KIFAP3 (KAP3/SMAP) notes

Summary

• Non-motor cargo-linking subunit: PMID:24338362
• Tail binding (UniProt): "Binds to the tail domain of the KIF3A/KIF3B heterodimer to form a heterotrimeric KIF3 complex and may regulate the membrane binding of this complex"
• SMAP = human KAP3; ER-area localization and SmgGDS binding PMID:8900189
• Chromosome link proposal PMID:9506951
• POPX2 phosphatase binds KAP3 PMID:24338362

Curation decisions

• 15 protein binding rows with KIF3A/KIF3B: MODIFY to kinesin binding (GO:0019894), which is KAP3's defining MF and is already supported by IPI from PMID:16298999.
• 17 other protein binding rows (HTP Y2H partners NCF2, NAA10, HOXB5, KANK2 etc.; SMC3): REMOVE.
• signal transduction and protein-containing complex assembly TAS (8900189): MARK_AS_OVER_ANNOTATED.
• Photoreceptor, ER/Golgi, dendritic/synaptic, chromosome and spindle terms: KEEP_AS_NON_CORE.

HPA cilium atlas vs module role

• HPA v25: Basal body (Approved); main locations Basal body; Microtubules.
• Module: lists KIFAP3 as a kinesin-2 subunit of an annoton whose function is plus-end-directed microtubule motor activity.
• Assessment: partial disagreement. KIFAP3 has no motor domain and does not possess motor activity. At the gene level the correct MF is kinesin binding / cargo adaptor. In GO terms KAP3 could at most contribute_to the complex's motor activity. core_functions therefore use kinesin binding (GO:0019894) plus participation in cilium organization and vesicle transport within kinesin II, and do not use GO:0008574. The basal-body localization in HPA fits kinesin-2 loading at the ciliary base. No change to modules/ made (outside scope); raised as a suggested question in the review.

Deep research

See below.
Falcon deep research succeeded (genes/human/KIFAP3/KIFAP3-deep-research-falcon.md). Key points (not independently re-verified against primary papers unless cached):
- [file:human/KIFAP3/KIFAP3-deep-research-falcon.md "KAP3 couples kinesin-2 to cargo-associated proteins and helps organize interactions between the motor’s C-terminal tails and transport machinery."]
- No catalytic activity: [file:human/KIFAP3/KIFAP3-deep-research-falcon.md "no catalytic reaction or small-molecule transport substrate should be assigned to KAP3 itself"] — this supports the decision not to give KIFAP3 motor activity.
- Chlamydomonas FLA3/KAP ortholog: [file:human/KIFAP3/KIFAP3-deep-research-falcon.md "its mutation dispersed KAP and the FLA10 motor from the basal-body/flagellar region"]; anterograde IFT frequency was reduced. This is ortholog evidence for a ciliary role.
- APC-mediated mRNA cargo and KAP3-dependent activation of KIF3A/B by APC (Webb et al. 2025, reported in the deep research; not cached) would be a candidate non-ciliary cargo-adaptor role. Not used for annotations.

2026-11-05 ORGANELLES ER batch 2 (endoplasmic reticulum rows)

• Rows: GO:0005783 IEA (GO_REF:0000107, Ensembl projection from mouse P70188) and TAS (PMID:8900189), both KEEP_AS_NON_CORE, located_in.
• Projection source (QuickGO): mouse Kifap3 has a single GO:0005783 annotation, MGI IDA from PMID:19384852 (fetched; full text). Pre-embedding immuno-EM of endogenous KAP3 in mouse photoreceptors PMID:19384852.
• TAS source is abstract only PMID:8900189.
• KAP3 is the soluble cargo-binding kinesin-II subunit (no signal peptide, no TM): a recruited cytosolic-face pool, so it stays at the root with no ER-membrane row (cf. TRAF3, A1CF).
• Outcome: root; both rows stay KEEP_AS_NON_CORE, reasons record the check.