# PN dossier: CDK5RAP3

- review_batch: proteostasis-batch-2026-06-07
- review_yaml: genes/human/CDK5RAP3/CDK5RAP3-ai-review.yaml
- PN workbook rows: 3

## PN row 1: Translation | Cytosolic translation | Ribosome-associated QC | UFMylation
- UniProt: Q96JB5
- In branches: TR, ALP, UPS
- PN-node mapping records (path + ancestors):
    - [type] Translation|Cytosolic translation|Ribosome-associated QC|UFMylation
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0071569 protein ufmylation]
        rationale: This PN RQC type denotes UFM1 conjugation in ribosome quality control. Protein ufmylation is the shared process target.
    - [group] Translation|Cytosolic translation|Ribosome-associated QC
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0006515 protein quality control for misfolded or incompletely synthesized proteins]
        rationale: The PN ribosome-associated quality-control group covers surveillance and disposal of stalled or defective nascent-chain translation products. GO lacks a dedicated ribosome-associated QC term in the local cache, so the broader protein-quality-control process is the best supported target.
    - [class] Translation|Cytosolic translation
        status=context_only scope=too_broad_to_propagate GO=[GO:0002181 cytoplasmic translation]
        rationale: The PN class Cytosolic translation is centered on the cytoplasmic translation apparatus and process, but it also houses supporting machinery such as ribosome biogenesis factors. The GO process term is a useful high-level label for the class, but propagating it to all members would over-annotate genes whose PN placement is through assembly or maturation context rather than core cytoplasmic translation.
    - [branch] Translation
        status=context_only scope=too_broad_to_propagate GO=[GO:0006412 translation]
        rationale: The PN Translation branch is organized around the translation apparatus and immediately associated cotranslational quality-control systems. GO translation is the closest high-level process label, but the PN branch also contains adjacent machinery such as ribosome biogenesis and nascent-chain handling. Keeping this relationship is useful for interpretation, but it is too broad to project safely onto every member.

## PN row 2: Autophagy-Lysosome Pathway | Autophagy substrate selection | Selective autophagy receptor | ERphagy
- UniProt: Q96JB5
- In branches: TR, ALP, UPS
- Notes: Receptor for selective autophagy. Binds to ATG8 and ubiquitinated or degron-contaning substrates. Active in ERphagy
- PN references (titles):
    - Regulatory events controlling ER-phagy - ScienceDirect
    - Full article: C53 is a cross-kingdom conserved reticulophagy receptor that bridges the gap betweenselective autophagy and ribosome stalling at the endoplasmic reticulum (tandfonline.com)
- PN-node mapping records (path + ancestors):
    - [type] Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|ERphagy
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0061709 reticulophagy]
        rationale: The PN uses the community label ERphagy for selective autophagy of the endoplasmic reticulum, while GO uses the synonym reticulophagy. Receptor members of this PN category are suitable for propagation to the GO reticulophagy process.
    - [group] Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a broad PN taxonomy container. The descendants mix components, regulators, context labels, and mechanistic leaves, so propagation should come only from narrower curated nodes.
    - [class] Autophagy-Lysosome Pathway|Autophagy substrate selection
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a broad substrate-selection container. GO has useful targets for specific receptor, cargo-adaptor, and selective-autophagy leaves, but this class mixes marking, recognition, receptor regulation, and unknown roles and should not propagate as one term.
    - [branch] Autophagy-Lysosome Pathway
        status=no_mapping scope= GO=[]
        rationale: Reviewed as the top-level PN branch. It is a project taxonomy umbrella rather than a direct GO assertion; all propagation must come from manually curated child nodes.

## PN row 3: Ubiquitin Proteasome System | E3 ubiquitin and UBL ligases | UBL modifier cofactors | UFMylation cofactor
- UniProt: Q96JB5
- In branches: TR, ALP, UPS
- Signature domains: (none)
- Auxiliary domains: IPR008491
- PN references (titles):
    - 36121123
- PN-node mapping records (path + ancestors):
    - [type] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|UBL modifier cofactors|UFMylation cofactor
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a UPS taxonomy container. Its descendants mix catalytic roles, complex membership, binding domains, regulators, adaptors, and substrate-context labels, so a single propagating GO assertion would overstate the shared biology.
    - [group] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|UBL modifier cofactors
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a UPS taxonomy container. Its descendants mix catalytic roles, complex membership, binding domains, regulators, adaptors, and substrate-context labels, so a single propagating GO assertion would overstate the shared biology.
    - [class] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases
        status=context_only scope=too_broad_to_propagate GO=[GO:0061630 ubiquitin protein ligase activity]
        rationale: This class is a genuine E3-ligase context, but its descendants include catalytic ligases, cullin scaffolds, substrate receptors, adaptors, cofactors, regulators, and UBL modifier systems. A class-level propagation would over-annotate.
    - [branch] Ubiquitin Proteasome System
        status=no_mapping scope= GO=[]
        rationale: Reviewed as the top-level UPS branch. It is a project taxonomy umbrella rather than a direct GO assertion; UPS propagation must come from manually curated child nodes.

## Projected GO annotations (3)
- GO:0006515 protein quality control for misfolded or incompletely synthesized proteins | scope=ok_for_propagation_to_go | goa_status=new_to_goa | from=Translation|Cytosolic translation|Ribosome-associated QC
- GO:0071569 protein ufmylation | scope=ok_for_propagation_to_go | goa_status=already_in_goa_exact | from=Translation|Cytosolic translation|Ribosome-associated QC|UFMylation
- GO:0061709 reticulophagy | scope=ok_for_propagation_to_go | goa_status=supported_by_goa_regulation | from=Autophagy-Lysosome Pathway|Autophagy substrate selection|Selective autophagy receptor|ERphagy