Genuine gene seeding completed from UniProt O60716 and current QuickGO records: 95 raw records produce 91 grouped assertions, 55 references and 32 product entries. The seed source objects and original grouping are preserved separately. The selected main boundary is 980669d44911afeca6c093c06bf0c73732e853a3; all 51 existing source-cache files, two GO-CAM sources and their index remain exact.
The configured Falcon research attempt failed authentication. Its configured perplexity-lite fallback returned HTTP 401 with an insufficient-quota response. Both genuine failures and the terminal wrapper receipt are saved in the isolated evidence packet. No provider report was synthesized. Publication caching ran concurrently and completed successfully. Manual research is recorded here and in a compact source index.
The official 32 products were reconstructed independently from all six UniProt alternative-sequence features and matched the separately fetched all-isoform FASTA. Their lengths range from 589 to 968 residues. Alternative initiation and splicing do not demonstrate equal Rho regulation, nuclear localization, cadherin binding or any other activity. Historical construct names will be checked against source sequences and stated endpoints.
The standing ClinGen project rule retains supported generic protein binding as non-core when no evidenced specific replacement is established; inaccessible or unadjudicated interactions remain uncertain.
All 91 seeded assertions have individual decisions. The two existing experimental claims for Kaiso-family and PLEKHA7 binding remain uncertain because their exact target assays were not recovered; absent literal joins are not negative interaction results. Supported generic associations remain non-core where no more informative activity is established, following the standing ClinGen project rule. Specific partner classes are used for cadherins, receptor tyrosine kinases, phosphatases and the DNA-binding factor Kaiso. Co-IP, proximity labeling, tagged reporters and complex membership keep their original evidential limits.
Cadherin stabilization is directly supported by p120 depletion/rescue and surface-turnover experiments PMID:14610055(https://pubmed.ncbi.nlm.nih.gov/14610055/). Human cell assays and mixed-species rescue are distinguished. The deposited structure 3L6Y from PMID:20371349 is human p120 4A with a deletion and N-terminal GSPEF, not an intact product or proof of equal activity across all variants. The DSG3 study concerns a p120-associated free surface pool; it does not establish p120 incorporation into mature desmosomes. The cadherin-24 long/short associations remain separate source assertions.
The actual current PTHR10372 tree has 322 nodes, 164 leaves and a 16-node target path. Its exact 968-residue target MSA reproduces the official sequence. All six literal on-path IBDs agree with the seeded source sets. Target self-evidence is legitimate and donor counts were not used as a proxy for confidence. Complete donor queries yield 1,200 records and 52 annotation/source joins; repeated aliases remain aliases rather than independent experiments. A first WormBase projection used the wrong cross-reference field; the corrected GeneId-based projection and the original attempt are both retained. The two ARBA rules were evaluated branch by branch, and both have genuine target matches.
The endothelial source PMID:33972531(https://pmc.ncbi.nlm.nih.gov/articles/PMC8110786/) shows p120 on the intracellular VE-cadherin tail. The inherited GO:0098632 term instead describes binding to another cell's extracellular component, so cadherin binding replaces that molecular-function assertion. The original mouse donor and GO-CAM bytes remain intact. Positive angiogenic migration context is retained separately; the correction does not deny process participation through intracellular junctional work.
The full operative indexed original PMID:20123964(https://pubmed.ncbi.nlm.nih.gov/20123964/) was recovered beyond its partial cached extraction. Positive LPP3 association and density-dependent signaling are retained, while direct phosphatase inhibition remains unresolved. p120 depletion reduces branching; the paper's LPP3 interventions do not establish p120 as a negative branching regulator. The GLUT4 study PMID:21998202(https://pubmed.ncbi.nlm.nih.gov/21998202/) uses mouse p120 in 3T3-L1 cells; reduced transporter surface delivery is distinct from direct glucose-flux measurement and from an established p120–GLUT4 sequestration interface. The three AMPA-trafficking assertions remain uncertain because target-specific full-source evidence was not recovered.
The parotid exosome assignment is supported by the genuine publisher workbooks from PMID:19199708(https://doi.org/10.1021/pr800658c). Table S2, sheet Paratid Exosomes, Excel row 526 identifies CTNND1/old IPI00182469.2. Table S1 rows 4194–4195 contain the two target peptides. These peptides match 24 and 32 current official products, respectively; the old 1AB label is not unique isoform evidence. Detection in a fraction is retained without assigning exosome-biogenesis activity. The exact target in the older midbody screen remains unverified.
Two original studies directly measure mouse p120 inhibition of Rho GDP release PMID:10980705(https://www.nature.com/articles/ncb0900_637.pdf), PMID:17194753(https://pmc.ncbi.nlm.nih.gov/articles/PMC1820477/). The earlier paper explicitly retained a possible co-purifying-factor caveat; the later direct-binding and GDP-inhibition assays, truncations and regulatory-site mutants strengthen the performed-activity conclusion. This supports one new human molecular-function assertion by sequence inference (ISS), not a human IDA or a new biological-process claim. The separate Rho core states that inferential basis. The proposed cytosol/membrane switching scheme remains a model; the core retains broad cytoplasm rather than claiming a newly proved cytosol-only mechanism.
The later paper cites mouse Z17804.1/CAA79078.1, a 911-residue sequence. Among all 32 human products, the best global alignment is current O60716-8, 912 residues, with 887 identical paired residues and full query coverage. Historical mouse 1B is not current human O60716-6 (941 residues). Tested regulatory tyrosines and the basic motif are conserved, with product-specific exceptions. The reproducible analysis retains archived sequences, locked dependencies, generic scripts, complete results and an independent control-gene run. Sequence correspondence is not a functional measurement of every product or authentication of an experimental plasmid.
The bounded core/product consultation, including its original-source recovery, was independently completed by brca2_science and reproduced before integration. ROOT independently completed the nonjunction and Rho consultations. The owner read the complete reports, read ledgers and recommendations and reproduced their read-only verifiers; those attributed primary reads are not relabeled as personal whole-paper reads. Owner primary reads, actual interaction-record/ROGID reconstruction, donor joins, tree, rules, HPA text and Reactome component paths are recorded separately in the immutable TMP packet.
The compact public source index provides repository/public locators and essential access, construct and interpretation limits. It omits raw databases and repeated review/reference mirrors. Full-text availability is distinguished from actual selected-section reading and target-panel verification. Genuine failed access routes and provider failures are preserved in the research packet; no source cache is repaired by authored prose. Short primary anchors occur once in the review YAML, with at most 25 words per source across the candidate, notes and index. This notes appendix does not repeat those quotations.
SYNGAP1 is a reviewed Ras/Rap GTPase-activating protein (UniProt Q96PV0). The positive curated anti-bait co-IP records therefore support GTPase activating protein binding, with the target table/panel and purified-interface limits retained. This does not assign GAP catalysis to p120. Nuclear localization in PMID:20123964 is accepted as a location observation, without an activity requirement. The DEP1 refinement is based on the demonstrated phosphatase partner class; receptor binding itself can be intracellular.
The authored RhoGDI ISS assertion now explicitly records enables and mouse ortholog P30999. Later independent binding and GDP assays strengthen the activity evidence and address, rather than strengthen, the earlier co-purifying-factor caveat. All 91 original source objects, 32 official products and primary quotations are unchanged. The first scientific snapshot and the genuine ordinary status derivation remain preserved separately.
The exact published 91 source assertions, additional ISS assertion, 32 official products, caches and analysis artifacts remain unchanged. This amendment changes only the phosphatase-inhibitor action (row 67, UNDECIDED to MARK_AS_OVER_ANNOTATED), clarifies source scope, and records a biological knowledge gap. UNDECIDED remains permitted for a genuinely unclear annotation as well as being required for inaccessible relevant evidence; access is not its sole use.
The complete indexed main Methods/Results/Discussion of PMID:20123964 was reread, including the main assay captions. Methods describe LEF1 reporters, coimmunoprecipitation, far-western/pull-down, localization and cellular phenotypes; Results Figures 3 and 7–10 establish signaling suppression and LPP3 association. No lipid-substrate turnover experiment with and without p120 is described in that main assay scope. Phosphatase-defective LPP3 retaining signaling separates the reporter from catalytic activity; it does not show that p120 cannot inhibit catalysis. The specific inhibitor assignment therefore exceeds what these experiments demonstrate. The positive binding and signaling findings are preserved. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC2838065/; no figure-pixel or supplement read is claimed.
PMID:21998202 target Results, Methods and Figure 6/7 captions were reread. Mouse p120 in 3T3-L1 cells reduces GLUT4 surface trafficking; RPTPμ coexpression alters p120 distribution and restores trafficking. The Rho/Rac mechanism is discussed, not demonstrated to be a GDP-dissociation-inhibition mechanism for this phenotype. GO:0140311 requires binding the sequestered protein, and the preserved GO-CAM 613aae0000000885 identifies SLC2A4 as input. This source-specific uncertainty remains UNDECIDED. Neither the independent Rho GDI evidence nor trafficking inhibition establishes a p120–GLUT4 sequestration interface.
The preserved UniProt Q3UIL6 identity record resolves the row 16 partner as mouse Plekha7 (1118 aa). Species is now explicit in the prose; the literal IPI supporting entity is untouched, and non-human identity is not negative interaction evidence. PMID:18343367 row 88 now states that the deletion is in DSG3’s intracellular association region rather than CTNND1. Its original full-assay access limit and curator deference remain explicit.
The description now states biology without the research-provenance phrasing. PMID:10980705 original Figure 5 Results and Discussion distinguish a cadherin-free Rho-inhibitory pool from cadherin-bound stabilization. The cadherin-fragment competition suppresses branching; endogenous uncoupling uses ezrin localization as an indirect Rho readout. This is a source-scoped constraint, not proof that every human product follows an identical switch. The separate core retains the mouse-assay/human-inference boundary. A BIOLOGY gap and purified-human-product GDP-release experiment now express the unresolved product, cadherin-occupancy and phosphorylation dependence. No redundant Rho-binding annotation is added.
All existing supporting excerpts remain unchanged, with no new quotations or repeated snippets in this addendum. The compact source index carries public source locators and these finite conclusions; the original raw evidence remains in the immutable research packet. Spoke/complex-association records retain their existing assay limits rather than becoming purified direct-interface claims. The prior history entry is append-only and is not rewritten for its spacing defects.