PIKFYVE encodes the phosphoinositide 5-kinase that converts phosphatidylinositol 3-phosphate to phosphatidylinositol 3,5-bisphosphate (and phosphatidylinositol to phosphatidylinositol 5-phosphate) on endosomal membranes. The full-length enzyme (about 2100 residues) is recruited to endosomes by its PtdIns3P-binding FYVE finger, works in a complex with the scaffold VAC14 and the phosphatase FIG4, and controls endolysosomal maturation, phagosome-lysosome fusion, melanosome biogenesis and neutrophil chemotaxis and ROS production. This entry, A0A9L0JQ61, is not the full-length kinase: its 460-residue sequence corresponds to the short human PIKFYVE splice isoform 3 (96% identity), which keeps the N-terminal region and the DEP domain but lacks most of the FYVE finger, the chaperonin-like domain and the entire PIPK catalytic domain. It is the product of a non-canonical transcript of the same donkey gene, whose canonical 2108-residue product (A0A8C4L106) it matches at 99.6% identity over its whole length. The function of this short isoform has not been characterized; it may not be a stable protein, and if it is, any role it has would come from its N-terminal and DEP regions rather than from lipid-kinase activity.
Summary: 1-phosphatidylinositol-3-phosphate 5-kinase activity, combined from InterPro (PIKfyve family and PIKfyve DEP entries) and the PANTHER node PTN001347166. The activity belongs to the C-terminal PIPK domain of full-length PIKFYVE; this 460-residue isoform contains no part of that domain.
Reason: The family and DEP-domain signatures are shared with the full-length kinase, but the catalytic domain (human 1758-2084) is absent from this product, which corresponds to human isoform 3 (truncated at residue 548). An enzyme activity cannot be assigned to a protein that lacks its catalytic domain. The gene's full-length products (separate entries; Ensembl canonical A0A8C4L106) do carry this activity, and the PANTHER subfamily placement (PTHR46715:SF1, shared with human and mouse PIKFYVE) is correct at the gene level.
The catalytic domain is encoded only by the canonical and other full-length transcripts, so the gene's lipid-kinase function belongs to those products.
Summary: TreeGrafter vesicle membrane from PTN001347166. Full-length PIKFYVE is targeted to late endocytic membranes through its FYVE finger binding PtdIns3P.
Reason: Six of the eight zinc-binding cysteines of the FYVE finger are absent, so the targeting mechanism of the full-length protein is unavailable; whether the short isoform associates with vesicle membranes (for example through its DEP domain) is not known. Neither transfer nor refutation is supported.
Summary: TreeGrafter neutrophil chemotaxis from PTN001347166, derived from the requirement for PIKFYVE kinase activity in neutrophils.
Reason: The neutrophil phenotypes of PIKFYVE are attributed to its PI(3,5)P2-producing activity (and are probed with the kinase inhibitors apilimod and YM201636); this product lacks the catalytic domain, so there is no basis to assign it this process.
Summary: TreeGrafter cytoplasmic vesicle from PTN001347166.
Reason: As for vesicle membrane; the localization of the full-length kinase depends on the FYVE finger, which this isoform largely lacks, and no localization data exist for the short isoform.
Summary: TreeGrafter melanosome organization from PTN001347166.
Reason: Melanosome biogenesis depends on PIKFYVE lipid-kinase activity controlling endosome-to-melanosome delivery; the kinase-less isoform cannot be assumed to do this work.
Summary: InterPro2GO intracellular signal transduction from the DEP domain (IPR000591), which the isoform retains.
Reason: The DEP-domain mapping is a generic association (DEP domains occur in many signalling proteins) and implies no specific activity. There is no evidence that the short PIKFYVE isoform transduces a signal; the role of the full-length kinase in hormone-induced signalling depends on its catalytic output.
Summary: TreeGrafter 1-phosphatidylinositol-5-kinase activity from PTN001347166, a second lipid-kinase activity of the full-length enzyme's PIPK domain.
Reason: Same domain-architecture objection as the PtdIns3P 5-kinase row; the TreeGrafter placement in the PIKFYVE family is right at the gene level but this isoform lacks the catalytic domain.
The catalytic domain is encoded only by the canonical and other full-length transcripts, so the gene's lipid-kinase function belongs to those products.
Summary: TreeGrafter phagosome-lysosome fusion from PTN001347166.
Reason: Phagosome maturation and fusion with lysosomes require PI(3,5)P2 synthesis by full-length PIKFYVE; this product lacks the catalytic domain and the endosomal FYVE targeting module.
It also lacks the chaperonin-like domain (human 616-868) and the entire PIPK catalytic domain (human 1758-2084).
GO:1903426 regulation of reactive oxygen species biosynthetic process
IEA GO_REF:0000118
REMOVE
Summary: TreeGrafter regulation of reactive oxygen species biosynthetic process from PTN001347166, from the neutrophil ROS phenotype of PIKFYVE inhibition or loss.
Reason: As for neutrophil chemotaxis; the ROS phenotype reflects loss of PI(3,5)P2 production, which this isoform cannot catalyze.
Q: Is the short PIKFYVE isoform (human isoform 3, donkey A0A9L0JQ61) translated as a stable protein, and if so does it act as a regulator, for example a dominant-negative competitor of full-length PIKFYVE for VAC14/FIG4 or membrane sites?
Suggested Experiments
Experiment: Detect the short PIKFYVE isoform protein in equine or human tissues with an isoform-specific antibody or targeted proteomics of its unique NSLQHPQEN junction peptide, and test whether its expression alters PI(3,5)P2 levels or endolysosome size.
Knowledge Gaps
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The molecular function, if any, of the short kinase-less PIKFYVE isoform (DEP domain retained, FYVE finger largely and PIPK domain wholly absent) is unknown.
BIOLOGY
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Assessment of the single ProtNLM2 GO prediction for donkey PIKFYVE entry A0A9L0JQ61 (DONKEY40 cohort). The 460-residue input is a non-canonical splice product of the donkey PIKFYVE gene (canonical product A0A8C4L106), not the full-length phosphoinositide kinase: alignment shows it is the counterpart of the short human PIKFYVE splice isoform 3 (96.08% identity), lacking the PIPK catalytic domain, the chaperonin-like domain and most of the FYVE finger, while retaining the DEP domain. The predicted phosphatidylinositol phosphate biosynthetic process transfers the full-length enzyme's catalytic output (the ProtNLM2 evidence record cites a phmmer match to full-length mouse Pikfyve Q9Z1T6) to a protein that cannot catalyze it; because a non-catalytic contribution through the retained DEP-containing region is neither shown nor excluded, it is scored UNC. Non-GO ProtNLM2 output for this accession, not scored here: subcellular location "Nucleus", whose evidence record is a weak phmmer match (score 26.2) to Drosophila Dishevelled (P51140), a DEP-domain protein; full-length PIKFYVE is an endosomal membrane protein, and no data place the short isoform in the nucleus. No function text was emitted.
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-10-14
Review rationale: Full-length PIKFYVE contributes to phosphatidylinositol phosphate biosynthesis by synthesizing PtdIns(3,5)P2 and PtdIns5P through its C-terminal PIPK domain. The selected donkey protein is the product of a non-canonical transcript corresponding to human isoform 3, which ends at residue 548 and contains no part of the PIPK domain (human 1758-2084), so it cannot perform the catalytic step. That excludes the gene's main mode of participation, but it does not exclude every other mode. The short product also lacks the Cpn60_TCP1 (chaperonin-like) domain, which the PAS-complex study identifies as a major, not the sole, determinant of ArPIKfyve(VAC14)-Sac3(FIG4) association, and it lacks the complete FYVE finger that targets the enzyme to endosomes. It retains the N-terminal region and the DEP domain (donkey 277-352), whose contribution to the PAS complex or to lipid synthesis has been neither shown nor excluded. No study characterizes the short isoform, and endogenous human PIKfyve was detected as a single molecular species, so a binding or regulatory contribution is unsupported but not refuted. The prediction most likely transfers the full-length enzyme's output through the shared N-terminal and DEP region, and the term cannot be validated or refuted for this product, so it is scored UNC. At the gene level the claim is not novel, because the canonical donkey product A0A8C4L106 already carries phosphatidylinositol metabolic process and PI(3,5)P2 metabolic process annotations.