ER-phagy

Selective autophagy of the endoplasmic reticulum: a scoped project

AI Gene Review · projects/ER_PHAGY · SCOPING · 2026

Bottom line

  • Scoped, not started. No ER-phagy module and no review made for this project.
  • 16 seed/related human genes listed; 8 COMPLETE, 2 DRAFT, 2 INITIALIZED, 4 not started.
  • The defining receptors RETREG1 (FAM134B), RTN3, CCPG1, TEX264 have no review yet.
  • GO-CAM already covers one UFMylation/CYB5R3 reticulophagy branch.

The biology

Schematic from the gene roles listed on the project page. Membrane receptors and soluble cargo adaptors bind LC3B/GABARAP through LIR- or UDS-type motifs.

Why this is worth doing

  • A young field: many receptors were characterized from the mid-2010s into the 2020s, so GO coverage is likely to lag.
  • Receptors are dual-function membrane proteins (SEC62 is a translocon subunit; ATL3 an ER-fusion GTPase), so the core-vs-non-core call matters.
  • Disease links: hereditary sensory neuropathy (RETREG1/FAM134B), ER storage disease, flavivirus infection.

Where the candidate genes stand

What the existing reviews already say

  • SEC62: IMP reticulophagy (GO:0061709) kept as KEEP_AS_NON_CORE; the core function is the Sec61 translocon.
  • CALCOCO1, RETREG2, UBAC2: ER-phagy receptor/adaptor reviews now add core reticulophagy biology.
  • CDK5RAP3: captures the UFM1-dependent positive regulation of reticulophagy.
  • ATL3: a reticulophagy projection was not promoted to a new annotation; the review keeps ER membrane fusion as core and asks for receptor-mutant rescue experiments.
  • ERN1: COMPLETE ER-stress review; GABARAP, MAP1LC3B are DRAFT; ULK1, ATG9A are INITIALIZED.

Next steps

  1. just fetch-gene human RETREG1 (and RTN3, CCPG1, TEX264); review them first.
  2. Decide whether an ER-phagy receptor/adaptor module is warranted, alongside modules/phagophore_assembly_site.yaml.

Read more: projects/ER_PHAGY.md · genes/human/SEC62/ · genes/human/ATL3/ · genes/human/CALCOCO1/