Phase-1 review — consolidated recommended edits (auto-extracted)

Generated from the per-gene section files in _sections/. Tags: [YAML] gene-review change · [MAP] PN mapping/projection · [WB] upstream PN workbook · [REF] reference hygiene. Nothing here was applied automatically — staged for curator adjudication.

• genes with [YAML] recommendations: 65
• genes with [MAP] recommendations: 148
• genes with [REF] recommendations: 39
• genes with [WB] recommendations: 3

Genes with gene-review (YAML) change recommendations

ATP6V0A1, AZI2, BCL2L13, BNIP3L, CALCOCO1, CALR3, CAND1, CCDC47, CHIC2, CLCN7, CLGN, CNOT4, CSNK1D, DCAF10, DDA1, DDB2, DNAJC6, DTL, EIF5A, FAF2, FBXL8, FBXO16, FBXO27, FBXO47, FBXO8, FBXW5, GIGYF1, GLMN, GTPBP2, GTPBP6, LRSAM1, MAP1S, MEFV, NAA30, NAA35, NAA38, NAA40, NBR1, NEMF, NLRX1, NPLOC4, NUFIP1, P4HA3, PPIB, RACK1, RETREG2, RNF166, RNF170, RNF185, RNF41, RNF5, SEC62, SEC63, SERPINH1, SIAH1, STIP1, STUB1, TCF25, TRIM13, TRIM16, TRIM17, TRIM5, TXNDC11, TXNDC16, UBAC2

Per-gene tagged recommendations

AATF

• Verdict: Subunit contradiction — PN over-reaches (LSU projection on an SSU factor); review correctly rejects pre-60S. Recommended edits:** [MAP] Do not project GO:0030687 to AATF; re-bucket AATF under an SSU-processome/pre-40S PN node or suppress the pre-60S type mapping for this gene.

ABCF2

• Verdict: Consistent (review conservatively rejects the PN RQC projection). Recommended edits:** [REF] Reconcile UniProt accession — PN dossier/workbook uses A0A090N7X1 but the canonical reviewed entry and review YAML use Q9UG63; update the PN workbook to Q9UG63. [MAP] Keep GO:0006515 non-propagating for ABCF2.

ABRAXAS2

• Verdict: Consistent on BRISC; PN DNA-repair projection over-reaches and is correctly declined; review's p53-DDR/IFN NEW terms are sound. Recommended edits:** [MAP] Do not project GO:0006281 DNA repair to ABRAXAS2; the supported DNA-damage role is GO:0043517 (p53-class DDR signaling), already added in the review.

ABTB1

• Verdict: Consistent; PN substrate-adaptor activity correctly held back (no substrate), review adds verified CRL3 complex + cullin-binding terms. Recommended edits:** [MAP] Keep GO:1990756 non-propagating for ABTB1 pending substrate evidence (review's GO:0031463/GO:0097602 are the correct landing terms). Optional [REF]: consider adding PMID:15071497 / PMID:23912815 (PN-cited Cul3 reviews) to the review references for completeness.

ABTB3

• Verdict: PN Cul3-adaptor projection over-reaches (domain-only, contradicted by synaptic-function evidence); review correctly rejects GO:1990756. Recommended edits:** [MAP] Suppress GO:1990756 projection for ABTB3 (no CUL3/CRL3/substrate evidence); retain the group mapping for genes with direct support (e.g. ABTB2).

ADRB2

• Verdict: PN direct-lipophagy projection over-reaches; review correctly retains positive-regulation-of-lipophagy and declines GO:0061724 (RAB7 is the direct factor). Recommended edits:** [MAP] Keep ADRB2 mapping at GO:1904504 positive regulation of lipophagy; do not propagate direct GO:0061724 lipophagy.

AFG3L2

• Verdict: Consistent; PN GO:0035694 correctly adopted as NEW; PN matrix (GO:0005759) projection correctly overruled at gene level. Recommended edits:** none required. Optional [MAP]: flag mitochondrial-proteostasis "Matrix protease" group GO:0005759 as too specific for inner-membrane matrix-facing proteases (consider GO:0005743 or no_mapping).

AGK

• Verdict: Consistent; PN TIM22 (GO:0042721) adopted; PN class GO:0015031 protein transport too broad — review's GO:0045039 is the correct narrower call. Recommended edits:** none required. Optional [MAP]: confirm class-level GO:0015031 stays gene-gated in favor of compartment-specific insertion/import terms.

AGR2

• Verdict: Consistent; PN GO:0003756 projection validated and added via MODIFY; only nuance is the pseudo-PDI catalysis debate (review mitigates via mixed-disulfide evidence). Recommended edits:** none required; [REF] optionally note in review that AGR2 is a non-canonical CXXS PDI-family member (catalytic isomerase activity debated) to pre-empt over-reading GO:0003756.

AGR3

• Verdict: PN PDI projection (GO:0003756) over-reaches for AGR3; correctly overruled — best-supported role is Ca-dependent ciliary beat regulation. Recommended edits:** none to YAML. [MAP]: flag ER-proteostasis "Protein disulfide isomerases" group GO:0003756 as requiring gene-level catalytic gating; AGR3 (DCYQS, no CXXC) should be excluded/no_mapping.

AHCTF1

• Verdict: Consistent; PN nuclear pore (GO:0005643) adopted; PN class GO:0015031 protein transport over-reaches for an NPC-assembly factor — review's GO:0051292 + GO:0003682 are the correct calls. Recommended edits:** none required. [MAP]: flag class-level GO:0015031 for the Nuclear proteostasis|Protein transport node as too broad for structural NPC-assembly factors; consider gene-gating. [WB]: optionally reconsider AHCTF1's inclusion in the PN source list (assembly factor, weak proteostasis link).

AHR

• Verdict: PN UPS/CUL4-adaptor projection (GO:1990756) over-reaches; correctly NOT propagated to AHR (left as open question). Core TF/nuclear-receptor function fully captured. Recommended edits:** none to YAML. [MAP]: keep AHR/ARNT/TBL3 and PAS subtypes no_mapping; gate the Cul4A/Cul4B substrate-adaptor group GO:1990756 behind per-gene review (AHR is the cautionary case). [REF]: optionally fetch/verify PN PMID:17392787 & 28416634 to substantiate or retire the AHR UPS placement.

AIP

• Verdict: Consistent; PN PPIase (GO:0003755) projection correctly overruled with direct biochemical evidence; cochaperone role captured more specifically as GO:0051879. Recommended edits:** none required. Optional [MAP]: note FKBP-type PPIase group GO:0003755 over-projects to catalytically-dead members (AIP); flag for gene-level gating.

AIPL1

• Recommended edits:** [MAP] Flag GO:0003755 PPIase as a known false-positive for AIPL1 in the PPIase group/type mapping notes (gene-level exclusion), so the FKBP-type propagation does not re-assert PPIase activity on AIPL1.

AIRE

• Recommended edits:** [MAP] Mark AIRE (and other PHD-"other" members) as a gene-level exception to the RING-variant→GO:0061630 propagation, or downgrade that subtree to context_only, since PHD-reader members are not demonstrated catalytic E3s. [REF] Adjudicate PMID:14734522 and PMID:15150263 (the PN E3 references) — fetch full text and record a reference_review before any E3 verdict.

AKIRIN1

• Recommended edits:** [MAP] Split the adaptors|Akirin type so GO:0070628 proteasome binding propagates to AKIRIN2 only; mark AKIRIN1 as no_mapping (nuclear transcription cofactor, no proteasome-binding evidence).

AMBRA1

• Recommended edits: [MAP] Downgrade the CMA-enhancer type→GO:1904716 to context_only (or mark AMBRA1 a gene-level exclusion) so positive-CMA is not auto-projected without LAMP2A/HSPA8 substrate-uptake evidence, consistent with the review's withholding.

ANKFY1

• Recommended edits:** none to ANKFY1-ai-review.yaml. [MAP] exclude ANKFY1 from the Cul3-substrate-receptor GO:1990756 projection (no CUL3/adaptor evidence; function is Rab5/PI3P endosomal + ATG2A autophagy). Consider re-homing ANKFY1's proteostasis placement to ALP.

ANKZF1

• Recommended edits:** none to ANKZF1-ai-review.yaml. [MAP] do not propagate GO:0035694 from the mito "Organelle-specific protein degradation" class to ANKZF1 (Vms-pathway leaf is no_mapping; gene-level evidence is RQC/stress-translocation, not mito proteolysis).

ARF1

• Recommended edits:** none to ARF1-ai-review.yaml. [MAP] flag PN "COPI coating and uncoating" subtype to not project GO:0030126 (CC membership) to regulatory GTPases such as ARF1; restrict to coatomer subunits.

ARL8A

• Recommended edits:** none to ARL8A-ai-review.yaml. [MAP] do not propagate GO:0061906 to ARL8A from the autophagosome-localization leaf until direct ARL8A-dependent autophagosome positioning is shown; ARL8A's shared target is lysosome localization.

ARL8B

• Recommended edits:** none to ARL8B-ai-review.yaml (it already flags both issues). [MAP] do not propagate GO:0061906 to ARL8B (autophagy role captured by GO:0061909). [REF] PN/curators: correct GO:0007059 origin reference PMID:14871887 → PMID:15331635 (GIE/ARL8 study).

ARNT

• Verdict: PN UPS adaptor projection over-reaches and is correctly rejected in-review. Recommended edits:** exempt ARNT from GO:1990756 group propagation at the mapping layer [MAP].

ATP23

• Verdict: MOSTLY CONSISTENT — IMS location good; class-level catabolic projection mis-flavored for an assembly/processing peptidase. Recommended edits:** [MAP] mark GO:0035694 class projection as not_for_propagation to ATP23 (gene is processing/assembly, not catabolism); review's GO:0034982 is the correct process term.

ATP6V0A1

• Recommended edits:** [YAML] Consider aligning the GO:0046610 NEW-row evidence code between ATP6V0A1 (IC) and ATP6V0C (TAS) for consistency across the V0 PN refinements (low priority; both are defensible).

ATP6V0A4

• Verdict: PN LYSOSOMAL PROJECTION OVER-REACHES for a4 (renal-apical, not lysosomal); review correctly declined. Recommended edits:** [MAP] flag GO:0046610 + GO:0007042 leaf/type projections as not_for_propagation to ATP6V0A4 (no a4-specific lysosomal evidence; isoform is apical-PM targeted); keep GO:0033179 (V0 domain, already in GOA).

ATP6V1A

• Verdict: Consistent / ADD GO:0046612 (verified) as more-specific CC; no contradictions. Recommended edits:** [MAP] align subtype complex target GO:0033176 → GO:0046611 (lysosomal V-ATPase complex, already ACCEPTed in review) for specificity.

ATP6V1B1

• Mapping strategy: The shared V-ATPase node maps to lysosomal terms generically, but B1 is a tissue-restricted plasma-membrane isoform — analogous to the TOMM20/HSPA8/RAB7A "too broad" precedent. [MAP]** flag B1 as an exception to lysosomal projection (scope=too_broad/wrong_compartment for this isoform); the generic vacuolar V1 term (GO:0000221, already in review) is the safe target.
• Verdict: OVER-REACH — PN lysosomal projection (GO:0046612/GO:0007042) is wrong-compartment for this apical-plasma-membrane kidney isoform. Recommended edits:** [MAP] exempt ATP6V1B1 from lysosomal-acidification/lysosomal-V1 projection; restrict to vacuolar V1 domain + plasma-membrane/renal acid-secretion terms already in the review.

ATP6V1D

• Verdict: Consistent / ADD GO:0046612 (verified) as more-specific CC; review exceeds PN scope (cilia) without conflict. Recommended edits:** [MAP] align subtype complex target GO:0033176 → GO:0046611 (lysosomal V-ATPase complex, already ACCEPTed for D).

ATP6V1E1

• Verdict: Consistent / ADD GO:0007042 + GO:0046612 (verified, new to E1 GOA); review also makes an unrelated REMOVE for a mis-attributed citation. Recommended edits:** [MAP] consider subtype complex GO:0033176 → GO:0046611 (already ACCEPTed for E1) for specificity.

ATP6V1E2

• Mapping strategy: Like B1/G3, E2 is a tissue-restricted isoform whose specialized compartment is not the lysosome (TOMM20/HSPA8/RAB7A "too broad" precedent applies). [MAP]** flag E2 as an exception to lysosomal projection; safe target is the generic catalytic/V1 complex term (GO:0033178, already in review). Acrosome remains non-core/IEA.
• Verdict: OVER-REACH — PN lysosomal projection wrong-compartment for this testis/acrosome isoform (and acrosome itself is IEA-only). Recommended edits:** [MAP] exempt ATP6V1E2 from lysosomal-acidification/lysosomal-V1 projection; restrict to vacuolar/catalytic V1 complex terms; keep acrosome as non-core.

ATP6V1G2

• Mapping strategy: Tissue-restricted neuronal isoform; lysosomal projection is over-broad (TOMM20/HSPA8/RAB7A precedent). [MAP]** flag G2 as an exception — its acidification specialization is synaptic-vesicle (GO:0097401), not lysosomal; safe complex target is GO:0000221/GO:0016471 (already in review).
• Verdict: OVER-REACH — PN lysosomal projection wrong-compartment for this brain/synaptic-vesicle isoform; correct acidification term (GO:0097401) already present. Recommended edits:** [MAP] exempt ATP6V1G2 from lysosomal-acidification/lysosomal-V1 projection; route to synaptic-vesicle acidification + vacuolar V1 complex terms already in the review.

ATP6V1G3

• Mapping strategy: Tissue-restricted plasma-membrane isoform; lysosomal projection over-broad (TOMM20/HSPA8/RAB7A precedent). [MAP]** flag G3 as an exception — safe targets are vacuolar V1 domain/complex (GO:0000221/GO:0016471) + plasma-membrane acid-secretion context already in the review; the specific G3-a-subunit ATPase-binding (GO:0051117) is the mechanistically informative core, not lysosomal acidification.
• Verdict: OVER-REACH — PN lysosomal projection wrong-compartment for this apical-plasma-membrane kidney isoform. Recommended edits:** [MAP] exempt ATP6V1G3 from lysosomal-acidification/lysosomal-V1 projection; restrict to vacuolar V1 complex + plasma-membrane/renal acid-secretion terms already in the review.

AZI2

• Verdict: Consistent biology, but PN xenophagy projection over-reaches for a TBK1-adaptor/regulator. Recommended edits:** [MAP] downgrade AZI2's contribution to the Xenophagy node from xenophagy (GO:0098792, involved_in) to regulation of xenophagy (GO:1904415) — AZI2 is a TBK1-recruiting adaptor, not a cargo receptor. [YAML] optionally add GO:1904415 regulation of xenophagy (involved_in) supported by PMID:30459273 to reflect the NDP52/TAX1BP1-TBK1 bridging role; do not add bare GO:0098792.

BAG2

• Verdict: NEF classification sound and already captured; the UPS "adaptor → proteasome binding" projection is unsupported for BAG2. Recommended edits:** [MAP] do not project GO:0070628 proteasome binding onto O95816 (BAG2 binds HSP70 and CHIP, not the proteasome); its UPS role is already covered by GO:0031625 / GO:0031397 in the review.

BCL2L13

• Verdict: Consistent; mitophagy process correctly added (note it is already IEA in UniProt GOA). Key finding: the review's proposed NEW "mitophagy receptor activity" duplicates existing GO:0140580. Recommended edits:** [YAML][REF] replace the BCL2L13 proposed_new_term with existing GO:0140580 mitochondrion autophagosome adaptor activity (add as core MF, supported by PMID:26146385); [MAP] note GO:0000423 is already UniProt-IEA, so goa_status is closer to "already_in_goa" than "new_to_goa".

BNIP3L

• Verdict: Consistent; mitophagy process already captured. Key finding: the review's proposed NEW "mitophagy receptor activity" term duplicates the existing GO:0140580. Recommended edits:** [YAML][REF] replace the BNIP3L proposed_new_term "mitophagy receptor activity" with the existing GO:0140580 mitochondrion autophagosome adaptor activity (add as core MF, supported by PMID:20200478).

CACUL1

• Recommended edits:** Suppress/except the Cullin-group GO:0160072 projection for CACUL1; mark the node mapping as not-inherited for this degenerate member. [MAP]

CACYBP

• Verdict: Domain-based misclassification — CACYBP is a Siah1 E3-ligase adaptor / S100A6-binding protein, not a demonstrated HSP90 cochaperone; Hsp90-binding projection is unsupported. Recommended edits:** [MAP] remove/flag GO:0051879 projection onto Q9HB71 and reconsider the HSP90-cochaperone placement; the gene's shared MF is better represented by molecular adaptor activity (GO:0060090) / ubiquitin protein ligase binding, already in the review.

CALCOCO1

• Recommended edits:** [YAML] Add GO:0061709 reticulophagy (BP, involved_in) to CALCOCO1 existing/core annotations — currently new_to_goa and the validated core process. [YAML] Replace proposed_new_terms "reticulophagy/Golgiphagy receptor activity" with existing GO:0160247 autophagy cargo adaptor activity (and GO:0038024 cargo receptor activity) as the molecular_function for the core receptor role. [REF] Add the EMBO J "CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy" PMID (named in PN dossier) to the review references.

CALR

• Verdict: OVER-REACHES — reject projected GO:0006487 for CALR (true lectin-chaperone function already captured). Recommended edits:** [MAP] do not propagate GO:0006487 to CALR; re-map the shared "Lectin chaperone" type node to a binding/chaperone term (GO:0030246 / GO:0036503), covering CALR+CANX together.

CALR3

• Recommended edits:** [MAP] Do not propagate GO:0006487 to CALR3; remap N-glycosylation system group to a folding/glycoprotein-QC term or leave chaperone members unmapped. [MAP] Reconsider the Lectin chaperone leaf for CALR3 (documented lectin-independent). [YAML] No glycosylation annotation for CALR3.

CAMLG

• Verdict: GET-pathway placement sound and already captured by a more specific gene-level term; PPIase classification is a misassignment — CAML binds cyclophilin B but is not a PPIase. Recommended edits:** [MAP] flag CAMLG as a non-member of the PN "Peptidyl-prolyl isomerases / Cyclophilin type" node, or block GO:0003755 projection onto P49069 (binds cyclophilin, no isomerase activity).

CAND1

• Verdict: Consistent and the strongest ADD case of the six — GO:1990757 (real) is a defensible new MF for CAND1, matching both PN and the review's positive-regulator framing. Recommended edits:** [YAML] consider adding GO:1990757 ubiquitin ligase activator activity to CAND1 existing/core (currently only proposed as a bespoke new term); [REF] confirm PN reference 23453757 and add to the review if it supports the activator role.

CAND2

• Verdict: Substantively consistent; PN activator mapping (GO:1990757) over-reaches and conflicts with the review's non-catalytic/context-inhibitory exchange-factor framing. Prefer review's GO:0097602 + GO:0010265. Recommended edits:** [MAP] downgrade CAND2 type/subtype GO:1990757 mapping toward exchange-factor/cullin-binding (GO:0097602) or context_only, rather than "activator". [REF] add PMID:40011427 to CAND2 review references (currently only cited via falcon report).

CANX

• Verdict: OVER-REACHES — projected GO:0006487 mis-assigns an enzymatic process to a lectin chaperone; reject for CANX (true function already captured). Recommended edits:** [MAP] do not propagate GO:0006487 to CANX; re-map the "Lectin chaperone" type node to a binding/chaperone term (e.g. GO:0030246 carbohydrate binding / GO:0036503 ERAD pathway).

CCDC47

• Verdict: Consistent; PN adds the precise complex term. Recommended edits:** [YAML] ADD GO:0160005 PAT complex (part_of, IPI/IDA, PMID:32814900/PMID:36261522) to CCDC47 existing_annotations and core_functions.in_complex — it is the exact, more-specific complex vs the review's GO:0160064. [MAP] keep GO:0044743/GO:0015031 as context-only (broader than review's GO:0160063/GO:0045048).

CCDC50

• Verdict: CONSISTENT conclusion (GO:0160247 ADD agreed by both); evidence sources diverge. Recommended edits:** [REF] add the CCDC50/NLRP3 autophagic-degradation EMBO reports paper to the review references and as supporting_text for the proposed GO:0160247 receptor MF.

CDK5RAP3

• Recommended edits:** None required; optionally note GO:0006515 is a broader sibling of the review's GO:0072344/GO:0032790 and should not displace them. [MAP]

CGRRF1

• Recommended edits:** Suppress/flag the RING-group GO:0061630 projection for CGRRF1 (unproven catalytic activity; one in vitro assay negative); if retained, mark as homology-only/unverified rather than ok_for_propagation. [MAP]

CHIC2

• Verdict: UNDER-CAPTURED by review — PN ADD is justified. Recommended edits:** [YAML] add PMID:40796662 to references and add a NEW/proposed annotation GO:0000151 (part_of, "STUB1-CHIC2 complex") and an adapter/molecular-function note; [REF] flag that the review's "function undefined" framing is now superseded by the STUB1-CHIC2 adapter finding.

CLCN7

• Recommended edits:** [YAML] Add an existing_annotations/proposed_new_terms entry or core_functions.directly_involved_in for GO:0007042 lysosomal lumen acidification (involved_in, supported_by PMID:18449189), framed as contributory.

CLGN

• Recommended edits:** [MAP] Do not propagate GO:0006487 from N-glycosylation system to lectin-chaperone members (CLGN); remap the group to a folding/glycoprotein-QC term or leave lectin chaperones unmapped. [YAML] No glycosylation annotation should be added to CLGN.

CLPX

• Recommended edits:** [MAP] Reconsider [class] projection GO:0035694 → use GO:0030163 protein catabolic process (matches GOA + ClpXP biology; GO:0035694's definition is lysosome-like-organelle specific). [MAP] Optionally extend the PN node to reflect CLPX's GO:0006783 heme biosynthesis chaperone role.

CNOT4

• Verdict: CONSISTENT — defensible ADD of GO:0006515 (protein QC) to capture the RQC role. Recommended edits:** [YAML] consider adding GO:0006515 (involved_in, from PMID:29861391 ABCE1/co-translational QC) as a proposed_new_term or NEW annotation to align with the PN RQC projection.

CNPY3

• Recommended edits:** [MAP] Correct goa_status for GO:0051879 on the CNPY3 row from more_specific_than_existing_goa to new_to_goa (no Hsp90-binding annotation exists in CNPY3 GOA). (Review already proposes GO:0051879 + the full chaperone/TLR NEW set; no YAML change needed.)

CSNK1D

• Verdict: UNDER-CAPTURED autophagy role; PN ADD (GO:0000045) plausible but PMID-unverified. Recommended edits:** [REF] resolve the PN row's title-only citations to PMIDs and confirm human (not just yeast Hrr25) evidence; [YAML] if confirmed, add GO:0000045 (involved_in) and reframe the SEC23/COPII annotations to note an autophagosome-membrane-input role alongside secretion.

CSNK2B

• Verdict: ROW-1 OVER-REACHES (yeast UTP-C orthology); ROW-2 acceptably no_mapping. Recommended edits:** [MAP] downgrade row-1 SSU-processome/ribosome-biogenesis projection (GO:0032040/GO:0042254) to context_only/no_mapping for human CSNK2B pending human evidence; [WB] human CSNK2B SSU-processome membership unverified (PubMed: 0 hits).

CWC27

• Verdict: Inconsistent — PN propagates positive GO:0003755 PPIase activity onto a curated dead pseudo-enzyme that GOA annotates as NOT|GO:0003755. Recommended edits:** [MAP] exclude CWC27 from the cyclophilin-type GO:0003755 propagation (CWC27 is a catalytically inactive pseudo-PPIase; GOA = NOT|GO:0003755, PMID:20676357); represent CWC27 via its scaffold/spliceosome role instead.

CYB5R4

• Verdict: Inconsistent — PN HSP90-cochaperone placement / GO:0051879 over-reaches and is unsupported by the review. Recommended edits:** [MAP] exclude CYB5R4 from GO:0051879 Hsp90 protein binding propagation (CS/p23 domain is structural-homology only; no Hsp90-binding evidence); flag the PN "HSP90 cochaperone" classification as domain-based, not functional. [REF] none.

DCAF10

• Recommended edits:** Add GO:1990756 (ubiquitin-like ligase-substrate adaptor activity) as the molecular_function on DCAF10's core_function, inferred by homology/DCAF-family membership. [YAML]

DDA1

• Verdict: Consistent; GO:0160072 (scaffold) is a defensible-but-borderline add vs the review's GO:0005198. Recommended edits:** [YAML] optionally add GO:0160072 to DDA1 core MF (or reconcile GO:0005198 vs GO:0160072) to align the review with the PN scaffold projection.

DDB1

• Verdict: Biology consistent but PN MF mapping mis-categorized. Recommended edits:** [MAP] retarget DDB1 "Cullin adaptor" node from GO:1990756 to GO:0160072 (scaffold), matching the review's accepted MF and existing GOA.

DDB2

• Verdict: Consistent; PN GO:1990756 (receptor) is correctly categorized and a defensible add. Recommended edits:** [YAML] consider adding GO:1990756 to DDB2 as the explicit DCAF substrate-receptor MF (complements existing GO:0004842 contributes_to), aligning with the PN projection.

DDRGK1

• Verdict: Consistent and high quality; only the broad GO:0006515 RQC projection over-reaches relative to existing specific GOA terms. Recommended edits:** [MAP] drop/downgrade GO:0006515 projection for DDRGK1 (specific RQC terms GO:0072344/GO:0032790 already in GOA and reviewed).

DENR

• Verdict: Mapping mismatch — PN "translation termination" + GO:0006415 contradicts DENR's reinitiation/recycling biology (already in GOA as GO:0002188). Recommended edits:** [MAP] do not project GO:0006415 to DENR; reclassify the PN node as translation reinitiation/40S recycling (GO:0002188 already in GOA).

DNAJB13

• Recommended edits:** [MAP] Exclude DNAJB13 from the J-domain containing HSP70 cochaperone GO:0030544 projection (catalytically-divergent, no HSP70-binding evidence; function is structural radial-spoke). [MAP] Re-examine its ER-branch placement (protein is axonemal, not ER-resident).

DNAJC10

• Verdict: Row1 consistent/captured; Row2 over-reaches (PDI isomerase ≠ ERdj5 reductase). Recommended edits:** [MAP] retarget DNAJC10 row2 from GO:0003756 (PDI activity) to GO:0015035 (protein-disulfide reductase activity), or exclude ERdj5 from the "Protein disulfide isomerases" PN group as a reductase exception.

DNAJC11

• Verdict: PN over-reaches — DNAJC11 is a structural MIB/cristae protein, not a demonstrated HSP70 cochaperone. Recommended edits:** [MAP] remove/exempt DNAJC11 from GO:0030544 propagation under the "J-domain containing HSP70 cochaperone" type; its propagating terms are GO:0140275 / GO:0042407.

DNAJC12

• Verdict: Consistent; PN GO:0030544 defensible and already realized in the review. Recommended edits:** [MAP] (minor) correct DNAJC12 projected goa_status from more_specific_than_existing_goa to new_to_goa (GOA lacks the GO:0031072 parent).

DNAJC13

• Verdict: Cochaperone identity consistent; GO:0030544 defensible but inferred. Recommended edits:** [MAP] (minor) correct DNAJC13 projected goa_status to new_to_goa; optionally co-propagate GO:0001671 (ATPase activator activity) to match the review's core MF.

DNAJC14

• Verdict: PN over-reaches — Hsp70 binding unverified; DNAJC14's supported function is GPCR ER export. Recommended edits:** [MAP] do not propagate GO:0030544 to DNAJC14 (mark cochaperone MF unverified); retain GO:0050780 / GO:0001664 as the gene-level MF.

DNAJC16

• Verdict: Over-reaches for this gene — Hsp70 binding is domain-inferred only, no HSP70 partner shown; flag as family-level inference, not new_to_goa. Recommended edits:** [MAP] downgrade DNAJC16's GO:0030544 projection from new_to_goa confident annotation to family/ISS-level inference (no experimental HSP70 binding); note the established function (autophagosome-size regulation) lies outside this HSP70-cochaperone node.

DNAJC17

• Verdict: Plausible family inference but over-reaches as confident projection; gene's real function (spliceosome/RNA) sits outside the HSP70-cochaperone node. Recommended edits:** [MAP] mark DNAJC17's GO:0030544 as family/domain-level inference (no experimental HSP70 binding); correct the "more_specific_than_existing_goa" tag (existing GOA MF is RNA binding, not an HSP70 parent).

DNAJC22

• Verdict: Consistent family-level inference; GO:0030544 is a defensible more-specific candidate but unverified experimentally — flag as ISS/family inference rather than confident new annotation. Recommended edits:** [MAP] retain GO:0030544 for DNAJC22 but mark as family/domain-level inference (no experimental HSP70 binding; Wurst-orthology basis only).

DNAJC27

• Verdict: Consistent core review; PN placement over-emphasizes the J-domain. GO:0030544 is a defensible inferred ADD but not core. Recommended edits:** [MAP] change goa_status from more_specific_than_existing_goa to new_to_goa (no existing chaperone-binding GOA term to refine).

DNAJC28

• Verdict: Consistent on function (uncharacterized J-protein); GO:0030544 defensible inferred ADD. Recommended edits:** [MAP] change goa_status to new_to_goa; [MAP] reconcile ER vs mitochondrial branch placement (review predicts mitochondrial targeting).

DNAJC30

• Verdict: Over-reach. GO:0030544 projection is unsupported for DNAJC30 (a complex-I repair / ATP-synthase auxiliary factor). Recommended edits:** [MAP] do not propagate GO:0030544 to DNAJC30 (family-level over-inference; gene-level GO:0051082 + GO:0019899 already capture its biology); [MAP] if retained, downgrade goa_status to new_to_goa and mark as IBA/family-inferred only.

DNAJC4

• Verdict: Family-level J-co-chaperone call sound; GO:0030544 is a defensible-but-unverified ADD; mitochondrial placement and the GO:0030544-vs-GO:0051082 MF mismatch need reconciling. Recommended edits:** [MAP] reconcile Hsp70 protein binding (GO:0030544) projection with the review's GO:0051082 unfolded protein binding — both are family-level/unverified; prefer GO:0030544 only if asserted as predicted, not experimental. [MAP][WB] verify the Mitochondrial-branch assignment — no mitochondrial localization evidence appears in the review or notes.

DNAJC5

• Verdict: Fully consistent; PN Hsp70-binding story already captured as core MF (GO:0030544). Recommended edits: none required; optionally [MAP] note that CSPalpha is the prototypical synaptic/secretory-vesicle CSP, so the ER-branch placement is an umbrella rather than its primary compartment.

DNAJC5G

• Verdict: Family-level call sound; GO:0030544 is a defensible-but-unverified ADD; harmonize MF term with the CSP family. Recommended edits:** [MAP] reconcile the GO:0030544 (PN) vs GO:0051082 (review) MF choice across the CSP paralogs — for consistency with DNAJC5/DNAJC5B, GO:0030544 Hsp70 protein binding is preferable, asserted as predicted/family-level (not experimental).

DNAJC6

• Verdict: Consistent and well-supported; PN's GO:0030544 is a defensible more-specific ADD over the review/GOA's GO:0031072. Recommended edits:** [YAML][MAP] consider replacing/supplementing GO:0031072 heat shock protein binding with the more specific GO:0030544 Hsp70 protein binding in the review core MF (auxilin's documented partner is HSPA8/HSC70), aligning with the PN projection.

DNAJC7

• Verdict: Fully consistent; row2 already captured, row1 GO:0030544 a defensible-but-secondary more-specific ADD. Recommended edits:** [MAP] note that for DNAJC7 the broader GO:0031072 (joint HSP70/HSP90 binding) is the better umbrella than the HSP70-only GO:0030544; consider also projecting the well-supported GO:0001671 ATPase activator activity (review core MF, in GOA) from the J-domain node.

DRG2

• Verdict: GTPase biology is solid, but the PN RQC placement and GO:0006515 projection are unsupported for DRG2. Recommended edits:** [MAP] do not project GO:0006515 (protein QC) to DRG2 — no RQC/surveillance evidence; GTPase activity (GO:0003924) is the supported core.

DTL

• Verdict: Consistent; PN GO:1990756 is correctly categorized and a defensible more-specific add over the review's GO:0030674. Recommended edits:** [YAML] optionally add/swap GO:1990756 as the DCAF substrate-receptor MF (more specific than GO:0030674), aligning with the PN projection.

EEF2K

• Verdict: Clear mis-mapping — EEF2K is the eEF2 kinase, not a translation elongation factor; GO:0003746 should not be projected. Recommended edits:** [MAP] remove GO:0003746 projection for EEF2K; if a shared process is wanted use GO:0045900 negative regulation of translational elongation. Core MF GO:0004686 already in GOA.

EIF2D

• Verdict: Mapping mismatch — PN "translation termination" + GO:0006415 contradicts EIF2D's initiation/recycling biology already in GOA. Recommended edits:** [MAP] do not project GO:0006415 to EIF2D; reclassify PN node toward reinitiation/40S recycling (GO:0001731 / GO:0032790 already in GOA).

EIF3J

• Verdict: Initiation placement consistent and correct; RQC-group GO:0006515 projection over-reaches (EIF3J is a recycling accessory, not a protein-QC factor). Recommended edits:** [MAP] drop GO:0006515 projection for EIF3J (or substitute GO:0032790 ribosome disassembly if a recycling term is wanted).

EIF4E2

• Verdict: Biology consistent; one node-level contradiction (PN GO:0016281 vs review REMOVE). RQC story already captured more precisely. Recommended edits:** [MAP] flag the EIF4E2 "eIF4F complex" type→GO:0016281 projection as inappropriate (4EHP cannot bind eIF4G / is not an eIF4F component — see review REMOVE of GO:0016281); do not propagate GO:0016281 to O60573.

EIF5A

• Verdict: Consistent; elongation core fully captured. GO:0006515 RQC umbrella is defensible but mildly over-reaching for a general elongation factor and is absent from the review. Recommended edits:** [MAP] treat the EIF5A RQC-group→GO:0006515 projection as low-confidence (eIF5A is an elongation factor with a supportive RQC-cofactor role, not a dedicated surveillance factor); optionally [YAML] consider adding eIF5A's RQC-cofactor role only if curator deems UniProt's CAT-tailing statement annotation-worthy.

ERLIN1

• Recommended edits:** [MAP] Replace/qualify the GO:0000151 group projection with GO:0000835 "ER ubiquitin ligase complex" (CC) for the ERLIN/RNF170 assembly, noting ERLINs are non-catalytic BAND 7 subunits. [YAML, optional] Consider adding MF GO:0160072 "ubiquitin ligase complex scaffold activity" to core_functions for the adaptor role.

ERLIN2

• Recommended edits:** [MAP] Replace/qualify the GO:0000151 group projection with GO:0000835 "ER ubiquitin ligase complex" (CC), noting ERLINs are non-catalytic BAND 7 subunits. [YAML, optional] Consider adding MF GO:0160072 "ubiquitin ligase complex scaffold activity" to core_functions.

ERO1A

• Verdict: Consistent at the (corrected) gene/type level; GO:0016971 validated and captured. The lingering group-level GO:0003756 projection over-reaches and should not land on ERO1A. Recommended edits:** [MAP] suppress/override the GO:0003756 projection for ERO1A (and ERO1B) so the PDI-reoxidation oxidase children inherit only GO:0016971, not the parent isomerase term (matches the already-corrected type node and the review's oxidase-vs-isomerase distinction).

ERO1B

• Verdict: Consistent at the (corrected) gene/type level; GO:0016971 validated and captured. The group-level GO:0003756 projection over-reaches and should not land on ERO1B (same fix as ERO1A). Recommended edits:** [MAP] suppress/override the GO:0003756 projection for ERO1B so PDI-reoxidation oxidase children inherit only GO:0016971 (consistent with the corrected type node and the review's explicit oxidase-not-isomerase / not-reductase stance).

ERP27

• Verdict: Contradiction — PN projects GO:0003756 (new_to_goa) onto a gene whose review explicitly NEGATES that exact term (no CXXC, catalytically inactive). PN over-reaches; review is correct. Recommended edits:** [MAP] remove/suppress the GO:0003756 projection for ERP27 (it is a non-catalytic PDI-family member; the term is correctly a NOT annotation). If a positive mapping is wanted, target GO:0051082 unfolded protein binding and/or GO:0051087 protein-folding chaperone binding (both OLS-real, both already in the review's core_functions).

ERP29

• Verdict: OVER-REACHES / CONTRADICTED — reject projected GO:0003756 for ERP29; the gene is a non-catalytic PDI member whose function is already captured by GO:0051087. Recommended edits:** [MAP] do not propagate GO:0003756 to ERP29 (it carries a curated NOT for this term); exclude non-catalytic PDI-family members from the group's isomerase projection or re-map ERP29 to GO:0051087 protein-folding chaperone binding.

FAF2

• Recommended edits:** [YAML] (optional) add GO:0035694 mitochondrial protein catabolic process (involved_in; mitoTAD/mito membrane-protein extraction, PMID:41258083) as a non-core BP to mirror the PN projection. [REF] PN-cited PMID:18438607 (UBX row) absent from review — verify whether gene-specific or a UBX-family review.

FBXL16

• Verdict: CONSISTENT-WITH-CAVEATS / ACCEPT degradative mapping. Flag: non-canonical F-box (no detectable CUL1). Proposed stabilizer term is candidate/unverified. Recommended edits:** none to YAML [no change]; [MAP] annotate node that FBXL16 is non-canonical (SKP1+ / CUL1-negative) so GO:1990756 propagation is treated as tentative for this member.

FBXL3

• Verdict:** CONSISTENT / ACCEPT mapping. No edits required; the MODIFY→GO:1990756 pattern is correctly applied. Optional [REF]: PN-row reference PMID:15340381 not reflected in review (placeholder only).

FBXL8

• Verdict: MAPPING CONSISTENT but YAML gap. Recommended edits:** [YAML] add GO:1990756 as action: NEW in FBXL8 existing_annotations (mirror FBXL7/FBXL12) so the PN-projected adaptor MF is materialized; [MAP] consider noting the non-canonical (no-LRR) status on the F-box|LRR subtype for FBXL8.

FBXO10

• Recommended edits:** none to FBXO10-ai-review.yaml. [MAP] none — node mapping and review concur.

FBXO15

• Recommended edits:** none to FBXO15-ai-review.yaml. [MAP] none — node mapping and review concur.

FBXO16

• Recommended edits:** [YAML] consider adding GO:1990756 as a NEW MF existing_annotation (currently FBXO16 carries no MF annotation; the adaptor activity lives only in core_functions) — mirrors the explicit NEW done for FBXO15. [MAP] none.

FBXO17

• Recommended edits:** none to FBXO17-ai-review.yaml (ERAD MARK_AS_OVER_ANNOTATED and NEW carbohydrate-binding are sound). [MAP] for the FBA subfamily, prefer GO:0030246 (lectin) as the informative MF at gene level rather than propagating the generic GO:1990756; do not propagate ERAD (GO:0036503) from the FBA node to FBXO17.

FBXO2

• Recommended edits:** none to FBXO2-ai-review.yaml. [MAP] Optionally annotate FBA-lectin F-box subfamily nodes so carbohydrate binding (GO:0030246) is recognized as their distinguishing MF alongside the generic GO:1990756.

FBXO21

• Recommended edits:** none to FBXO21-ai-review.yaml. [MAP] none — node mapping and review concur.

FBXO27

• Recommended edits: [YAML] In FBXO27-ai-review.yaml, replace the proposed_new_terms "lysophagy" entry with a reference to existing GO:0062093 lysophagy (verified real), and set core_function #3 directly_involved_in to GO:0062093 (more specific than GO:0016236 macroautophagy). [YAML] Optionally MODIFY the ERAD IBA (GO:0036503) toward GO:0097466 ubiquitin-dependent glycoprotein ERAD pathway** if retained.

FBXO40

• Verdict: Consistent; correct F-box MODIFY pattern; defensible verified NEW BP (GO:0046627). ACCEPT review. Recommended edits:** none required; optionally [REF] upgrade PMID:22033112 to VERIFIED if full text read.

FBXO41

• Verdict: Consistent; well-evidenced verified NEW terms. ACCEPT review. Recommended edits:** none for YAML; optionally [MAP] note FBXO41 auxiliary domain may be C2H2/coiled-coil rather than LRR in the PN workbook.

FBXO43

• Verdict: Review correct; PN node mis-files FBXO43 and over-reaches with GO:1990756. Recommended edits:** [MAP] exclude FBXO43/EMI2 from the GO:1990756 substrate-adaptor projection and flag as non-canonical F-box / APC/C inhibitor (core MF GO:1990948), mirroring FBXO5/EMI1.

FBXO47

• Verdict: Consistent at MF label; meiotic biology appropriately added (GO:0007129) with honest UNDECIDED on SCF catabolism. ACCEPT review. Recommended edits:** none required; optionally [REF] verify Hua 2019 / Guan 2022 / Ma 2024 PMIDs and [YAML] convert the label-only bouquet term to a real GO ID if one exists (e.g. via OLS) before promotion.

FBXO5

• Recommended edits:** none to FBXO5-ai-review.yaml (review is correct). [MAP] Flag FBXO5/EMI1 as a non-canonical F-box (APC/C inhibitor) so GO:1990756 is NOT propagated to it; its core MF is GO:1990948 ubiquitin ligase inhibitor activity.

FBXO6

• Recommended edits:** none to FBXO6-ai-review.yaml. [MAP] As for FBXO2, FBA-lectin subfamily nodes could carry GO:0030246 as the distinguishing MF in addition to GO:1990756.

FBXO8

• Recommended edits:** [YAML] consider adding GO:1990756 as a NEW existing_annotation (MF) to make the adaptor activity an explicit annotation, not only a core_functions entry (FBXO8 currently has no curated SCF-adaptor MF in GOA; the only MF is the IEA GEF term, kept non-core). [MAP] none.

FBXW4

• Verdict: Row1 CONSISTENT (ADD GO:1990756). Row2 PN node OVER-REACHES. Recommended edits:** [MAP] change Row2 group Ubiquitin and UBL binding|E3 ligase projection for FBXW4 from GO:0061630 ubiquitin protein ligase activity to GO:0043130 ubiquitin binding, or set no_mapping — PMID:21070969 documents WD40 ubiquitin BINDING (regulating F-box turnover), not catalytic ligase activity; F-box proteins are non-catalytic.

FBXW5

• Verdict: MOSTLY CONSISTENT; one substrate gap. Recommended edits:** [YAML] Note the PN ALP SEC23B/autophagy axis in FBXW5 notes/description and assess the eLife "ULK1-FBXW5-SEC23B nexus" paper; if it supports a direct SCF(FBXW5)→SEC23B degradation event, consider adding it as a substrate (and a regulation-of-autophagy non-core process) — verify the PMID first. [REF] add the eLife SEC23B reference.

FBXW7

• Verdict: Rows 1–2 CONSISTENT; Row3 PN node OVER-REACHES (contradicts the review's own over-annotation call). Recommended edits:** [MAP] change Row3 Ubiquitin and UBL binding|E3 ligase projection for FBXW7 from GO:0061630 ubiquitin protein ligase activity to GO:0043130 ubiquitin binding or no_mapping — PMID:21070969 = WD40 ubiquitin BINDING controlling F-box auto-turnover, not catalytic ligase; the FBXW7 review already marks ubiquitin binding as over-annotated.

FBXW8

• Verdict: Rows 1–2 CONSISTENT (GO:1990756 already in GOA, both CUL1+CUL7 contexts validated); Row3 PN node OVER-REACHES. Recommended edits:** [MAP] change Row3 Ubiquitin and UBL binding|E3 ligase projection for FBXW8 from GO:0061630 ubiquitin protein ligase activity to GO:0043130 ubiquitin binding or no_mapping — PMID:21070969 = WD40 ubiquitin BINDING / F-box auto-turnover, not ligase catalysis; structure (PMID:35982156) shows FBXW8 is non-catalytic.

FKBP5

• Verdict: Consistent on core; PN's autophagy role is documented but intentionally non-propagating, so no required edit. Recommended edits:** none required; optionally note the FKBP5-autophagy/BECN1 paper in notes/references for completeness [REF]. Do not propagate GO:0035032/GO:0016236 (regulator, too broad) [MAP].

FKBP8

• Verdict: Consistent; all PN molecular roles captured; only nuance is mitophagy process (GO:0000423) vs regulation (GO:1901524) granularity. Recommended edits:** [MAP] optionally retarget the Mitophagy-receptor leaf projection from GO:0000423 to GO:1901524 regulation of mitophagy to match FKBP8's experimental (IDA) evidence and the review.

FKBPL

• Verdict: Consistent; PN GO:0051879 projection validated and added as the core MF; subtype-level PPIase correctly withheld. Recommended edits:** none required; [REF] optionally add PMID:15664193 (Jascur et al., WISp39/HSP90/p21) as an explicit reference entry in the review YAML to anchor the GO:0051879 core function (currently it is only in notes, with the YAML core_function relying on UniProt text).

GCN1

• Verdict: Highly consistent on core sensor/ISR/RQC biology; PN story already captured (review is more granular: GO:0140469, GO:0072344, GO:0170011). One over-reach. Recommended edits:** [MAP] qualify the eEF1A-ubiquitination type→GO:0016567 projection — GCN1 promotes (does not catalyze) eEF1A ubiquitination; project as involved_in RQC (GO:0072344) rather than as GCN1's own protein-ubiquitination activity. [REF] consider adding the PN-cited GCN1 developmental PLOS Genetics paper to the review references (currently absent) or noting its relevance is non-core.

GIGYF1

• Verdict: Fully consistent; PN RQC story already captured more precisely (GO:0045947 + NEW GO:0008190). GO:0006515 is a defensible umbrella, not an over-reach. Recommended edits:** [YAML] for paralog consistency, consider whether GIGYF1 warrants GO:0072344 (rescue of stalled cytosolic ribosome) as GIGYF2's review carries it — the underlying PMID:33053355/RQC evidence is shared (curator judgment; optional).

GLMN

• Verdict: Fully consistent; PN inhibitor mapping (GO:1904667) is well-aligned with the review (GO:0055105) — no over-reach, no missing-NEW pressure on the core function. Recommended edits:** [YAML] optional — anchor the proposed "negative regulation of cIAP-mediated inflammasome activation" term to the now-existing GO:0141086 (verify scope) as the closest existing parent/match. No mapping change required.

GTPBP1

• Verdict: Biology consistent; PN's GO:0072344 "Ribosomal rescue" mapping over-reaches vs the review's surveillance/decay framing (GO:0071025 present in GOA; GO:0072344 absent). Recommended edits:** [MAP] do not project GO:0072344 (rescue of stalled cytosolic ribosome) onto GTPBP1 — its evidenced role is mRNA surveillance/exosomal decay (GO:0071025/GO:0061014), not ribosome rescue; reclassify the PN row from "Ribosomal rescue" to "other RQC processes" (RQC-group→GO:0006515 still applies). [REF] PMID:30108131 supports surveillance, not rescue — note the interpretive divergence.

GTPBP2

• Verdict: Consistent; PN rescue story is real NEW pressure (GOA lacks a correct BP). Recommended edits:** add GO:0072344 rescue of stalled cytosolic ribosome to proposed_new_terms (or as a NEW annotation) [YAML]; consider adding Ishimura 2014 Science to references for the PELO-rescue/neurodegeneration evidence [REF].

GTPBP6

• Verdict: Mostly consistent on biogenesis (already captured, review narrower); row-2 stalled-ribosome-rescue projection over-reaches vs the recycling evidence. Recommended edits:** keep GO:7770016 as context-only / do not propagate to GTPBP6 unless stalled-ribosome evidence is found [MAP]; optionally add a mitochondrial-ribosome-recycling process annotation (anchored to PMID:34135319 dual-role) to capture row 2 accurately [YAML].

HBS1L

• Verdict: Fully consistent; PN rescue story already captured (more specifically) — no NEW pressure. Recommended edits:** none warranted; treat group-node GO:0006515 as context-only/entailed for HBS1L (do not add as a separate annotation) [MAP].

HSPA13

• Verdict: Atypical HSP70; PN's GO:0140662 foldase projection is contradicted by the truncated SBD and peptide-independent ATPase — over-reaches. Recommended edits:** [MAP] do not project GO:0140662 ATP-dependent protein folding chaperone (nor GO:0044183) onto P48723 (PMID:8131751 truncated peptide-binding domain, peptide-independent ATPase); its evidenced MFs are GO:0016887 ATP hydrolysis activity and GO:0032182 ubiquitin-like protein binding.

HSPA14

• Verdict: RAC/cotranslational-folding projection sound and already captured; HSP70-type GO:0140662 is borderline-defensible (atypical Ssz1p-like HSP70) but should carry the caveat. Recommended edits:** [MAP] keep GO:0051083 for the RAC subtype (already covered); for the HSP70-type GO:0140662 projection, scope to co-translational folding and note HSPA14's Ssz1p-like atypia (intrinsic foldase activity uncertain) rather than asserting canonical ATP-dependent refolding.

HSPB3

• Verdict: sHSP placement sound but PN MF target mischaracterizes holdases as foldases; mito row unsupported. Recommended edits:** [MAP] retarget GO:0044183 → GO:0140309 unfolded protein holdase activity (or GO:0051082) for sHSP nodes on Q12988; [MAP] do not project a mitochondrial chaperone term onto HSPB3 (no mitochondrial localization evidence).

HSPB7

• Verdict: sHSP membership correct but the GO:0044183 foldase projection is contradicted by direct evidence; over-reaches. Recommended edits:** [MAP] do not project GO:0044183 protein folding chaperone onto Q9UBY9 (HSPB7 demonstrably does not refold; PMID:19464326); if a shared sHSP MF is desired use GO:0140309 unfolded protein holdase activity / GO:0051082 unfolded protein binding, and mark HSPB7 a non-canonical exception.

HSPB8

• Verdict: CASA/aggrephagy projection sound and already captured; sHSP foldase MF over-reaches, mito row unsupported. Recommended edits:** [MAP] retarget sHSP GO:0044183 → GO:0140309 / GO:0051082 on Q9UJY1; [MAP] do not project a mitochondrial chaperone term onto HSPB8 (no mito localization). CASA row needs no change.

HSPB9

• Verdict: sHSP placement defensible by homology but the GO:0044183 foldase projection over-reaches (wrong activity class + no demonstrated chaperone activity). Recommended edits:** [MAP] do not project GO:0044183 (foldase) onto Q9BQS6; if the sHSP node propagates an MF use GO:0140309 / GO:0051082 as inference, and note HSPB9's only experimental MF is GO:0045503 dynein light chain binding.

HYPK

• Verdict: Mostly consistent; PN's catalytic N-terminal-acetylation projection over-reaches for a NatA-modulator. Recommended edits:** treat node GO:0006474 as context-only for HYPK (do not propagate the catalytic process term); keep the review's GO:0010699 inhibitor activity + GO:0031415 NatA complex as the accurate captures [MAP].

LMAN1

• Recommended edits:** [MAP] Do not propagate GO:0006487 (protein N-linked glycosylation) to LMAN1 from the "N-glycosylation system" group — LMAN1 binds/transports high-mannose glycoproteins, it does not perform N-linked glycosylation; flag the group node as over-broad (mixes installers/processors/readers).

LMAN1L

• Recommended edits:** [MAP] Suppress GO:0006487 (protein N-linked glycosylation) propagation to LMAN1L — predicted lectin/cargo receptor, no N-glycosylation activity, and transcript-level-only evidence; do not introduce a new biosynthesis annotation on an uncharacterized paralog.

LMAN2

• Recommended edits:** [MAP] Do not propagate GO:0006487 (protein N-linked glycosylation) to LMAN2/VIP36 — it is a high-mannose glycan-reading sorting receptor (transport/retrograde QC), not an N-linked-glycosylation enzyme; flag the "N-glycosylation system" group node as over-broad.

LMAN2L

• Recommended edits:** [MAP] Do not propagate GO:0006487 (protein N-linked glycosylation) to LMAN2L/VIPL — it is an ER-resident high-mannose lectin / ER-export regulator, not an N-glycosylation enzyme; flag the "N-glycosylation system" group node as over-broad (and a poor fit for a non-cycling ER resident).

LRSAM1

• Recommended edits:** [YAML] add GO:0098792 xenophagy (BP, involved_in) — the base process is absent though GO:1904417 (its positive-regulation child) is already accepted as core; cite PMID:23245322.

LTN1

• Verdict: Fully consistent; PN story already captured (review more specific) — no NEW pressure. Recommended edits:** none required for terms; treat group-node GO:0006515 as context-only/entailed (LTN1 has the specific GO:1990116) [MAP]; optionally add PMID:19489725 (PN row-2 reference) to references if it supports the Listerin RQC/neurodegeneration role [REF].

MAN1B1

• Recommended edits:** [MAP] Correct MAN1B1's group projection of GO:0006487 — mark goa_status as NOT entailed_by_goa_closure (GO:0140277/GO:1904380 do not subsume GO:0006487); MAN1B1 is an N-glycan-processing enzyme, not an N-linked-glycosylation (attachment) enzyme.

MAP1S

• Recommended edits:** [YAML] Add GO:0000423 mitophagy (involved_in) supported_by PMID:21262964 (LRPPRC/Parkin link; defective-mitochondria accumulation) and GO:0035973 aggrephagy (involved_in) supported_by the PN-cited tandfonline/Cancer Research MAP1S-autophagy papers — fetch and add those PMIDs to references first (verify the tandfonline "MAP1S enhances autophagy to suppress tumorigenesis" PMID and the AACR Cancer Research PMID before citing). [MAP] No mapping-status change needed; both type→GO propagations are correct.

MAP3K20

• Verdict: Consistent; ribotoxic-stress sensor role already well captured — PN group GO:0006515 over-reaches for a signaling kinase. Recommended edits:** treat group-node GO:0006515 as context-only for MAP3K20 (do not propagate the protein-QC catabolic process to a sensor/signaling kinase) [MAP]; no YAML changes needed.

MEFV

• Recommended edits:** [YAML] consider adding GO:0160247 autophagy cargo adaptor activity (MF) for the TRIM20 precision-autophagy receptor role (PMID:26347139) — currently captured only as non-core positive-regulation-of-autophagy. [MAP] annotate the RING-group node (or a ringless-TRIM exclusion) so GO:0061630 does NOT auto-propagate to "Pyrin, ringless, SPRY" members lacking a functional RING; the review's over-annotation flag on GO:0061630 should be honored by the mapping.

MKRN2

• Verdict: Over-reach on the RQC branch (paralog inheritance from MKRN1). E3-ligase placement consistent. Recommended edits:** [MAP] do not project GO:0006515 / GO:1990116 onto MKRN2 from the RQC node — no human-experimental RQC evidence; flag MKRN2's RQC-node membership as paralogy-driven (PARALOG_OVERANNOTATION) pending the suggested iCLIP/ribosome-profiling experiment.

NAA30

• Verdict: Consistent and high-quality. Optional ADD of BP GO:0006474 to the review to mirror the PN projection. Recommended edits:** Add existing/new BP annotation GO:0006474 (N-terminal protein amino acid acetylation, involved_in) to NAA30 review [YAML].

NAA35

• Verdict: Consistent, high-quality. Internal note vs YAML mismatch: notes say PMID:32296183 (TRIM7) protein-binding should be MARK_AS_OVER_ANNOTATED, but YAML uses KEEP_AS_NON_CORE (minor, defensible either way). Recommended edits:** Add BP GO:0006474 (involved_in, auxiliary subunit of the acetylating complex) to NAA35 review [YAML]; optionally reconcile PMID:32296183 action with notes (KEEP_AS_NON_CORE vs MARK_AS_OVER_ANNOTATED) [YAML].

NAA38

• Verdict: Consistent, high-quality. Same minor notes-vs-YAML mismatch as NAA35: notes say HT protein-binding PMID:25416956/PMID:32814053 should be MARK_AS_OVER_ANNOTATED, YAML uses KEEP_AS_NON_CORE. Recommended edits:** Add BP GO:0006474 (involved_in, auxiliary subunit) to NAA38 review [YAML]; optionally reconcile PMID:25416956 / PMID:32814053 protein-binding actions with notes [YAML].

NAA40

• Verdict: Placement biologically off (histone NAT mis-filed under nascent-peptide husbandry); generic GO:0006474 over-reaches relative to the histone-specific terms already present. Recommended edits:** Re-home NAA40/NatD from "N-terminal acetylation of nascent peptide" to a histone/chromatin PN node, or replace the projected generic GO:0006474 with a histone-N-terminal-acetylation-specific framing [MAP]; do not add generic GO:0006474 to the review (histone-specific MFs suffice) [YAML]; PMID:25732826 already flagged WRONG_IDENTIFIER — candidate for removal/replacement [REF].

NBR1

• Verdict: CONSISTENT and convergent — review already adds GO:0160247 NEW. Minor: consider adding GO:0000425 pexophagy BP to match PN projection. Recommended edits:** consider [YAML] add existing/new GO:0000425 pexophagy (involved_in) to NBR1 review to mirror PN projection and SQSTM1 co-receptor evidence.

NEMF

• Verdict: Consistent, high-quality; PN projection of GO:0006515 is a defensible ADD (distinct QC aspect, verified absent from GOA and not an ancestor of existing terms). Recommended edits:** Add GO:0006515 (protein quality control for misfolded or incompletely synthesized proteins, involved_in) to NEMF review to mirror the PN projection [YAML].

NLRX1

• Recommended edits:** [REF/WB] obtain and assess the PN-cited "Listeria hijacks host mitophagy through a novel mitophagy receptor" (Nat Immunol) — it is absent from the review; it is the sole basis for the NLRX1 LIR/mitophagy-receptor claim and for GO:0000423. [YAML] if verified, add GO:0000423 mitophagy (and reconcile with the review's existing GO:0010508 proposed_new_term, which currently frames the autophagy role generically via TUFM rather than as mitophagy).

NPLOC4

• Verdict: Consistent, high-quality; core captured, DUB correctly suppressed, one ComplexPortal mis-citation already flagged. Recommended edits:** Optionally add GO:0006515 (involved_in, non-core) to mirror the RQC-group projection [YAML]; PMID:39329031 already flagged WRONG_IDENTIFIER on GO:0034098/GO:0043161/GO:1904949 — replace with a correct p97 complex reference [REF].

NUFIP1

• Verdict: Consistent; ribophagy ADD already implemented in review; only the proposed bespoke MF term over-reaches. Recommended edits:** [YAML] drop the proposed_new_terms "ribophagy receptor activity" entry — the existing GO:0034517 ribophagy (BP) + GO:0160247 autophagy cargo adaptor activity (MF), both already in the review's core_functions, fully capture the role (mirrors the BNIP3L/CALCOCO1 "use existing terms, don't mint new" precedent).

OPTN

• Verdict: CONSISTENT on mitophagy/xenophagy (review more specific); PN aggrephagy (GO:0035973) over-reaches / likely group-note carryover. Recommended edits:** [MAP] reconsider OPTN membership in the Aggrephagy receptor leaf (GO:0035973 new_to_goa) — unsupported by OPTN-specific evidence; demote to context or drop.

OTUD3

• Recommended edits:** [MAP] Do not propagate GO:0006515 (protein QC) to OTUD3 from the RQC-group node — OTUD3 antagonizes ZNF598-driven 40S ubiquitination (negative RQC regulator), so an involved_in protein quality control assertion mis-states direction; flag as do-not-project.

P4HA3

• Recommended edits:** [YAML] Consider adding a peptidyl-proline-hydroxylation / collagen-biosynthetic-process entry to P4HA3 proposed_new_terms (GO:0018401 / GO:0032964) for parity with P4HA1/P4HA2 and to match the PN projection.

P4HB

• Verdict: Consistent; PDI core validated; collagen role real but already captured via finer P4H-complex terms, making GO:0032964 a broader optional addition. Recommended edits:** [MAP] consider downgrading the ER-collagen-processing leaf projection (GO:0032964) to context/non-propagating for P4HB (it acts as the non-catalytic structural beta-subunit; the review's GO:0004656 contributes_to + GO:0016222 part_of are the more accurate, already-present representation).

PELO

• Recommended edits:** none required. [MAP] (optional) treat GO:0006515 for PELO as broader/redundant given GO:0072344 already exact in GOA+review.

PPIB

• Verdict: CONSISTENT — GO:0003755 already captured (correct); GO:0032964 is a sound NEW addition. Recommended edits:** [YAML] consider adding GO:0032964 collagen biosynthetic process (involved_in) to PPIB existing/proposed terms, supported by PMID:39245686 + OI9 genetics, to align the review with the defensible PN projection.

RACK1

• Recommended edits:** [YAML] Consider adding a note/annotation on the RACK1-ATG5 autophagy-regulator role (PN-cited) and the pre-40S/biogenesis association if literature supports — both are absent from the current review. [MAP] Do NOT auto-project GO:0042254/GO:0030688 to RACK1 from the biogenesis/pre-40S node without gene-level evidence (RACK1 framed as structural/RQC scaffold, not an assembly factor); GO:0006515 broader than the exact GO:0072344 already present. [REF] RACK1-ATG5 paper (resolve to a PMID) missing from review references.

RETREG2

• Recommended edits:** [YAML] add GO:0061709 reticulophagy (BP, involved_in; the specific process for this ER-phagy receptor) — currently absent; more precise than the accepted generic GO:0061753. Cite PMID:26040720/PMID:34338405.

RNF14

• Recommended edits:** none required. [REF] (optional) check PN-cited PMID:17367545 (RBR row) — absent from review; verify whether it adds RNF14-specific support or is a family review. [MAP] GO:0006515 broader than the exact RQC terms already annotated.

RNF166

• Recommended edits:** [YAML] none required for the PN story — the review already proposes GO:0098792 xenophagy (NEW). Optionally [REF] check PN row3's PMID:17990982 (UIM characterization), absent from the review, if a UIM ubiquitin-reader MF is desired.

RNF170

• Recommended edits:** [YAML] add GO:0000151 ubiquitin ligase complex (or child GO:0000835 ER ubiquitin ligase complex; part_of, PMID:21610068/38782601 ERLIN1/2 association) as a non-core CC — currently absent from the review. [REF] verify PN row-3 reference "41481136" — does not resolve as a valid PMID (likely garbled); confirm intended citation.

RNF185

• Recommended edits:** [YAML] (optional) add GO:0000151 ubiquitin ligase complex (or child GO:0000835 ER ubiquitin ligase complex; part_of, PMID:32738194) and GO:0000423 mitophagy (involved_in, PMID:21931693) as non-core annotations to mirror the PN projections. [MAP] consider GO:0000835 ER ubiquitin ligase complex as a more precise target for the membralin-complex node.

RNF25

• Recommended edits:** none required. [REF] (optional) check PN-cited PMID:19489725 (RING row) — absent from review; verify whether it adds RNF25-specific support or is a family review. [MAP] GO:0006515 broader than the exact RQC terms already annotated.

RNF41

• Recommended edits:** [REF/WB] obtain/assess the PN-cited CLEC16A-RNF41-USP8 beta-cell mitophagy paper (and UniProt's PMID:24949970 late-mitophagy citation) — both absent from the review; they are the basis for GO:0000423. [YAML] if verified, add GO:0000423 mitophagy (regulation-of-mitophagy may fit better given RNF41's late/fusion-stage role) — currently the mitophagy role is mentioned in description but unannotated and uncited.

RNF5

• Recommended edits:** none required. [YAML] (optional) consider adding GO:2000785 regulation of autophagosome assembly (IMP/IDA, PMID:23093945) as a non-core BP to mirror the PN projection. [REF] PN-cited PMID:19489725 (RING row) absent from review — verify it is a family review, not gene-specific.

SEC11A

• Recommended edits:** [MAP] At the "ER signal peptidase" node, annotate that catalytic subunits SEC11A/SEC11C additionally project signal peptidase MF (GO:0009003 / GO:0004252), distinct from accessory subunits — so the node does not flatten catalytic vs accessory members.

SEC11C

• Recommended edits:** [MAP] Same node-level note as SEC11A: flag that catalytic subunits SEC11A/SEC11C project signal peptidase MF (GO:0009003 / GO:0004252) distinct from the non-catalytic SPCS subunits.

SEC62

• Recommended edits:** [YAML] Add GO:0005784 Sec61 translocon complex (part_of/located_in, translocon-associated) to SEC62 existing_annotations/core_functions, matching the PN-projected term and the verified GO definition (TRAP-inclusive).

SEC63

• Recommended edits:** [YAML] Add MF GO:0030544 Hsp70 protein binding (enables; J-domain stimulation of BiP/HSPA5) to SEC63 existing_annotations + core_functions, supported by H132/HPD mutagenesis and PMID:29719251/36459117. [YAML] Optionally add GO:0005784 Sec61 translocon complex CC to mirror the PN node.

SERPINH1

• Verdict: Consistent and high-quality. Recommended edits:** optionally add GO:0032964 collagen biosynthetic process (KEEP_AS_NON_CORE) to align with PN, since it captures HSP47's ER-upstream role better than the existing GO:0030199 fibril-organization term [YAML]; otherwise no change.

SGTA

• Verdict: Consistent; PN adds breadth only, no new defensible term. Recommended edits:** none required; treat GO:0015031 and GO:0031072 as broader-than-review and do not propagate (gene-level GO:0006620/GO:0071816/GO:0051879 already finer) [MAP].

SIAH1

• Recommended edits:** [YAML] Add a mitophagy annotation GO:0000423 (NEW, qualifier involved_in) for the PINK1-SIAH1-SNCAIP PRKN-independent pathway, supported_by the Szargel et al. 2016 HMG paper — first fetch/verify the PMID (Szargel HMG 2016; cache currently lacks it) and add it to references; mark UNDECIDED→NEW only after full-text confirmation. [REF] Keep the existing PMID:11863358 WRONG_IDENTIFIER flag (no change); optionally re-anchor the zinc IDA's primary support note to PMID:16085652.

SPCS1

• Recommended edits:** [MAP] At the "ER signal peptidase" class, prefer GO:0006465 signal peptide processing over GO:0015031 protein transport as the BP projection for accessory subunits (SPCS1/2), reflecting that SPCS1 acts downstream of ER targeting (matches review MODIFY of GO:0045047→GO:0006465).

SPCS2

• Recommended edits:** [MAP] At the "ER signal peptidase" class, prefer GO:0006465 signal peptide processing over GO:0015031 protein transport as the BP projection for accessory subunits (SPCS1/2). Optionally [REF] note PMID:39565596 (Spc2/SPCS2 substrate-selection) supports a substrate-selectivity contribution beyond bare membership.

STIP1

• Verdict: Consistent on the chaperone core but review under-covers the ALP/CMA story PN documents. Recommended edits:** consider adding GO:0061684 / GO:0061740 / GO:0061738 as KEEP_AS_NON_CORE pending full-text verification of HOP-specific evidence [YAML]; cite the CMA review [REF]. Do not add GO:0031072 (broader, already entailed) [MAP].

STUB1

• Verdict: Consistent and high-quality; one warranted addition (aggrephagy). Recommended edits:** add GO:0035973 aggrephagy as KEEP_AS_NON_CORE supported by CASA literature [YAML]; optionally cite PMID:40796662 / CASA review in references [REF].

TANK

• Verdict: OVER-REACH — PN projects GO:0000423 mitophagy (new_to_goa) onto TANK with no support in review/notes; TANK is an indirect regulatory scaffold of TBK1. Recommended edits:** [MAP] drop/demote TANK's "Autophagy receptor regulation|Mitophagy"→GO:0000423 projection (indirect, single-paper, regulatory-subunit role) — at most a regulation-of-mitophagy context, not a direct mitophagy annotation; do not add to the review without TANK-specific evidence.

TBK1

• Verdict: CONSISTENT on biology; PN's bare GO:0000423 mitophagy projection is scope drift for a regulator — review's positive-regulation terms are better. Recommended edits:** [MAP] for TBK1 the "Autophagy receptor regulation|Mitophagy" node should project a regulation term (GO:1901526 positive regulation of mitophagy, verified real) rather than the bare process GO:0000423; do not add GO:0000423 involved_in to the kinase review.

TCF25

• Recommended edits:** none required. [YAML] (optional) GO:0006515 protein quality control for misfolded or incompletely synthesized proteins could be added as an involved_in process term to better surface TCF25's RQC role (currently only catabolic/regulation/complex terms present); supported by PMID:30244831.

TRIM13

• Verdict: Consistent; ERAD/RING already captured; reticulophagy ADD warranted (regulatory framing preferable). Recommended edits:** [YAML] add GO:0061709 reticulophagy (or GO:0140500 regulation of reticulophagy, matching the regulatory evidence) involved_in, supported by PMID:22178386 — currently new_to_goa and more specific than the existing GO:0016239.

TRIM16

• Verdict: Consistent; lysophagy ADD warranted; RING-less caveat correctly handled. Recommended edits:** [MAP] fix the Lysophagy node rationale — GO:0062093 lysophagy exists; add it as the process target alongside GO:0160247. [YAML] upgrade the review's NEW GO:0030674 adaptor MF to the more specific GO:0160247 autophagy cargo adaptor activity, and add GO:0062093 lysophagy (involved_in, PMID:27693506) as the specific process. [YAML] retain GO:0061630 only as the atypical B-box autoubiquitination capture (do not assert RING catalytic ligase function).

TRIM17

• Verdict: Consistent; cargo-adaptor MF upgrade warranted; RING ligase already captured. Recommended edits:** [YAML] upgrade the GO:0030674 adaptor MF to the more specific GO:0160247 autophagy cargo adaptor activity (supported by PMID:27562068/25127057), scoped to midbody autophagy. [REF] consider adding PMID:22023800 (MCL1/ZWINT, neuronal apoptosis) to references to support the core MCL1-degradation function.

TRIM5

• Verdict: Consistent; xenophagy ADD warranted; RING ligase already captured. Recommended edits:** [YAML] add GO:0098792 xenophagy (involved_in, supported by PMID:25127057) as a more-specific child of the existing autophagy annotation. [YAML] optionally upgrade the GO:0030674 adaptor MF to the more specific GO:0160247 autophagy cargo adaptor activity for the capsid-receptor role.

TXNDC11

• Recommended edits:** [MAP] Flag TXNDC11 in the "Protein disulfide isomerases" group as a non-canonical reductase: do not propagate GO:0003756 to it; project GO:0015035 protein-disulfide reductase activity instead. [YAML] Optionally tighten the TXNDC11 proposed_new_terms to GO:0097466 (ubiquitin-dependent glycoprotein ERAD pathway) as the precise BP, and drop the GO:0003756 alternative wording in favor of GO:0015035.

TXNDC16

• Recommended edits:** [MAP] Exclude TXNDC16 (Q9P2K2) from the GO:0003756 protein disulfide isomerase activity projection (redox-inactive PDI-family member, no CXXC) — flag as member-level exception under the "Protein disulfide isomerases" group, do NOT project to GOA. [YAML] none required (review correctly omits a catalytic MF).

UBAC2

• Recommended edits:** [YAML] add GO:0000151 ubiquitin ligase complex (part_of; LMBR1L-AMFR/GP78-UBAC2 complex, PMID:31073040) as a non-core CC — currently absent from the review. [MAP] none — node mapping is correct; complex (not catalytic) target for the non-catalytic subunit is the right call.

UFSP1

• Recommended edits:** [MAP] do not project group-level GO:0006515 (PQC for misfolded/incompletely synthesized proteins) onto UFSP1 — UFSP1 is a cytosolic UFM1-maturation/deUFMylase enzyme, not a ribosome-associated misfolded-protein QC factor (contrast UFSP2/RPL26).

UFSP2

• Recommended edits:** [MAP] the RQC-group GO:0006515 projection is acceptable for UFSP2 but redundant/broader than the review's existing GO:0072344 (rescue of stalled cytosolic ribosome) and GO:0032790 (ribosome disassembly); prefer those narrower IDA-supported terms when representing UFSP2's RQC role.

UPF1

• Recommended edits:** [MAP] for UPF1, replace/avoid the group projection GO:0006415 (translational termination, = peptide release) with GO:0006449 (regulation of translational termination), which is already in UPF1 GOA and is the accurate frame; UPF1's core remains NMD (GO:0000184) + RNA helicase (GO:0003724).

UPF2

• Recommended edits:** [MAP] do NOT project GO:0006415 (translational termination) onto UPF2 — it is an NMD adaptor recruited downstream of termination, not a peptide-release factor; the type-level no_mapping should win. UPF2 is already correctly anchored on GO:0000184 (NMD).

UPF3A

• Recommended edits:** [MAP] do NOT project GO:0006415 (translational termination) onto UPF3A; UPF3A is a partial NMD antagonist (negated GO:0000184; GO:2000623 negative regulation of NMD; GO:0140311 sequestering). The type-level no_mapping should win, and any node-level frame must respect its negative/antagonist directionality.

UPF3B

• Recommended edits:** [MAP] do NOT project GO:0006415 (translational termination) onto UPF3B — it is an EJC/NMD adaptor acting downstream of termination, already correctly anchored on GO:0000184 and GO:2000624 (positive regulation of NMD). Type-level no_mapping should win.