KDELR3

gene
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Summary

KDELR3 (KDEL endoplasmic reticulum protein retention receptor 3, HGNC:6306) is a protein-coding gene on chromosome 22q13.1, encoding ER lumen protein-retaining receptor 3 (O43731). Receptor for the C-terminal sequence motif K-D-E-L that is present on endoplasmic reticulum resident proteins and that mediates their recycling from the Golgi back to the endoplasmic reticulum.

This gene encodes a member of the KDEL endoplasmic reticulum protein retention receptor family. Retention of resident soluble proteins in the lumen of the endoplasmic reticulum (ER) is achieved in both yeast and animal cells by their continual retrieval from the cis-Golgi, or a pre-Golgi compartment. Sorting of these proteins is dependent on a C-terminal tetrapeptide signal, usually lys-asp-glu-leu (KDEL) in animal cells, and his-asp-glu-leu (HDEL) in S. cerevisiae. This process is mediated by a receptor that recognizes, and binds the tetrapeptide-containing protein, and returns it to the ER. In yeast, the sorting receptor encoded by a single gene, ERD2, is a seven-transmembrane protein. Unlike yeast, several human homologs of the ERD2 gene, constituting the KDEL receptor gene family, have been described. KDELR3 was the third member of the family to be identified. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 11015 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 42 total
  • MANE Select transcript: NM_006855

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6306
Approved symbolKDELR3
NameKDEL endoplasmic reticulum protein retention receptor 3
Location22q13.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000100196
Ensembl biotypeprotein_coding
OMIM619900
Entrez11015

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000216014, ENST00000409006, ENST00000471268, ENST00000862991, ENST00000943543, ENST00000943544

RefSeq mRNA: 2 — MANE Select: NM_006855 NM_006855, NM_016657

CCDS: CCDS13972, CCDS46705

Canonical transcript exons

ENST00000216014 — 5 exons

ExonStartEnd
ENSE000011228323848249638483447
ENSE000018382693846809638468324
ENSE000036269003848121238481464
ENSE000036334443847959338479751
ENSE000036337523847452338474623

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 98.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.8657 / max 358.8421, expressed in 1467 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
19225829.42761464
1922570.4381288

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097998.98gold quality
parotid glandUBERON:000183197.70gold quality
periodontal ligamentUBERON:000826697.32gold quality
stromal cell of endometriumCL:000225596.89gold quality
pancreatic ductal cellCL:000207994.44gold quality
jejunal mucosaUBERON:000039993.72gold quality
skin of hipUBERON:000155492.85gold quality
mucosa of sigmoid colonUBERON:000499392.60gold quality
parietal pleuraUBERON:000240092.50gold quality
germinal epithelium of ovaryUBERON:000130490.77gold quality
pleuraUBERON:000097790.68gold quality
cartilage tissueUBERON:000241890.23gold quality
rectumUBERON:000105289.79gold quality
gall bladderUBERON:000211089.64gold quality
colonic mucosaUBERON:000031789.63gold quality
deciduaUBERON:000245089.49gold quality
calcaneal tendonUBERON:000370189.26gold quality
smooth muscle tissueUBERON:000113588.62gold quality
ileal mucosaUBERON:000033188.61gold quality
epithelial cell of pancreasCL:000008387.68gold quality
duodenumUBERON:000211487.62gold quality
choroid plexus epitheliumUBERON:000391187.62gold quality
visceral pleuraUBERON:000240187.61gold quality
mucosa of paranasal sinusUBERON:000503087.36gold quality
renal glomerulusUBERON:000007487.30gold quality
saliva-secreting glandUBERON:000104486.90gold quality
nasal cavity mucosaUBERON:000182686.53gold quality
ascending aortaUBERON:000149686.49gold quality
corpus epididymisUBERON:000435986.43gold quality
thoracic aortaUBERON:000151586.37gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-13yes27.30
E-CURD-112yes16.80
E-ANND-3yes8.99
E-CURD-10no800.96
E-MTAB-7052no641.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting KDELR3, 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-4262100.0073.263931
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-453199.9969.703181
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-651-3P99.9473.485177
HSA-MIR-381-3P99.9371.872854
HSA-MIR-314399.9371.963104
HSA-MIR-30099.9271.762856
HSA-MIR-430299.8967.941187
HSA-MIR-137-3P99.8774.742401
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-6715A-3P99.8368.051473
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-430799.8270.453374
HSA-MIR-205-5P99.8170.051557
HSA-MIR-63699.8069.581500
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-548A-3P99.7670.583524

Literature-anchored findings (GeneRIF, showing 1)

  • Cell-type-specific differences in KDEL receptor clustering in mammalian cells. (PMID:32645101)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriokdelr3ENSDARG00000040912
danio_rerioKDELR3ENSDARG00000104519
mus_musculusKdelr3ENSMUSG00000010830
rattus_norvegicusKdelr3ENSRNOG00000013577
drosophila_melanogasterKdelRFBGN0267330
caenorhabditis_elegansWBGENE00001331
caenorhabditis_elegansWBGENE00016195

Paralogs (2): KDELR1 (ENSG00000105438), KDELR2 (ENSG00000136240)

Protein

Protein identifiers

ER lumen protein-retaining receptor 3O43731 (reviewed: O43731)

Alternative names: KDEL endoplasmic reticulum protein retention receptor 3

All UniProt accessions (1): O43731

UniProt curated annotations — full annotation on UniProt →

Function. Receptor for the C-terminal sequence motif K-D-E-L that is present on endoplasmic reticulum resident proteins and that mediates their recycling from the Golgi back to the endoplasmic reticulum.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus membrane. Cytoplasmic vesicle. COPI-coated vesicle membrane.

Domain organisation. Binds the C-terminal sequence motif K-D-E-L in a hydrophilic cavity between the transmembrane domains. This triggers a conformation change that exposes a Lys-rich patch on the cytosolic surface of the protein. This patch mediates recycling from the Golgi to the endoplasmic reticulum, probably via COPI vesicles.

Similarity. Belongs to the ERD2 family.

Isoforms (2)

UniProt IDNamesCanonical?
O43731-11yes
O43731-22

RefSeq proteins (2): NP_006846, NP_057839 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000133ER_ret_rcptFamily

Pfam: PF00810

UniProt features (25 total): topological domain 8, transmembrane region 7, region of interest 3, site 3, chain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O43731-F191.420.78

Functional residue map

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

Catalytic / active sites (3): 5 (interaction with the k-d-e-l motif on target proteins); 117 (interaction with the k-d-e-l motif on target proteins); 193 (important for recycling of cargo proteins with the sequence motif k-d-e-l from the golgi to the endoplasmic reticulum)

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-381038XBP1(S) activates chaperone genes
R-HSA-6807878COPI-mediated anterograde transport
R-HSA-6811434COPI-dependent Golgi-to-ER retrograde traffic

MSigDB gene sets: 209 (showing top): REACTOME_UNFOLDED_PROTEIN_RESPONSE_UPR, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, PATIL_LIVER_CANCER, GOBP_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM, MAHAJAN_RESPONSE_TO_IL1A_DN, ONKEN_UVEAL_MELANOMA_UP, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_MAINTENANCE_OF_LOCATION, GOCC_COATED_VESICLE, GOBP_MAINTENANCE_OF_PROTEIN_LOCALIZATION_IN_ORGANELLE, E4F1_Q6

GO Biological Process (4): protein retention in ER lumen (GO:0006621), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (3): KDEL sequence binding (GO:0005046), ER lumen protein retrieval receptor activity (GO:0046923), protein binding (GO:0005515)

GO Cellular Component (9): Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), cis-Golgi network (GO:0005801), transport vesicle (GO:0030133), COPI-coated vesicle membrane (GO:0030663), Golgi apparatus (GO:0005794), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
IRE1alpha activates chaperones1
ER to Golgi Anterograde Transport1
Golgi-to-ER retrograde transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
endomembrane system3
intracellular membrane-bounded organelle3
transport2
Golgi apparatus2
maintenance of protein localization in endoplasmic reticulum1
Golgi vesicle transport1
intracellular protein localization1
establishment of protein localization1
cellular process1
ER lumen protein retrieval receptor activity1
signal sequence receptor activity1
binding1
bounding membrane of organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cytoplasmic vesicle1
COPI-coated vesicle1
Golgi-associated vesicle membrane1
coated vesicle membrane1
cellular anatomical structure1
intracellular vesicle1

Protein interactions and networks

STRING

842 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KDELR3CUL7Q14999446
KDELR3TMEM229BQ8NBD8443
KDELR3TMEM131LA2VDJ0436
KDELR3MANFP55145395
KDELR3YIF1AO95070394
KDELR3SEC31AO94979377
KDELR3PPFIA1Q13136366
KDELR3CREB3L1Q96BA8362
KDELR3SEC24DO94855360
KDELR3ARF4P18085357
KDELR3AGAP5A6NIR3355
KDELR3IL2RGP31785353
KDELR3PREBQ9HCU5351
KDELR3COPB2P35606340
KDELR3CREB3L2Q70SY1339

IntAct

31 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
TMEM63AAP3D1psi-mi:“MI:0914”(association)0.530
GPR17IPO8psi-mi:“MI:0914”(association)0.530
ESYT2psi-mi:“MI:0914”(association)0.350
CRELD1TMEM223psi-mi:“MI:0914”(association)0.350
SLC22A4RTL8Cpsi-mi:“MI:0914”(association)0.350
KDELR3SLC4A2psi-mi:“MI:0914”(association)0.350
FFAR1SLC12A8psi-mi:“MI:0914”(association)0.350
GPR182SLC12A8psi-mi:“MI:0914”(association)0.350
REEP5ESYT2psi-mi:“MI:0914”(association)0.350
DUOXA2TMEM131Lpsi-mi:“MI:0914”(association)0.350
GPR45VWA8psi-mi:“MI:0914”(association)0.350
KDELR3POTEFpsi-mi:“MI:0914”(association)0.350
OPALINFAM171A2psi-mi:“MI:0914”(association)0.350
SLC1A1UBXN8psi-mi:“MI:0914”(association)0.350
ATP2A3UBXN8psi-mi:“MI:0914”(association)0.350
SPPL2BHAS3psi-mi:“MI:0914”(association)0.350
VIPR1SLC33A1psi-mi:“MI:0914”(association)0.350
SLC2A1SLC33A1psi-mi:“MI:0914”(association)0.350
LPAR2EI24psi-mi:“MI:0914”(association)0.350
VIPR2EI24psi-mi:“MI:0914”(association)0.350
TSPAN2TPP1psi-mi:“MI:0914”(association)0.350
FPR2SCAMP3psi-mi:“MI:0914”(association)0.350
GP5MGST3psi-mi:“MI:0914”(association)0.350
TMEM72MGST3psi-mi:“MI:0914”(association)0.350
P2RY8BTAF1psi-mi:“MI:0914”(association)0.350
S1PR4NPC1psi-mi:“MI:0914”(association)0.350
BSCL2QSOX1psi-mi:“MI:0914”(association)0.350
CXCR4ESYT2psi-mi:“MI:0914”(association)0.350
SLC10A4ILVBLpsi-mi:“MI:0914”(association)0.350

BioGRID (68): KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), TMEM56 (Affinity Capture-MS), ALG8 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), LPCAT3 (Affinity Capture-MS), SLC4A2 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS), KDELR3 (Affinity Capture-MS)

ESM2 similar proteins: A0A097ZPD8, A0A0E3D8M2, A0A0E3D8Q2, A0A140JWT2, A0A1B7YCX1, A0A2I6PJ07, A0A3G9H8P0, A9JPE3, E3UBL6, J7FIJ6, K2RU64, M1VJS5, O42580, O43731, O44017, O76767, O94270, P18413, P18414, P24390, P33946, P33947, P33948, P35402, P48583, P9WEX1, P9WEX7, P9WEY0, Q09473, Q2KJ37, Q4WLD2, Q569A6, Q5U305, Q5XHA2, Q5ZKX9, Q611C8, Q66JF2, Q68ES4, Q6NRS2, Q6P257

Diamond homologs: O42580, O43731, O44017, O76767, O94270, P18413, P18414, P24390, P33946, P33947, P33948, P35402, P48583, Q09473, Q2KJ37, Q569A6, Q5U305, Q5XHA2, Q5ZKX9, Q611C8, Q66JF2, Q68ES4, Q6P257, Q6PAB8, Q6PEH1, Q6PFS5, Q76NM1, Q7ZXS5, Q86JE5, Q8R1L4, Q8VWI1, Q99JH8, Q9CQM2, Q9ZTN2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 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
G protein-coupled receptor signaling pathway97.6×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance30
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

900 predictions. Top by Δscore:

VariantEffectΔscore
22:38468296:G:GTdonor_gain1.0000
22:38468296:G:Tdonor_gain1.0000
22:38468305:G:GTdonor_gain1.0000
22:38468323:GG:Gdonor_gain1.0000
22:38468324:GG:Gdonor_gain1.0000
22:38474514:T:TAacceptor_gain1.0000
22:38474517:CCACA:Cacceptor_loss1.0000
22:38474518:CACAG:Cacceptor_loss1.0000
22:38474521:A:AGacceptor_gain1.0000
22:38474521:AGGC:Aacceptor_loss1.0000
22:38474522:G:GCacceptor_loss1.0000
22:38474522:G:GGacceptor_gain1.0000
22:38474615:G:GGdonor_gain1.0000
22:38474621:AAGG:Adonor_loss1.0000
22:38474622:AGG:Adonor_loss1.0000
22:38474623:GGTGA:Gdonor_loss1.0000
22:38481204:T:TAacceptor_gain1.0000
22:38481324:T:TAacceptor_gain1.0000
22:38481325:G:Aacceptor_gain1.0000
22:38482494:A:AGacceptor_gain1.0000
22:38482495:G:GGacceptor_gain1.0000
22:38468323:GGGT:Gdonor_loss0.9900
22:38468344:G:Tdonor_gain0.9900
22:38474515:G:Aacceptor_gain0.9900
22:38474522:GGC:Gacceptor_gain0.9900
22:38479589:TTA:Tacceptor_loss0.9900
22:38479590:TAG:Tacceptor_loss0.9900
22:38479591:AGGT:Aacceptor_gain0.9900
22:38479592:GGTG:Gacceptor_gain0.9900
22:38479747:TGGAG:Tdonor_loss0.9900

AlphaMissense

1401 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:38474571:G:TR47M0.993
22:38474537:A:CS36R0.991
22:38474539:C:AS36R0.991
22:38474539:C:GS36R0.991
22:38474561:T:CF44L0.990
22:38474563:C:AF44L0.990
22:38474563:C:GF44L0.990
22:38481258:C:AP133H0.990
22:38468255:G:CG8R0.987
22:38468256:G:AG8D0.987
22:38468264:A:CS11R0.987
22:38468266:C:AS11R0.987
22:38468266:C:GS11R0.987
22:38481237:T:CL126P0.987
22:38481240:A:TE127V0.987
22:38474571:G:CR47T0.985
22:38481248:G:CA130P0.985
22:38481258:C:GP133R0.985
22:38481228:C:TS123F0.984
22:38481249:C:AA130D0.984
22:38481440:T:CF194L0.983
22:38481442:C:AF194L0.983
22:38481442:C:GF194L0.983
22:38481336:G:CR159P0.982
22:38481257:C:TP133S0.980
22:38481356:T:AW166R0.980
22:38481356:T:CW166R0.980
22:38468267:C:GH12D0.979
22:38481241:A:CE127D0.979
22:38481241:A:TE127D0.979

dbSNP variants (sampled 300 via entrez): RS1000362297 (22:38482655 G>A), RS1000411664 (22:38483710 C>T), RS1000646102 (22:38473100 TAAAAAA>T,TA,TAA,TAAAAA), RS1000708027 (22:38472448 G>C), RS1000912400 (22:38472479 A>T), RS1000947925 (22:38469180 A>G), RS1000965588 (22:38472243 C>T), RS1001161070 (22:38479075 T>C), RS1001350243 (22:38467450 A>G), RS1001364321 (22:38477082 T>A), RS1001572632 (22:38471520 C>T), RS1001637643 (22:38467149 C>T), RS1001833126 (22:38472617 G>C), RS1001984096 (22:38479534 G>C), RS1002062063 (22:38477667 G>T)

Disease associations

OMIM: gene MIM:619900 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST007209_16Gallstone disease1.000000e-10
GCST007561_72Sleep duration4.000000e-08
GCST007576_168Chronotype2.000000e-08
GCST010244_327Triglyceride levels2.000000e-14

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008328chronotype measurement
EFO:0004530triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, affects cotreatment, increases expression, decreases expression5
Tretinoindecreases expression, increases expression3
sodium arseniteaffects methylation, increases expression2
Resveratroldecreases expression, affects cotreatment, increases expression2
Cyclosporineincreases expression2
Particulate Matterincreases expression, decreases expression, increases abundance2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
deoxynivalenoldecreases expression1
lead acetateincreases expression1
salinomycindecreases expression1
trichostatin Aincreases expression1
beta-lapachonedecreases expression1
cobaltous chloridedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
avobenzoneincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluoro-n-nonanoic aciddecreases expression1
K 7174increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001increases expression1
abrinedecreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
NSC 689534increases expression1
(+)-JQ1 compounddecreases expression1
Decitabineaffects expression1
Sunitinibdecreases expression1
Orlistatincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): gallstones