co-localization with a mitochondrial dye in human cells; the available abstract does not establish an isoform-specific mitochondrial pool. Retain this historical localization as non-core. In a distinct context, human CFAP410 (NM_004928.2) fused to EGFP and expressed in mouse photoreceptors localized to connecting cilia and showed a distribution complementary to a mitochondrial marker (PMID:26974433, Figure 6O–Q). This argues against universal mitochondrial localization, not against the original human-cell observation. Variant-induced respiratory defects do not themselves demonstrate mitochondrial residence or an intrinsic mitochondrial enzymatic function. Supporting Evidence: PMID:9325172 Immunofluorescence studies and co-staining with a mitochondrial-specific dye suggest the subcellular localization of the protein to mitochondria. PMID:26974433 We stained mitochondria by Kusabira-Orange fused with mitochondria localizing signal and found that subcellular distribution of the C21orf2-EGFP fusion protein was complementary to that of mitochondria (Fig 6O–6Q). |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: HPA immunofluorescence supports a cytosolic pool of CFAP410. Reason: The HPA subcellular page for ENSG00000160226, checked during this review, reports cytosol with supported reliability in A-431, U-251MG and U2OS cells. This agrees with the cytoplasmic localization in PMID:26290490. Retain cytosol alongside ciliary basal-body localization. HPA030284 ICC reliability is standard literature-supported validation, not enhanced knockdown/tag validation; its Western-blot result is uncertain. The independent cytoplasmic localization literature is therefore important corroboration. Supporting Evidence: PMID:26290490 C21ORF2 was observed to be localized to the cytoplasm in these cells |
| GO:0005886 plasma membrane | IDA PMID:21834987 Identification and characterization of a set of conserved an... | REMOVE | Summary: Remove the unsupported CFAP410 plasma-membrane IDA attributed to Bai2011; native plasma-membrane association remains an unresolved biological possibility. Reason: Complete full-text, Figure 8 image and supplementary-material inspection of PMID:21834987 establish that its GFP localization experiment tested ARC, FAM40A, FAM40B, FMNL3 and ZRANB1, not CFAP410. CFAP410 appears in the knockdown morphology screen, where cortical actin is measured; this is not a CFAP410 localization assay. Remove this evidence-specific annotation because its claimed direct-assay support is demonstrably misattributed. This decision follows inspection of the actual experiments and supplemental contents, not absence from an abstract or incompatibility with a ciliary role. Live QuickGO traces the row to UniProt on 20110926; mouse annotations transferred from human provide no independent experimental corroboration. The targeted OpenScientist audit corroborates the source mismatch. Its stronger claim that plasma-membrane localization is biologically contradicted is not adopted: no NOT annotation is proposed, and a native peripheral membrane pool remains a question for controlled experiments. Supporting Evidence: PMID:21834987 To investigate how overexpression of selected PMMs affected cell morphology and cytoskeletal organisation and to determine their localization, cDNAs for ARC, FAM40A, FAM40B, FMNL3 and ZRANB1 were cloned downstream of GFP and transfected into PC3 cells (Figure 8A). PMID:21834987 GFP-ARC, FAM40A, FAM40B and FMNL3 proteins showed cytoplasmic localization with some enrichment on the plasma membrane compared to GFP alone (Figure 8B). file:human/CFAP410/CFAP410-deep-research-openscientist.md No supplementary file reports any GFP or antibody localization of C21orf2/CFAP410 or any plasma-membrane assay of it. |
| GO:0032391 photoreceptor connecting cilium | IEA GO_REF:0000107 | ACCEPT | Summary: CFAP410 is localized to the photoreceptor connecting cilium. Reason: The mouse-to-human transfer is biologically consistent with direct immunohistochemistry of human, pig and mouse retina in PMID:26294103. PMID:26167768 also localizes the protein to the base of the mouse photoreceptor connecting cilium. Accept this conserved ciliary localization. Supporting Evidence: PMID:26294103 Immunohistochemical studies in human, pig and mouse retinas localised C21orf2 protein to the ciliary structures of the photoreceptor cell (the daughter basal body, the centriole adjacent to the basal body, and the connecting cilium). PMID:26167768 C21orf2 localises to the basal body in mIMCD3 and hTERT-RPE1 cells and to the base of the connecting cilium in mouse photoreceptors |
| GO:0032391 photoreceptor connecting cilium | ISS GO_REF:0000024 | ACCEPT | Summary: CFAP410 is localized to the photoreceptor connecting cilium. Reason: The mouse-to-human transfer is biologically consistent with direct immunohistochemistry of human, pig and mouse retina in PMID:26294103. PMID:26167768 also localizes the protein to the base of the mouse photoreceptor connecting cilium. Accept this conserved ciliary localization. Supporting Evidence: PMID:26294103 Immunohistochemical studies in human, pig and mouse retinas localised C21orf2 protein to the ciliary structures of the photoreceptor cell (the daughter basal body, the centriole adjacent to the basal body, and the connecting cilium). PMID:26167768 C21orf2 localises to the basal body in mIMCD3 and hTERT-RPE1 cells and to the base of the connecting cilium in mouse photoreceptors |
| GO:0036064 ciliary basal body | IDA GO_REF:0000052 | ACCEPT | Summary: CFAP410 localizes at the ciliary basal body, where it associates with ciliary proteins including NEK1. Reason: Basal-body localization is directly observed in human hTERT-RPE1 cells (PMID:26167768) and photoreceptor ciliary structures (PMID:26294103), and is also reported with supported reliability by HPA. The electronic and HPA rows are consistent with these independent experimental observations. HPA030284 is rated supported by literature rather than enhanced genetic validation, and its Western-blot result is uncertain; independent basal-body experiments provide the stronger grounding. Supporting Evidence: PMID:26167768 C21orf2 localises to the basal body in mIMCD3 and hTERT-RPE1 cells and to the base of the connecting cilium in mouse photoreceptors |
| GO:0036064 ciliary basal body | IDA PMID:26167768 An siRNA-based functional genomics screen for the identifica... | ACCEPT | Summary: CFAP410 localizes at the ciliary basal body, where it associates with ciliary proteins including NEK1. Reason: Basal-body localization is directly observed in human hTERT-RPE1 cells (PMID:26167768) and photoreceptor ciliary structures (PMID:26294103), and is also reported with supported reliability by HPA. The electronic and HPA rows are consistent with these independent experimental observations. Supporting Evidence: PMID:26167768 C21orf2 localises to the basal body in mIMCD3 and hTERT-RPE1 cells and to the base of the connecting cilium in mouse photoreceptors |
| GO:0036064 ciliary basal body | IDA PMID:26294103 C21orf2 is mutated in recessive early-onset retinal dystroph... | ACCEPT | Summary: CFAP410 localizes at the ciliary basal body, where it associates with ciliary proteins including NEK1. Reason: Basal-body localization is directly observed in human hTERT-RPE1 cells (PMID:26167768) and photoreceptor ciliary structures (PMID:26294103), and is also reported with supported reliability by HPA. The electronic and HPA rows are consistent with these independent experimental observations. Supporting Evidence: PMID:26294103 Immunohistochemical studies in human, pig and mouse retinas localised C21orf2 protein to the ciliary structures of the photoreceptor cell (the daughter basal body, the centriole adjacent to the basal body, and the connecting cilium). |
| GO:0036064 ciliary basal body | IEA GO_REF:0000120 | ACCEPT | Summary: CFAP410 localizes at the ciliary basal body, where it associates with ciliary proteins including NEK1. Reason: Basal-body localization is directly observed in human hTERT-RPE1 cells (PMID:26167768) and photoreceptor ciliary structures (PMID:26294103), and is also reported with supported reliability by HPA. The electronic and HPA rows are consistent with these independent experimental observations. Supporting Evidence: PMID:26167768 C21orf2 localises to the basal body in mIMCD3 and hTERT-RPE1 cells and to the base of the connecting cilium in mouse photoreceptors |
| GO:0097733 photoreceptor cell cilium | IEA GO_REF:0000120 | ACCEPT | Summary: CFAP410 is a photoreceptor ciliary protein. Reason: The broad electronic photoreceptor-cell-cilium assignment is supported by immunohistochemical studies of mammalian retina (PMIDs:26294103,27548899). This encompasses the separately supported connecting-cilium and outer-segment locations and is not an unsupported extension to all flagellar functions. Supporting Evidence: PMID:26294103 Immunohistochemical studies in human, pig and mouse retinas localised C21orf2 protein to the ciliary structures of the photoreceptor cell (the daughter basal body, the centriole adjacent to the basal body, and the connecting cilium). PMID:27548899 the protein localized to the photoreceptor cilia in the adult retina. |
| GO:1905515 non-motile cilium assembly | IMP PMID:37188479 Functional characterization of C21ORF2 association with the ... | NEW | Summary: CFAP410 is required for primary-cilium formation in human cells. Reason: CRISPR loss and rescue studies in ARPE-19 cells demonstrate a requirement for CFAP410 in primary ciliogenesis. Earlier knockdown/rescue experiments (PMID:26167768) and human neuronal studies (PMID:39703094) corroborate this role. Add this missing process annotation; this does not imply that CFAP410 is a ciliary motor or an enzyme. Supporting Evidence: PMID:37188479 Here, we show that ARPE-19 cells lacking C21ORF2, like cells lacking NEK1, also show major defects in ciliogenesis. |
| GO:0000724 double-strand break repair via homologous recombination | IMP PMID:26290490 The NEK1 interactor, C21ORF2, is required for efficient DNA ... | NEW | Summary: CFAP410 supports efficient homologous-recombination repair of DNA double-strand breaks. Reason: CFAP410 knockdown reduces HR reporter repair, and the 2015 study distinguishes this defect from NHEJ and G2 checkpoint activation. The HR requirement was independently reproduced in PMID:37188479. Add a process annotation, without attributing a DNA repair enzyme activity or direct recruitment to DNA lesions to this cytoplasmic NEK1-associated protein. Supporting Evidence: PMID:26290490 Knockdown of both C21ORF2 and NEK1 resulted in defective HR repair, as shown by significantly decreased percentages of GFP-positive (HR-repaired) cells |
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Download this section (compressed HTML)Q: Does CFAP410 directly bind NEK1 and regulate substrate selection, localization, stability or catalytic activity, and are these mechanisms shared between ciliogenesis and homologous recombination?
Q: Are reported mitochondrial and plasma-membrane pools isoform-, cell-type- or antibody-dependent, and do endogenous tagging and knockout controls confirm them?
Q: Are IFT and Hedgehog defects primary consequences of CFAP410 loss, or downstream effects of altered cilium assembly and structure?
Experiment: Reconstitute purified human NEK1 and CFAP410, compare wild-type and binding-disrupting variants for physical association, kinase kinetics and substrate phosphorylation, and rescue matched CFAP410-null cells with variants controlled for abundance.
Hypothesis: CFAP410 supports NEK1 function through a separable binding-dependent mechanism.
Type: Biochemical reconstitution and cellular rescue
Experiment: Compare endogenous isoform-aware tags in retinal epithelial cells, motor neurons and B cells, including EBV-transformed B cells. Confirm tagged-protein function and use CFAP410-null controls. Resolve membrane-associated signal from adjacent basal bodies/cilia by three-dimensional imaging with compartment markers, then test membrane association by orthogonal fractionation with plasma-membrane, mitochondrial, ER and cytosolic purity controls. Use extraction conditions that distinguish peripheral association from integral-membrane residence; extracellular surface labeling alone cannot assess a cytosolic peripheral pool.
Hypothesis: Native peripheral plasma-membrane association can be distinguished from basal-body/ciliary localization and may depend on isoform or cell context.
Type: Endogenous tagging, compartment-resolved imaging and controlled fractionation
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