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.
  • 12 candidate human genes listed; 5 already reviewed for other projects (SEC62, ATL3, ULK1, ATG9A, EIF2AK3).
  • The defining receptors RETREG1 (FAM134B), RTN3, CCPG1, TEX264 have no review yet.

The biology

Schematic from the gene roles listed on the project page. Receptors sit in different ER subdomains and bind LC3B/GABARAP through LIR motifs.

Why this is worth doing

  • A young field: most receptors were characterised 2017–2023, 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 (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.
  • 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.
  • ULK1, ATG9A: reviewed for the CONDENSATES phagophore-membrane audit, not for ER-phagy.

Next steps

  1. just fetch-gene human RETREG1 (and RTN3, CCPG1, TEX264); review them first.
  2. Review MAP1LC3B, GABARAP and ERN1.
  3. Decide whether an ER-phagy receptor module is warranted, alongside modules/phagophore_assembly_site.yaml.

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