DNAAF6

Summary: Human ciliary dysmotility is a consequence of defective dynein-arm assembly.

Reason: Patient nasal-cell imaging and ultrastructure in PMID:28041644 positively connect DNAAF6 deficiency to immotile cilia and loss of outer and inner dynein-arm components. Retain the existing movement involvement as a contextual output of assembly; it does not make DNAAF6 an ATP-driven motor or a mature axonemal force generator.

Summary: Human and zebrafish ciliary movement depends on DNAAF6-supported arm assembly.

Reason: PMID:28176794 reports severe human ciliary dysmotility, with residual disorganized movement in one affected individual, and virtually immotile zebrafish mutant cilia. The positive involvement assertion is retained contextually. Variable residual arm assembly and movement preclude an invariant all-or-none phenotype; the direct core mechanism is dynein-arm preassembly.

Summary: Verified BTAF1 binary binding has a supported narrower partner class.

Reason: The 2014 binary interaction map source and exact IntAct partner records support DNAAF6–BTAF1 binding (3 positive records, including validated two-hybrid EBI-10557406). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. The literal unreviewed Q2M1V9 sequence is exactly identical to reviewed BTAF1 O14981 (1,849 residues). Independent human BTAF1 biochemistry in PMID:9488487 establishes ATP hydrolysis, so ATPase binding is a justified partner-class refinement; ATP binding or a helicase-domain name alone was not used. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: ATPase binding

Summary: Verified CDKL3 binary binding has a supported narrower partner class.

Reason: The 2014 binary interaction map source and exact IntAct partner records support DNAAF6–CDKL3 binding (3 positive records, including validated two-hybrid EBI-10582386). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. The official Q8IVW4 record identifies a protein kinase domain and serine/threonine protein phosphorylation reactions, supporting the protein-kinase partner class. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: protein kinase binding

Summary: Verified CCAR1 binary binding has a supported narrower partner class.

Reason: The 2014 binary interaction map source and exact IntAct partner records support DNAAF6–CCAR1 binding (3 positive records, including validated two-hybrid EBI-10582876). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Official Q8IX12 evidence supports both transcriptional coactivator and corepressor roles mediated through regulatory protein complexes. The common transcription-coregulator class is used without assigning a transcriptional function to DNAAF6. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: transcription coregulator binding

Summary: Verified KAT5 binary binding has a supported narrower partner class.

Reason: The 2014 binary interaction map source and exact IntAct partner records support DNAAF6–KAT5 binding (3 positive records, including validated two-hybrid EBI-10598320). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Q92993 is the catalytic histone acetyltransferase KAT5. Binding to this enzyme permits the histone-acetyltransferase partner class, without implying DNAAF6 acetylation or NuA4 membership. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: histone acetyltransferase binding

Summary: Verified P2RX4 binary binding has a supported narrower partner class.

Reason: The 2014 binary interaction map source and exact IntAct partner records support DNAAF6–P2RX4 binding (3 positive records, including validated two-hybrid EBI-10608316). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Q99571 is an ATP-gated transmembrane cation channel. The verified binary pair supports the transmembrane-transporter partner class, without making DNAAF6 a channel regulator, ATPase or physiological extracellular ligand. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment. Classical Y2H does not recreate native membrane topology or demonstrate association with an assembled active channel; endogenous channel regulation remains untested.

Proposed replacements: transmembrane transporter binding

Summary: Verified KIF13A binary binding has a supported narrower partner class.

Reason: The 2014 binary interaction map source and exact IntAct partner records support DNAAF6–KIF13A binding (3 positive records, including validated two-hybrid EBI-10617376). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Q9H1H9 is the plus-end-directed microtubule motor KIF13A. The binary interaction supports kinesin binding; no cargo-transport function or a measured stoichiometric coefficient for DNAAF6 is inferred. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: kinesin binding

Summary: Human DNAAF2 and DNAAF4 interactions support assembly-factor association.

Reason: PMID:28041644 Figure 4 and its associated Methods identify sequence-confirmed human DNAAF2/KTU and DNAAF4/DYX1C1 constructs in Y2H, followed by reciprocal tagged co-immunoprecipitation in HEK293T cells. Both literal supporting entities are retained. These positive assembly-factor associations do not establish that either partner is itself a protein-folding chaperone or that DNAAF6 performs a distinct adaptor mechanism. Retain the supported binding without forcing a chaperone-binding replacement.

Summary: Human DNAI2 association supports dynein intermediate chain binding.

Reason: The literal partner Q9GZS0 is DNAI2. PMID:28176794 Figure 5c,d reports reciprocal tag-swapped co-immunoprecipitation of human DNAAF6 and DNAI2 in HEK293 cells, with empty-vector controls and loss of association for four DNAAF6 variants. This is coherent with the existing curated GO:0045505 assertion and assembly mechanism. Refine the generic pair to dynein intermediate chain binding; do not claim purified direct affinity, a mapped interface or independent folding activity.

Proposed replacements: dynein intermediate chain binding

Summary: Verified PRKAA2 binary binding has a supported narrower partner class.

Reason: The HuRI source and exact IntAct partner records support DNAAF6–PRKAA2 binding (3 positive records, including validated two-hybrid EBI-24427381). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. P54646 is the catalytic alpha-2 subunit of AMP-activated protein kinase, with established protein phosphorylation activity. The kinase partner class is justified; DNAAF6 is not thereby assigned AMPK regulatory activity. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: protein kinase binding

Summary: Positive QRICH1 binary interaction retained with bounded functional interpretation.

Reason: Three literal HuRI interaction records, including the validated two-hybrid record, support this pair; reference sequences match the recorded accessions. Official QRICH1 functions include DNA-associated transcriptional regulation and stabilization of transcription factors in the zincore complex. The evaluated evidence does not resolve a single DNA-binding transcription-factor or non-DNA-binding coregulator class appropriate to this pair; no broad transcription label is converted automatically into either binding subclass. Retain the positive generic binding assertion under the explicit project instruction; assay context alone is not evidence of a false positive.

Summary: Positive ARID4B isoform 3 binary interaction retained with bounded functional interpretation.

Reason: Three positive HuRI records include validated two-hybrid EBI-25261226, with reference-sequence matches to DNAAF6 and Q4LE39-3. The 1,153-residue ARID4B product replaces canonical residues 1150–1153 and lacks 1154–1312. The official ARID4B record combines DNA-binding and corepressor-complex roles and assigns mSin3A interaction to its C terminus. The evaluated evidence does not resolve the relevant coregulator role for this altered product under GO:0001221, whose definition distinguishes cofactors from direct DNA-binding regulators. Retain the positive binding as non-core without declaring this product inactive or the assay false.

Summary: Positive PID1 isoform 3 binary interaction retained with bounded functional interpretation.

Reason: Three literal HuRI interaction records, including the validated two-hybrid record, support this pair; reference sequences match the recorded accessions. The literal Q7Z2X4-3 partner is a reconstructed 168-residue product. Its PTB-domain family and growth phenotype do not by themselves establish an enzyme, transcription-factor or cytoskeletal-regulatory partner class. Retain the positive generic binding assertion under the explicit project instruction; assay context alone is not evidence of a false positive.

Summary: Verified binding to YAF2 Q8IY57-5, named isoform 2, supports a coregulator partner class.

Reason: Three positive HuRI records include validated two-hybrid EBI-24280196, with reference-sequence matches to DNAAF6 and Q8IY57-5. Despite its accession suffix, this 204-residue product is officially named isoform 2. Its insertion at canonical residue 50 retains all canonical residues and the RanBP2-type zinc-finger region. Independently established protein-mediated YAF2 coactivator/corepressor roles support transcription coregulator binding; the inspected function record does not establish a direct DNA-binding mechanism. This specifies the bound partner class, not equal regulatory activity of every YAF2 product, a DNAAF6 transcriptional function or a demonstrated native complex.

Proposed replacements: transcription coregulator binding

Summary: Verified GAS2L2 binary binding has a supported narrower partner class.

Reason: The HuRI source and exact IntAct partner records support DNAAF6–GAS2L2 binding (4 positive records, including validated two-hybrid EBI-24324266). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Q8NHY3 regulates microtubule dynamics and microtubule–actin coupling, satisfying the cytoskeletal-regulatory partner definition. The source additionally records positive MAPPIT EBI-25293365 / IM-25472-162598 in human HEK293T cells. No cytoskeletal regulatory action is transferred from GAS2L2 to DNAAF6. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: cytoskeletal regulatory protein binding

Summary: Positive TSEN15 binary interaction retained with bounded functional interpretation.

Reason: Three literal HuRI interaction records, including the validated two-hybrid record, support this pair; reference sequences match the recorded accessions. Q8WW01 is a non-catalytic subunit of the tRNA-splicing endonuclease complex. Its membership in an enzyme complex does not make the individual binding partner an endonuclease or establish that the assay captured the complete complex. Retain the positive generic binding assertion under the explicit project instruction; assay context alone is not evidence of a false positive.

Summary: Verified KAT5 binary binding has a supported narrower partner class.

Reason: The HuRI source and exact IntAct partner records support DNAAF6–KAT5 binding (3 positive records, including validated two-hybrid EBI-24444209). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Q92993 is the catalytic histone acetyltransferase KAT5, independently establishing the narrower partner class. No acetylation substrate relationship or NuA4 membership is inferred. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: histone acetyltransferase binding

Summary: Verified RNF39 binary binding has a supported narrower partner class.

Reason: The HuRI source and exact IntAct partner records support DNAAF6–RNF39 binding (3 positive records, including validated two-hybrid EBI-24330220). Participant reference-sequence checksums match the literal source accessions; fusion tags remain assay features. Q9H2S5 is an E3 ubiquitin protein ligase, with an official ubiquitin-transfer reaction and experimentally grounded target ubiquitination. The binary pair supports E3-ligase binding without implying that DNAAF6 is a ligase substrate or regulator. The replacement specifies the binding partner class in this assay, not endogenous complex membership or established physiological deployment.

Proposed replacements: ubiquitin protein ligase binding

Summary: Positive POLDIP2 binary binding supports cytoskeletal regulatory protein binding.

Reason: Three positive HuRI records, including validated two-hybrid EBI-24406330, support DNAAF6 binding to the sequence-matched Q9Y2S7 partner. Independent human aortic smooth-muscle experiments in PMID:30354218 establish POLDIP2-dependent actin–vinculin association and focal-adhesion maturation through NOX4-dependent regulation, without demonstrating direct actin crosslinking by POLDIP2. GO:0005519 therefore describes the measured binding more specifically. The screen does not establish that DNAAF6 regulates the cytoskeleton or participates in the POLDIP2–NOX4 pathway; native interaction context remains unresolved.

Proposed replacements: cytoskeletal regulatory protein binding

Summary: Experimentally grounded phylogeny supports cytoplasmic localization.

Reason: Human Q9NQM4 leaf PTN002501283 descends from PTN000472342 in PTHR21083. The saved IBD names fly, mouse, trypanosome and human descendants; target experimental evidence is legitimate grounding, not circularity. Human nasal-cell staining places DNAAF6 in the cytoplasm with trans-Golgi enrichment, while mouse germ-cell imaging independently supports a cytoplasmic pool. Retain cytoplasm to cover this broader assembly compartment without equating it to soluble cytosol or an exclusive location.

Summary: Human imaging supports cytoplasm with trans-Golgi enrichment.

Reason: Human nasal-cell staining places DNAAF6 in the cytoplasm with trans-Golgi enrichment, while mouse germ-cell imaging independently supports a cytoplasmic pool. Retain cytoplasm to cover this broader assembly compartment without equating it to soluble cytosol or an exclusive location. PMID:28176794 Figure 5 establishes TGN46 co-localization; this does not specify Golgi-luminal topology or a role in secretion.

Summary: Correct official subcellular-location mapping preserves the cytoplasmic pool.

Reason: Human nasal-cell staining places DNAAF6 in the cytoplasm with trans-Golgi enrichment, while mouse germ-cell imaging independently supports a cytoplasmic pool. Retain cytoplasm to cover this broader assembly compartment without equating it to soluble cytosol or an exclusive location.

Summary: Mouse ortholog imaging positively supports the cytoplasmic transfer.

Reason: Q3KNI6 is mouse Dnaaf6/Pih1d3 and carries direct IDA cytoplasm evidence from PMID:24421334. The original compares wild-type and knockout testis, localizing the protein to spermatocytes and round spermatids rather than mature sperm. This is a positive ortholog transfer and is independently supported by human cytoplasmic imaging; the species-specific germ-cell expression pattern is not imposed universally on human DNAAF6.

Summary: Independent human imaging refines Golgi localization to the trans-Golgi network.

Reason: The current approved HPA record positively reports Golgi apparatus localization; its additional cell-context pools are preserved as source context. HPA itself does not resolve the trans-Golgi subcompartment. PMID:28176794 Figure 5a provides the independent target-level refinement: strong TGN46 co-localization and much less cis-Golgi GM130 overlap in human nasal cells, with confirmation in overexpression. GO:0005802 is part_of Golgi apparatus. This refinement does not erase cytoplasmic or other context-dependent pools or assert secretion activity.

Proposed replacements: trans-Golgi network

Summary: Independent human imaging refines Golgi localization to the trans-Golgi network.

Reason: The official SL-0132 mapping correctly supports Golgi apparatus and is not a mapping error. PMID:28176794 Figure 5a provides the independent target-level refinement: strong TGN46 co-localization and much less cis-Golgi GM130 overlap in human nasal cells, with confirmation in overexpression. GO:0005802 is part_of Golgi apparatus. This refinement does not erase cytoplasmic or other context-dependent pools or assert secretion activity.

Proposed replacements: trans-Golgi network

Summary: Human TGN46 co-localization establishes trans-Golgi enrichment.

Reason: PMID:28176794 Figure 5a compares endogenous human nasal-cell DNAAF6 with TGN46 and GM130. The late-Golgi marker overlaps strongly, whereas cis-Golgi overlap is much weaker; HEK293 overexpression provides additional confirmation. Accept trans-Golgi network localization without assuming luminal residence, an exclusive compartment or a secretory transport activity.

Summary: Positive sperm-motility involvement follows dynein-arm assembly.

Reason: The human leaf descends from the Euteleostomi node PTN002721091; the saved sperm-motility IBD is grounded in mouse and human experiments. DNAAF6-dependent assembly supports motile sperm flagella. Human affected males in PMID:28041644 have asthenozoospermia and immotile sperm; mouse Pih1d3 knockout in PMID:24421334 causes male infertility, impaired dynein arms and immotile sperm. Retain this positive physiological involvement as non-core relative to the molecular assembly step, without assigning DNAAF6 the dynein motor reaction.

Summary: Positive sperm-motility involvement follows dynein-arm assembly.

Reason: DNAAF6-dependent assembly supports motile sperm flagella. Human affected males in PMID:28041644 have asthenozoospermia and immotile sperm; mouse Pih1d3 knockout in PMID:24421334 causes male infertility, impaired dynein arms and immotile sperm. Retain this positive physiological involvement as non-core relative to the molecular assembly step, without assigning DNAAF6 the dynein motor reaction.

Summary: Positive sperm-motility involvement follows dynein-arm assembly.

Reason: The literal mouse Q3KNI6 donor carries direct IMP24421334 sperm-motility evidence. DNAAF6-dependent assembly supports motile sperm flagella. Human affected males in PMID:28041644 have asthenozoospermia and immotile sperm; mouse Pih1d3 knockout in PMID:24421334 causes male infertility, impaired dynein arms and immotile sperm. Retain this positive physiological involvement as non-core relative to the molecular assembly step, without assigning DNAAF6 the dynein motor reaction.

Summary: Human deficiency establishes a role in outer dynein-arm assembly.

Reason: PMID:28176794 combines human genotype, dynein-marker immunostaining and ultrastructure with zebrafish rescue/phenotypes. Human mutant cilia show impaired outer arm assembly, with variable residual structures across individuals. The protein contributes to the cytoplasmic assembly machinery; necessity is interpreted with its physical assembly-factor/IC associations, not as an autonomous motor or uniform loss of every arm component.

Summary: Human deficiency establishes a role in inner dynein-arm assembly.

Reason: PMID:28176794 combines human genotype, dynein-marker immunostaining and ultrastructure with zebrafish rescue/phenotypes. Human mutant cilia show impaired inner arm assembly, with variable residual structures across individuals. The protein contributes to the cytoplasmic assembly machinery; necessity is interpreted with its physical assembly-factor/IC associations, not as an autonomous motor or uniform loss of every arm component.

Summary: Valid phylogeny preserves the experimentally grounded intermediate-chain interaction.

Reason: The actual PTHR21083 human target path descends from PTN000472342, whose GO:0045505 IBD is seeded by the direct human DNAAF6–DNAI2 study. This expected target grounding is not circular. Preserve the curator's binding interpretation in the assembly context while retaining the tagged co-IP rather than purified-affinity scope.

Summary: Human DNAI2 interaction is a supported component of the assembly mechanism.

Reason: PMID:28176794 Figure 5c,d verifies human DNAI2 association by reciprocal tag-swapped co-IP. Wild-type DNAAF6 associates, whereas p.Asp133Tyr and three truncating variants lose this signal. Preserve the existing specific binding function; the data do not isolate a purified interface or demonstrate that mutant effects are solely loss of direct-contact residues.

Summary: Positive chaperone association is retained without a separate folding core.

Reason: IPR026697 is the DNAAF6 family, with a verified target match at residues 27–213 and an explicit GO:0051087 mapping. Native mouse testis co-immunoprecipitation in PMID:24421334 positively identifies Hsp70 and Hsp90 association with Pih1d3, and the human PMID:28041644 Y2H experiment corroborates HSP90 association using fragments. Retain chaperone binding as a supported contextual interaction, distinct from autonomous folding catalysis or a fully reconstructed R2TP complex.

Summary: Positive chaperone association is retained without a separate folding core.

Reason: The literal mouse Q3KNI6 donor carries direct IDA24421334 chaperone-binding evidence, not a propagated-only assertion. Native mouse testis co-immunoprecipitation in PMID:24421334 positively identifies Hsp70 and Hsp90 association with Pih1d3, and the human PMID:28041644 Y2H experiment corroborates HSP90 association using fragments. Retain chaperone binding as a supported contextual interaction, distinct from autonomous folding catalysis or a fully reconstructed R2TP complex.

Summary: Dynein-complex assembly is specified as outer and inner arm assembly.

Reason: The PTHR21083 human target descends from the valid PTN000472342 assembly IBD; fly, mouse, human and zebrafish experimental descendants ground the node. Refine the correct general axonemal dynein-complex assembly assertion to its verified outer-arm and inner-arm assembly children, supported independently in human DNAAF6. This preserves the source claim while avoiding duplication of a broad process in the core; it does not imply that every intermediate complex fails to form.

Proposed replacements: outer dynein arm assembly inner dynein arm assembly

Summary: Dynein-complex assembly is specified as outer and inner arm assembly.

Reason: IPR026697 is an actual target-matching DNAAF6 family with an explicit GO:0070286 mapping and cited human/mouse assembly studies. Refine the correct general axonemal dynein-complex assembly assertion to its verified outer-arm and inner-arm assembly children, supported independently in human DNAAF6. This preserves the source claim while avoiding duplication of a broad process in the core; it does not imply that every intermediate complex fails to form.

Proposed replacements: outer dynein arm assembly inner dynein arm assembly

Summary: Dynein-complex assembly is specified as outer and inner arm assembly.

Reason: PMID:28041644 human respiratory-cell phenotypes and dynein-component imaging establish assembly defects affecting outer and inner arms. Refine the correct general axonemal dynein-complex assembly assertion to its verified outer-arm and inner-arm assembly children, supported independently in human DNAAF6. This preserves the source claim while avoiding duplication of a broad process in the core; it does not imply that every intermediate complex fails to form.

Proposed replacements: outer dynein arm assembly inner dynein arm assembly

Summary: Dynein-complex assembly is specified as outer and inner arm assembly.

Reason: The literal mouse Q3KNI6 donor has direct IMP24421334 assembly evidence: outer arms are nearly absent and inner-arm loss is partial, with native intermediate-chain association still detectable. Refine the correct general axonemal dynein-complex assembly assertion to its verified outer-arm and inner-arm assembly children, supported independently in human DNAAF6. This preserves the source claim while avoiding duplication of a broad process in the core; it does not imply that every intermediate complex fails to form.

Proposed replacements: outer dynein arm assembly inner dynein arm assembly