# PN dossier: DDRGK1

- review_batch: proteostasis-batch-2026-06-07c
- review_yaml: genes/human/DDRGK1/DDRGK1-ai-review.yaml
- PN workbook rows: 4

## PN row 1: Translation | Cytosolic translation | Ribosome-associated QC | UFMylation
- UniProt: Q96HY6
- 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 | Marking substrates for selective autophagy | ERphagy | UFMylation of ER proteins
- UniProt: Q96HY6
- In branches: TR, ALP, UPS
- Notes: Involved in reticulophagy, brings UFL1 ligase to ER surface to UFMylate RPN1 and RPL26
- PN references (titles):
    - A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation - PubMed (nih.gov)
- PN-node mapping records (path + ancestors):
    - [subtype] Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy|ERphagy|UFMylation of ER proteins
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0061709 reticulophagy]
        rationale: This PN subtype captures a specific ER-cargo marking mechanism used in ERphagy. Because GO uses reticulophagy for ER autophagy, this subtype can propagate to reticulophagy.
    - [type] Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy|ERphagy
        status=mapped scope=ok_for_propagation_to_go GO=[GO:0061709 reticulophagy]
        rationale: The PN ERphagy marking category captures factors that mark ER cargo for selective autophagic turnover. GO uses reticulophagy for this pathway, so propagation to reticulophagy is appropriate.
    - [group] Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy
        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 | transmembrane
- UniProt: Q96HY6
- In branches: TR, ALP, UPS
- Signature domains: (none)
- Auxiliary domains: IPR019153
- PN references (titles):
    - 36121123
- PN-node mapping records (path + ancestors):
    - [subtype] Ubiquitin Proteasome System|E3 ubiquitin and UBL ligases|UBL modifier cofactors|UFMylation cofactor|transmembrane
        status=no_mapping scope= GO=[]
        rationale: Reviewed manually as a UPS source node. No single GO term is appropriate for direct propagation from this PN label without narrower context or gene-level evidence.
    - [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.

## PN row 4: Ubiquitin Proteasome System | Ubiquitin and UBL binding | E3 ligase / UBLM | UFMylation cofactor | UFM1 binding
- UniProt: Q96HY6
- In branches: TR, ALP, UPS
- Signature domains: PMID: 38383789
- Auxiliary domains: IPR019153
- PN references (titles):
    - 38383789
- PN-node mapping records (path + ancestors):
    - [subtype] Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase / UBLM|UFMylation cofactor|UFM1 binding
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a binding-branch UBL-modifier subtype. Because this context mixes catalytic ligases and cofactors, no direct GO propagation is made from this node.
    - [type] Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase / UBLM|UFMylation cofactor
        status=no_mapping scope= GO=[]
        rationale: Reviewed as a binding-branch UBL-modifier subtype. Because this context mixes catalytic ligases and cofactors, no direct GO propagation is made from this node.
    - [group] Ubiquitin Proteasome System|Ubiquitin and UBL binding|E3 ligase / UBLM
        status=context_only scope=too_broad_to_propagate GO=[GO:0019787 ubiquitin-like protein transferase activity]
        rationale: This binding-branch group records E3/UBL-modifier context, but it includes cofactors as well as catalytic ligases. Direct propagation should come from narrower enzyme-specific nodes.
    - [class] Ubiquitin Proteasome System|Ubiquitin and UBL binding
        status=context_only scope=too_broad_to_propagate GO=[GO:0140036 ubiquitin-modified protein reader activity]
        rationale: This class records ubiquitin/UBL-reader context, but the subtree mixes ubiquitin, SUMO, UBL-domain, domain-architecture, catalytic, signaling, trafficking, and nucleic-acid process buckets. It is useful context, not a safe direct propagation.
    - [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 (4)
- 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=already_in_goa_exact | from=Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy|ERphagy
- GO:0061709 reticulophagy | scope=ok_for_propagation_to_go | goa_status=already_in_goa_exact | from=Autophagy-Lysosome Pathway|Autophagy substrate selection|Marking substrates for selective autophagy|ERphagy|UFMylation of ER proteins