RETREG3

gene
On this page

Also known as DKFZp686B1036FLJ33806

Summary

RETREG3 (reticulophagy regulator family member 3, HGNC:27258) is a protein-coding gene on chromosome 17q21.2, encoding Reticulophagy regulator 3 (Q86VR2). Endoplasmic reticulum (ER)-anchored autophagy regulator which exists in an inactive state under basal conditions but is activated following cellular stress.

Predicted to enable endoplasmic reticulum-autophagosome adaptor activity. Involved in endoplasmic reticulum tubular network organization; positive regulation of neuron projection development; and reticulophagy. Located in endoplasmic reticulum tubular network. Part of protein-containing complex.

Source: NCBI Gene 162427 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 78 total — 1 likely-pathogenic
  • MANE Select transcript: NM_178126

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:27258
Approved symbolRETREG3
Namereticulophagy regulator family member 3
Location17q21.2
Locus typegene with protein product
StatusApproved
AliasesDKFZp686B1036, FLJ33806
Ensembl geneENSG00000141699
Ensembl biotypeprotein_coding
OMIM616498
Entrez162427

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 8 protein_coding, 5 nonsense_mediated_decay, 3 retained_intron

ENST00000309428, ENST00000585726, ENST00000585894, ENST00000586796, ENST00000586870, ENST00000588423, ENST00000589007, ENST00000589797, ENST00000590035, ENST00000590541, ENST00000591547, ENST00000593251, ENST00000875457, ENST00000875458, ENST00000917259, ENST00000955309

RefSeq mRNA: 1 — MANE Select: NM_178126 NM_178126

CCDS: CCDS11432

Canonical transcript exons

ENST00000309428 — 9 exons

ExonStartEnd
ENSE000013204924258783442587864
ENSE000028750774257951542582270
ENSE000034696834258267442582806
ENSE000034723144259205642592162
ENSE000035191994258676542586891
ENSE000035653394258512542585262
ENSE000035658274258349842583580
ENSE000036137414258605342586137
ENSE000038501994260908642609374

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 96.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.1876 / max 215.6569, expressed in 1817 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
16617222.18761817

Top tissues by expression

300 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183196.41gold quality
epithelium of nasopharynxUBERON:000195195.58gold quality
nasopharynxUBERON:000172895.56gold quality
gingival epitheliumUBERON:000194995.43gold quality
nippleUBERON:000203095.20gold quality
periodontal ligamentUBERON:000826694.88gold quality
nasal cavity epitheliumUBERON:000538494.66gold quality
gingivaUBERON:000182894.37gold quality
pylorusUBERON:000116694.16gold quality
body of pancreasUBERON:000115094.15gold quality
granulocyteCL:000009493.95gold quality
tendon of biceps brachiiUBERON:000818893.88gold quality
ileal mucosaUBERON:000033193.83gold quality
thymusUBERON:000237093.71gold quality
right testisUBERON:000453493.70gold quality
left testisUBERON:000453393.57gold quality
epithelium of mammary glandUBERON:000324493.48gold quality
superior surface of tongueUBERON:000737193.48gold quality
mammary ductUBERON:000176593.40gold quality
upper leg skinUBERON:000426293.38gold quality
penisUBERON:000098993.36gold quality
upper arm skinUBERON:000426393.35gold quality
tracheaUBERON:000312693.04gold quality
Brodmann (1909) area 23UBERON:001355492.93gold quality
mammalian vulvaUBERON:000099792.89gold quality
layer of synovial tissueUBERON:000761692.70gold quality
bloodUBERON:000017892.66gold quality
cardia of stomachUBERON:000116292.64gold quality
pharyngeal mucosaUBERON:000035592.61gold quality
germinal epithelium of ovaryUBERON:000130492.59gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.55

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NRF1

miRNA regulators (miRDB)

181 targeting RETREG3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-12118100.0065.881270
HSA-MIR-4533100.0069.482758
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-5193100.0067.261744
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-453499.9966.581907
HSA-MIR-150-5P99.9966.691976
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-302E99.9670.742669
HSA-MIR-6778-3P99.9667.292693

Literature-anchored findings (GeneRIF, showing 2)

  • We verified that NRF-1 positively regulates FAM134C and ENOX1, and negatively regulates C3orf10 in human neuroblastoma IMR-32 cells and primary rat cortical neurons. (PMID:23939472)
  • RTN4B interacting protein FAM134C promotes ER membrane curvature and has a functional role in autophagy. (PMID:33826365)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusRetreg3ENSMUSG00000017802
rattus_norvegicusRetreg3ENSRNOG00000020056

Protein

Protein identifiers

Reticulophagy regulator 3Q86VR2 (reviewed: Q86VR2)

All UniProt accessions (9): Q86VR2, K7EJ34, K7EJ42, K7ELM8, K7EMF4, K7ENF4, K7ENZ6, K7EPD0, K7EQI9

UniProt curated annotations — full annotation on UniProt →

Function. Endoplasmic reticulum (ER)-anchored autophagy regulator which exists in an inactive state under basal conditions but is activated following cellular stress. When activated, induces ER fragmentation and mediates ER delivery into lysosomes through sequestration into autophagosomes via interaction with ATG8 family proteins. Promotes ER membrane curvature and ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes. Required for collagen quality control in a LIR motif-dependent manner. Mediates NRF1-enhanced neurite outgrowth.

Subunit / interactions. Interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAP, GABARAPL1 and GABARAPL2. Interacts with CANX. Interacts with RTN4 isoform B.

Subcellular location. Endoplasmic reticulum membrane.

Domain organisation. The LIR motif interacts with ATG8 family proteins.

Induction. Induced by amino acid starvation but not by endoplasmic reticulum stress.

Similarity. Belongs to the RETREG family.

Isoforms (2)

UniProt IDNamesCanonical?
Q86VR2-11yes
Q86VR2-22

RefSeq proteins (1): NP_835227* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR043384RETREG1/3Family
IPR055258RETR3_RHDDomain
IPR057282RETREG1-3-like_RHDDomain

Pfam: PF24456

UniProt features (38 total): modified residue 16, topological domain 5, compositionally biased region 4, transmembrane region 4, region of interest 3, mutagenesis site 2, initiator methionine 1, chain 1, short sequence motif 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86VR2-F161.610.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (16): 2, 10, 26, 258, 260, 283, 285, 288, 293, 303, 307, 310, 313, 320, 360, 440

Mutagenesis-validated functional residues (2):

PositionPhenotype
445–450reduced formation of autophagosomes.
447–450abolishes interaction with atg8 family proteins, induction of er fragmentation and er degradation.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 195 (showing top): AAGCAAT_MIR137, TGCGCANK_UNKNOWN, GOBP_VACUOLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_NEUROGENESIS, GOBP_MACROAUTOPHAGY, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, MARTINEZ_RB1_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_ORGANELLE_ASSEMBLY, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, DOUGLAS_BMI1_TARGETS_DN, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_ENDOPLASMIC_RETICULUM_ORGANIZATION

GO Biological Process (7): positive regulation of neuron projection development (GO:0010976), collagen catabolic process (GO:0030574), reticulophagy (GO:0061709), endoplasmic reticulum tubular network organization (GO:0071786), autophagy (GO:0006914), endoplasmic reticulum organization (GO:0007029), substrate localization to autophagosome (GO:0061753)

GO Molecular Function (2): endoplasmic reticulum-autophagosome adaptor activity (GO:0140506), protein binding (GO:0005515)

GO Cellular Component (5): endoplasmic reticulum membrane (GO:0005789), protein-containing complex (GO:0032991), endoplasmic reticulum tubular network (GO:0071782), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
catabolic process2
endoplasmic reticulum subcompartment2
regulation of neuron projection development1
neuron projection development1
positive regulation of cell projection organization1
collagen metabolic process1
macroautophagy1
endoplasmic reticulum organization1
transmembrane transport1
process utilizing autophagic mechanism1
organelle organization1
endomembrane system organization1
autophagosome assembly1
establishment of localization in cell1
autophagosome-membrane adaptor activity1
endoplasmic reticulum-organelle membrane tether activity1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
cellular_component1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1430 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RETREG3GABARAPO95166793
RETREG3TEX264Q9Y6I9548
RETREG3CCPG1Q9ULG6537
RETREG3MANSC1Q9H8J5522
RETREG3TMEM171Q8WVE6502
RETREG3RTN3O95197495
RETREG3SEC62Q99442493
RETREG3LNPKQ9C0E8450
RETREG3RTN4Q9NQC3413
RETREG3ENOX1Q8TC92405
RETREG3CACFD1Q9UGQ2404
RETREG3MRFAP1L1Q96HT8402
RETREG3PACC1Q9H813399
RETREG3ENTREP1Q15884386
RETREG3ATL3Q6DD88380

IntAct

488 interactions, top by confidence:

ABTypeScore
RETREG3GABARAPL1psi-mi:“MI:0915”(physical association)0.830
GABARAPL1RETREG3psi-mi:“MI:0915”(physical association)0.830
ABHD16ARETREG3psi-mi:“MI:0915”(physical association)0.780
ARL6IP1RETREG3psi-mi:“MI:0915”(physical association)0.780
RETREG3MAP1LC3Apsi-mi:“MI:0915”(physical association)0.780
RETREG3ABHD16Apsi-mi:“MI:0915”(physical association)0.780
RETREG3ARL6IP1psi-mi:“MI:0915”(physical association)0.780
MAP1LC3ARETREG3psi-mi:“MI:0915”(physical association)0.780
RETREG3STAP1psi-mi:“MI:0915”(physical association)0.720
ATP5PBSLC19A2psi-mi:“MI:0914”(association)0.640
CCDC167RETREG3psi-mi:“MI:0915”(physical association)0.560
LRCH4RETREG3psi-mi:“MI:0915”(physical association)0.560
MOB2RETREG3psi-mi:“MI:0915”(physical association)0.560
TMEM65RETREG3psi-mi:“MI:0915”(physical association)0.560
CMTM3RETREG3psi-mi:“MI:0915”(physical association)0.560
YIPF1RETREG3psi-mi:“MI:0915”(physical association)0.560
CMTM5RETREG3psi-mi:“MI:0915”(physical association)0.560
HMOX2RETREG3psi-mi:“MI:0915”(physical association)0.560
ANKRD46RETREG3psi-mi:“MI:0915”(physical association)0.560

BioGRID (341): FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Two-hybrid), FAM134C (Affinity Capture-RNA), FAM134C (Affinity Capture-RNA), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), FAM134C (Affinity Capture-MS), JPH1 (Affinity Capture-MS), ATP12A (Affinity Capture-MS)

ESM2 similar proteins: A1L3T7, A2A699, A7YWL5, O70622, O75298, O94983, Q0P4Z1, Q16799, Q1L899, Q1LU99, Q2T9L4, Q3T1H8, Q3TES0, Q3UJB9, Q3ZAV8, Q4FZU8, Q4VAC9, Q5E9U3, Q5IS59, Q5RBI7, Q5XIS1, Q64548, Q66H43, Q68FE6, Q6NS82, Q6P2E9, Q6PDH0, Q6WN19, Q6ZQ29, Q6ZS17, Q76LL6, Q76N89, Q80Y50, Q86UU1, Q86VR2, Q8BG26, Q8CD60, Q8K0T0, Q8K330, Q8TE77

Diamond homologs: Q0P4Z1, Q3MHU5, Q5E9K8, Q5FVM3, Q6NS82, Q86VR2, Q8NC44, Q8VE91, Q9CQV4, Q9H6L5

SIGNOR signaling

3 interactions.

AEffectBMechanism
NRF1“up-regulates quantity by expression”RETREG3“transcriptional regulation”
NRF1up-regulatesRETREG3
RETREG3up-regulatesNeurite_outgrowth

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 125 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
vesicle fusion530.7×1e-04
endoplasmic reticulum organization521.5×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

78 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance67
Likely benign1
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3338057NM_001070.5(TUBG1):c.664A>C (p.Asn222His)Likely pathogenic

SpliceAI

2050 predictions. Top by Δscore:

VariantEffectΔscore
17:42582266:TAGGT:Tacceptor_gain1.0000
17:42582270:TC:Tacceptor_loss1.0000
17:42582271:C:CCacceptor_gain1.0000
17:42582668:CCTCA:Cdonor_loss1.0000
17:42582669:CTCAC:Cdonor_loss1.0000
17:42582670:TCACC:Tdonor_loss1.0000
17:42582671:CA:Cdonor_loss1.0000
17:42582673:C:CGdonor_loss1.0000
17:42582685:T:TAdonor_gain1.0000
17:42582803:CCAG:Cacceptor_gain1.0000
17:42582804:CAG:Cacceptor_gain1.0000
17:42582804:CAGC:Cacceptor_gain1.0000
17:42582807:C:CCacceptor_gain1.0000
17:42582808:T:Cacceptor_gain1.0000
17:42582808:T:TCacceptor_gain1.0000
17:42582821:A:Tacceptor_gain1.0000
17:42583493:GATAC:Gdonor_loss1.0000
17:42583494:ATACC:Adonor_loss1.0000
17:42583495:TACCT:Tdonor_loss1.0000
17:42583496:A:ATdonor_loss1.0000
17:42583497:C:CGdonor_loss1.0000
17:42583499:TGAGG:Tdonor_gain1.0000
17:42583576:GCGTA:Gacceptor_gain1.0000
17:42583577:CGTA:Cacceptor_gain1.0000
17:42583577:CGTAC:Cacceptor_gain1.0000
17:42583578:GTA:Gacceptor_gain1.0000
17:42583579:TA:Tacceptor_gain1.0000
17:42583580:ACTG:Aacceptor_loss1.0000
17:42583581:C:CCacceptor_gain1.0000
17:42583581:C:Gacceptor_loss1.0000

AlphaMissense

3029 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:42586783:T:AK162N0.997
17:42586783:T:GK162N0.997
17:42586135:G:CF169L0.996
17:42586135:G:TF169L0.996
17:42586137:A:GF169L0.996
17:42581873:A:CF447L0.995
17:42581873:A:TF447L0.995
17:42581875:A:GF447L0.995
17:42581874:A:CF447C0.994
17:42586123:G:CS173R0.993
17:42586123:G:TS173R0.993
17:42586125:T:GS173R0.993
17:42582717:G:CF300L0.990
17:42582717:G:TF300L0.990
17:42582719:A:GF300L0.990
17:42586784:T:AK162I0.989
17:42592086:A:GW106R0.989
17:42592086:A:TW106R0.989
17:42583507:G:CF267L0.988
17:42583507:G:TF267L0.988
17:42583509:A:GF267L0.988
17:42586122:A:GC174R0.988
17:42609141:A:GW62R0.988
17:42609141:A:TW62R0.988
17:42586134:A:GC170R0.987
17:42586136:A:GF169S0.986
17:42592098:A:GC102R0.986
17:42582236:A:CF326L0.983
17:42582236:A:TF326L0.983
17:42582238:A:GF326L0.983

dbSNP variants (sampled 300 via entrez): RS1000082779 (17:42605009 G>A,C), RS1000205705 (17:42589285 A>C,G), RS1000266418 (17:42604683 C>T), RS1000371644 (17:42599687 G>T), RS1000543364 (17:42604368 T>C), RS1000627953 (17:42579617 C>A), RS1000637859 (17:42605711 G>A,C), RS1000691492 (17:42597696 TCTC>T), RS1000847302 (17:42591270 T>C), RS1000999074 (17:42604588 G>A), RS1000999620 (17:42584134 T>A), RS1001113921 (17:42583876 C>T), RS1001232470 (17:42579943 A>G), RS1001240843 (17:42607020 TA>T), RS1001246946 (17:42579036 G>A)

Disease associations

OMIM: gene MIM:616498 | disease phenotypes: MIM:615412

GenCC curated gene-disease

Mondo (1): complex cortical dysplasia with other brain malformations 4 (MONDO:0014171)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009325_53Parkinson’s disease or first degree relation to individual with Parkinson’s disease1.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression3
Arsenicaffects methylation, decreases expression, increases abundance2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
testosterone enanthateaffects expression1
bisphenol Aincreases expression1
trichostatin Aaffects expression1
sodium arsenitedecreases expression, increases abundance1
perfluorooctanoic aciddecreases expression1
ochratoxin Adecreases expression1
potassium chromate(VI)increases expression1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
bisphenol Sincreases expression1
bisphenol AFincreases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, decreases expression1
Cadmiumincreases abundance, increases expression1
Caffeineaffects phosphorylation1
Estradioldecreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Vanadatesdecreases expression1

Cellosaurus cell lines

15 cell lines: 15 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D1IAH9 AAVS1-TRE3G-NGN2 RETREG3-/-Embryonic stem cellFemale
CVCL_D1IBH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/-Embryonic stem cellFemale
CVCL_D1ICH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/-Embryonic stem cellFemale
CVCL_D1IDH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- TEX264-/-Embryonic stem cellFemale
CVCL_D1IEH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- TEX264-/- CCPG1-/-Embryonic stem cellFemale
CVCL_D1IPH9 AAVS1-TRE3G-NGN2 RETREG3-/- Keima-RAMP4Embryonic stem cellFemale
CVCL_D1IQH9 AAVS1-TRE3G-NGN2 RETREG3-/- Keima-REEP5Embryonic stem cellFemale
CVCL_D1IRH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- Keima-RAMP4Embryonic stem cellFemale
CVCL_D1ISH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- Keima-REEP5Embryonic stem cellFemale
CVCL_D1ITH9 AAVS1-TRE3G-NGN2 RETREG3-/- RETREG2-/- RETREG1-/- Keima-RAMP4Embryonic stem cellFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.