DNAAF19

Summary: Laterality-dependent heart-looping phenotype.

Reason: Human CCDC103 variants and zebrafish schmalhans experiments in PMID:22581229 connect defective motile cilia with abnormal organ situs and heart looping. Retain this developmental consequence of the conserved assembly function; it does not establish a separate cardiac morphogenesis activity.

Summary: Human-protein rescue supports ciliary motility.

Reason: Wild-type human CCDC103 rescued zebrafish mutant motility and dynein arms; respiratory cilia from affected humans had variable motility defects. Retain cilium movement as a supported system-level consequence of arm assembly and attachment, without assigning motor ATPase activity to DNAAF19.

Summary: Inherited epithelial ciliary fluid-movement role.

Reason: The human leaf PTN002523902 descends from the stated PTN002005038 node in PTHR28572; current tree annotations and QuickGO retain this process. The available IBD snapshot does not contain the separate GO:0003351 line, so its complete historical donor trail was not recovered. Positive zebrafish epithelial-cilium and human respiratory motility evidence in PMID:22581229 supports retaining the contextual process. This is not rejection based on a short donor list.

Summary: HGS association in verified binary assays.

Reason: Three positive IntAct records include pairwise and validated Y2H for DNAAF19 and HGS (O14964; PMID:25416956). HGS is an endosomal sorting/signaling protein, not a kinase merely because its name contains tyrosine kinase substrate. The study does not establish DNAAF19 as an ESCRT subunit or signaling adaptor, and no more specific binding class is assigned here.

Summary: Binary binding to the homeobox transcription factor MEOX2.

Reason: The exact positive MEOX2 P50222 pair was verified in the original Y2H map and IntAct. Official MEOX2 biology includes DNA-dependent transcriptional regulation, supporting DNA-binding transcription factor binding. This class describes the binding partner; it does not make DNAAF19 a transcriptional regulator or establish a native nuclear role.

Proposed replacements: DNA-binding transcription factor binding

Summary: Binary binding to the VAC14 scaffold.

Reason: Verified pairwise/validated Y2H supports the DNAAF19–VAC14 Q08AM6 pair. Official VAC14 evidence establishes a scaffold that assembles and coordinates the PIKFYVE–FIG4 phosphoinositide regulatory complex. Scaffold protein binding is therefore more informative than generic binding; DNAAF19 membership in that native complex or control of its lipid enzymes was not tested.

Proposed replacements: scaffold protein binding

Summary: Binary association with R3HCC1L.

Reason: The exact Q7Z5L2 pair has three positive screening, pairwise and validated-Y2H records. The official partner record does not establish a specific molecular role sufficient for a narrower binding term. Retain the supported association as non-core without inferring chaperone or adaptor activity from a coiled-coil protein name.

Summary: Binary binding to the ATPase RUVBL2.

Reason: The exact Q9Y230 pair is supported by the original binary map and validated-Y2H record. Official RUVBL2 annotation includes experimentally supported ATP hydrolysis. GO:0051117 captures binding to this ATPase; the pair does not show that DNAAF19 hydrolyzes ATP, remodels chromatin, or modulates RUVBL2 catalysis.

Proposed replacements: ATPase binding

Summary: VAC14 binding retained in a variant assay.

Reason: PMID:29892012 Methods require a positive wild-type Y2H pair and exclude autoactivators before variant testing. IntAct EBI-22272037 maps the exact DNAAF19–VAC14 pair and records a non-disruptive VAC14 position-127 variant. With VAC14 independently established as a scaffold, refine the partner class to scaffold protein binding. The variant experiment is not proof of endogenous complex stoichiometry or phosphoinositide regulation by DNAAF19.

Proposed replacements: scaffold protein binding

Summary: HGS binding persists in the assayed DNAAF19 variant.

Reason: PMID:31515488 compares WT and variant ORFs with autoactivation controls and repeat disruption screens. Exact IntAct EBI-22141249 records the HGS pair and non-disruptive DNAAF19 position-27 variant rs149553827. Retain this positive binary association; neither a kinase-binding refinement nor a native signaling mechanism follows from the partner name.

Summary: VAC14 scaffold binding in WT/variant comparisons.

Reason: Exact IntAct EBI-22128811 records DNAAF19–VAC14 and non-disruptive DNAAF19 variants at positions 112 and 154 (rs371291293 and rs145457535). The original Methods explicitly compare WT and mutant interactions. The independent official VAC14 scaffold classification supports scaffold protein binding; these particular variants must not be equated with every change at residue 154 or with the pathogenic H154P mechanism.

Proposed replacements: scaffold protein binding

Summary: HuRI binary association with PNMA6A.

Reason: Three positive IntAct records, including validated Y2H, map the pair to P0CW24 (PNMA6A; historical PNMA6C naming). The partner has no established function in the inspected official record that supports a narrower molecular-function class. Retain this assay-supported interaction without assigning a native ciliary mechanism.

Summary: HuRI binding to the DNA-binding transcription factor PAX6.

Reason: The exact P26367 pair has positive pairwise and validated-Y2H records, with reference sequences independently authenticated. PAX6 is a DNA-binding transcription factor. Refine the binding class accordingly, while leaving endogenous co-localization, regulation and physiological significance unresolved.

Proposed replacements: DNA-binding transcription factor binding

Summary: HuRI binding to the PKA regulatory subunit PRKAR1B.

Reason: Five positive records support the P31321 pair across two Y2H configurations and validation. PRKAR1B is the cAMP-responsive regulatory subunit, not the catalytic protein kinase. A kinase-binding term would conflate those roles; retain the positive generic association without asserting that DNAAF19 regulates PKA.

Summary: HuRI binding to the homeobox transcription factor MEOX1.

Reason: The exact positive P50221 pair is supported by pairwise and validated Y2H. MEOX1 has established sequence-dependent promoter regulation, even though some reported transcriptional effects use other mechanisms. DNA-binding transcription factor binding states the justified partner class without transferring transcriptional activity to DNAAF19.

Proposed replacements: DNA-binding transcription factor binding

Summary: HuRI binary binding to sulfite oxidase.

Reason: The positive P51687 pair and reference sequences are verified. SUOX is an enzyme with an experimentally supported sulfite-oxidation reaction, so enzyme binding is an appropriate class refinement. The heterologous assay does not demonstrate a mitochondrial encounter, regulation of SUOX, or sulfite catalysis by DNAAF19.

Proposed replacements: enzyme binding

Summary: HuRI independently supports VAC14 scaffold binding.

Reason: The exact Q08AM6 pair has positive screening, pairwise and validated-Y2H records. VAC14 is a defined scaffold of the PIKFYVE–FIG4 regulatory complex, supporting GO:0097110. This independently corroborates binary binding without establishing endogenous incorporation or a lipid-metabolic function for DNAAF19.

Proposed replacements: scaffold protein binding

Summary: HuRI binary binding to the protein kinase PKN1.

Reason: The positive Q16512 pair is verified, and official PKN1 evidence establishes serine/threonine protein kinase catalysis. Protein kinase binding is the supported narrower class. The experiment does not show DNAAF19 phosphorylation or kinase regulation.

Proposed replacements: protein kinase binding

Summary: HuRI binding to GRIPAP1 with a sufficient-region annotation.

Reason: Eight positive records annotate GRIPAP1 residues 358–841 as a sufficient binding region. Their ROGIDs authenticate the full 841-residue reference parent, not the engineered fragment sequence. The official scaffold activity concerns processed C-terminal chain 599–841, but the contact within the larger annotated region has not been localized or linked to that activated chain. Retain the positive association without claiming recognition of a native signaling scaffold or DNAAF19 control of JNK.

Summary: HuRI binding to a sequence-verified MEOX2 clone.

Reason: The literal Q6FHY5 partner is retained. Its verified 303-residue sequence differs from reviewed MEOX2 P50222 only by deletion of one glutamine in the N-terminal tract; the homeodomain is unchanged. The positive validated-Y2H pair therefore supports DNA-binding transcription factor binding to this MEOX2 construct. This is not an accession rewrite or proof that all MEOX2 isoforms interact.

Proposed replacements: DNA-binding transcription factor binding

Summary: HuRI association with USHBP1.

Reason: The exact Q8N6Y0 pair has three positive screening, pairwise and validated-Y2H records. The inspected official USHBP1 record does not establish a narrower partner class; its harmonin-binding name does not make DNAAF19 a scaffold or actin regulator. Retain the positive interaction as non-core.

Summary: HuRI association with reticulocalbin-3.

Reason: The exact Q96D15 pair and reference sequence are verified. RCN3 is described as a probable ER chaperone, but this screen does not establish a chaperone-recognition mechanism and the inspected partner annotation does not settle that class. Retain the positive generic interaction; neither compartment mismatch alone nor a tentative functional label justifies removal or a confident refinement.

Summary: HuRI association with the specified CENPN isoform.

Reason: The three positive records explicitly identify Q96H22-3. Its C-terminal replacement was reconstructed against the official sequence and the ROGID matches. Preserve this product-specific partner identity; the screen does not show that DNAAF19 belongs to the centromere complex or binds a nucleosome.

Summary: HuRI binary binding to the lipid enzyme PLAAT1.

Reason: The exact positive Q9HDD0 pair is verified. Official PLAAT1 evidence establishes phospholipase and acyltransferase catalysis, supporting enzyme binding. No lipid reaction or regulation of that enzyme is assigned to DNAAF19 from the pair.

Proposed replacements: enzyme binding

Summary: HuRI binding to the cytoskeletal regulator PICK1.

Reason: The exact Q9NRD5 binary pair is supported by three positive records. Independently, PICK1 regulates actin reorganization through Arp2/3-dependent mechanisms. GO:0005519 describes binding to that established partner class; it does not imply that DNAAF19 itself inhibits Arp2/3 or regulates neuronal morphology.

Proposed replacements: cytoskeletal regulatory protein binding

Summary: Primary AP-MS supports a contextual GRIPAP1 association.

Reason: The paper-linked primary U2OS AP-MS graph contains CCDC103 bait node 582992, GRIPAP1 prey node 566184 and edge 582996. The original Methods use tagged-bait affinity capture and mass spectrometry, so this is an experimentally supported association rather than an embedding prediction. It does not establish direct contact or processed-chain specificity; retain generic binding as non-core, consistent with the independently positive HuRI pair with a broader sufficient-region annotation.

Summary: Extracellular localization is an unsupported automatic process-to-location inference.

Reason: The exact GO_REF:0000120 row derives from GO:0003351 and GO:0060287, which describe ciliary movement of extracellular fluid or organizer flow. Those process participants can act from the axoneme inside the ciliary membrane; the checked GO:0005576 definition requires the protein itself to be outside the plasma membrane. Positive cytoplasmic/axonemal evidence supports DNAAF19 as an intracellular assembly/attachment factor. This identified mapping conflates the moved fluid with the protein location, rather than being an experimental secretion result.

Summary: Conserved cytoplasmic pool accompanies axonemal assembly.

Reason: The official cytoplasmic localization is consistent with the assembly role. PMID:22581229 directly localizes zebrafish Ccdc103 to cytoplasm and axonemes; Chlamydomonas fractionation independently finds a cytoplasmic pool. The zebrafish Q6DGB6 donor has the matching IDA annotation. Retain this conserved location without describing the microscopy as a direct human-protein localization assay.

Summary: Conserved cytoplasmic pool accompanies axonemal assembly.

Reason: The official cytoplasmic localization is consistent with the assembly role. PMID:22581229 directly localizes zebrafish Ccdc103 to cytoplasm and axonemes; Chlamydomonas fractionation independently finds a cytoplasmic pool. The zebrafish Q6DGB6 donor has the matching IDA annotation. Retain this conserved location without describing the microscopy as a direct human-protein localization assay.

Summary: Conserved cytoplasmic pool accompanies axonemal assembly.

Reason: The official cytoplasmic localization is consistent with the assembly role. PMID:22581229 directly localizes zebrafish Ccdc103 to cytoplasm and axonemes; Chlamydomonas fractionation independently finds a cytoplasmic pool. The zebrafish Q6DGB6 donor has the matching IDA annotation. Retain this conserved location without describing the microscopy as a direct human-protein localization assay.

Summary: Conserved axonemal localization supports the attachment mechanism.

Reason: The stated Q6DGB6 donor has direct zebrafish axonemal microscopy in PMID:22581229. Chlamydomonas Ccdc103 persists on axonemes after high-salt extraction and in strains deficient in dynein arm/docking components. This supports a conserved axonemal assembly/attachment location, with the ortholog species explicit.

Summary: Inherited laterality role follows ciliary dysfunction.

Reason: Target descent from PTN002005038 and its GO:0007368 IBD are verified. Human target experimental evidence is a legitimate seed, not circular support. Human situs variation and zebrafish rescue substantiate the contextual developmental process; retain it outside the arm-assembly core.

Summary: Retain the supported motile-cilium location.

Reason: SL-0117 correctly places DNAAF19 in motile cilia, consistent with the conserved positive localization and motility evidence in PMID:22581229. Motile cilium and axoneme describe complementary location axes: GO:0005930 does not retain the motility distinction and is not a checked descendant of GO:0031514. Keep the original motile-cilium assertion alongside independently supported axonemal localization, without restricting it to 9+2 cilia.

Summary: Generalize outer-arm membership to an axonemal attachment location.

Reason: IPR042422 is an exact target family match (residues 3–241), but its GO:0036157 mapping places the protein within the outer arm. The original fractionation instead shows persistence on axonemes lacking arm/docking components and after arm extraction. Refine to axoneme, the supported compartment, without asserting a solved attachment interface or categorical exclusion from every transient arm-associated complex.

Proposed replacements: axoneme

Summary: Human-protein rescue directly supports outer-arm assembly.

Reason: Zebrafish mutants lose outer arms and wild-type human CCDC103 restores them in PMID:22581229; human respiratory material independently shows variable outer-arm defects. This is a performed assembly/attachment role, not merely a downstream motility phenotype.

Summary: Conserved inner-arm assembly is retained with allele-specific limits.

Reason: The target descends from PTN002005038 and the GO:0036159 IBD explicitly uses human Q8IW40 experimental grounding. Zebrafish loss of both arms and rescue by human CCDC103 support this function. Preserved DNALI1 staining in selected human patients does not demonstrate universal absence of an inner-arm role; it limits claims of complete IDA loss in every allele.

Summary: Human CCDC103 restores inner arms in the zebrafish rescue system.

Reason: The source directly tests human wild-type CCDC103 in zebrafish mutants that lack inner and outer arms and reports restoration of dynein arms. Retain inner-arm assembly, while noting that native human patient evidence is stronger for outer arms and some examined patients preserve DNALI1 localization.

Summary: Homodimerization is a measured self-association mechanism.

Reason: PMID:22581229 detects apparent dimers of human protein in respiratory cells and after expression in fish, and purified Chlamydomonas protein forms dimers. PMID:31858719 independently shows that human residues 68–94 confer dimerization on LC1 fusions. Retain the existing activity in the integrated assembly core, without equating fragment dimers with a solved native polymer architecture or functional equivalence of the short predicted isoform.

Summary: Organizer ciliary flow links the assembly defect to laterality.

Reason: The cited paper documents motility and laterality defects and rescue, supporting the curator inference connecting the two. Retain this organismal context outside the assembly core; it does not mean that DNAAF19 is a secreted organizer signal or an extracellular protein.

Summary: Refine general axonemal dynein assembly to both arm classes.

Reason: The broad assembly assertion is sound. Zebrafish mutants lack outer and inner dynein arms, and human CCDC103 restores arms in the rescue experiment. Use the two supported arm-assembly terms instead of the broader parent. Native human defects remain allele dependent, with stronger outer-arm evidence and some preserved IDA markers.

Proposed replacements: outer dynein arm assembly inner dynein arm assembly

Summary: Refine general axonemal dynein assembly to both arm classes.

Reason: The broad assembly assertion is sound. Zebrafish mutants lack outer and inner dynein arms, and human CCDC103 restores arms in the rescue experiment. Use the two supported arm-assembly terms instead of the broader parent. Native human defects remain allele dependent, with stronger outer-arm evidence and some preserved IDA markers.

Proposed replacements: outer dynein arm assembly inner dynein arm assembly

Summary: Digestive-tract laterality is a supported developmental context.

Reason: Human situs abnormalities and zebrafish laterality defects in PMID:22581229 support this annotation. The mechanistic link is motile ciliary assembly and flow; the phenotype does not establish a separate digestive-tract patterning activity for the protein.

Summary: Direct microtubule association demonstrated with purified human protein.

Reason: PMID:25572396 directly tests bacterially expressed His10-tagged human CCDC103 with purified bovine-brain microtubules. In the sedimentation assay, CCDC103 remains soluble without microtubules and co-sediments with preformed or assembling microtubules; little or no binding to free tubulin dimers is observed. Cold-stability measurements and a minimal two-component EM reconstruction support this physical interaction. Methods and Figures 7A–C/8 distinguish these human-protein assays from the Chlamydomonas axoneme-extract assay in Figure 7D. This specific binding assertion is not covered by the existing named protein-partner pairs and does not establish native human polymer geometry, the dynein interface, or equivalent activity of the predicted short product.