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COPZ2

gene
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Also known as MGC23008

Summary

COPZ2 (coat protein complex I subunit zeta 2, HGNC:19356) is a protein-coding gene on chromosome 17q21.32, encoding Coatomer subunit zeta-2 (Q9P299). The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network.

This gene encodes a member of the adaptor complexes small subunit family. The encoded protein is a subunit of the coatomer protein complex, a seven-subunit complex that functions in the formation of COPI-type, non-clathrin-coated vesicles. COPI vesicles function in the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Source: NCBI Gene 51226 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 9 total
  • MANE Select transcript: NM_016429

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19356
Approved symbolCOPZ2
Namecoat protein complex I subunit zeta 2
Location17q21.32
Locus typegene with protein product
StatusApproved
AliasesMGC23008
Ensembl geneENSG00000005243
Ensembl biotypeprotein_coding
OMIM615526
Entrez51226

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 13 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000579263, ENST00000580174, ENST00000580409, ENST00000581637, ENST00000581756, ENST00000583414, ENST00000584955, ENST00000585182, ENST00000612370, ENST00000621465, ENST00000861305, ENST00000861306, ENST00000861307, ENST00000861308, ENST00000861309, ENST00000861310, ENST00000965149, ENST00000965150, ENST00000965151

RefSeq mRNA: 1 — MANE Select: NM_016429 NM_016429

CCDS: CCDS74092

Canonical transcript exons

ENST00000621465 — 9 exons

ExonStartEnd
ENSE000035031074802847248028510
ENSE000035837654802912548029176
ENSE000035900294803215648032233
ENSE000036037834803321148033302
ENSE000036572044803268648032741
ENSE000036603364803386348033944
ENSE000036794834802616748026475
ENSE000037206974803766748037797
ENSE000037445514803685148036925

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 99.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.2761 / max 430.3076, expressed in 1539 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
16662331.27611539

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818899.21gold quality
right coronary arteryUBERON:000162597.63gold quality
periodontal ligamentUBERON:000826697.63gold quality
ascending aortaUBERON:000149697.39gold quality
thoracic aortaUBERON:000151597.38gold quality
aortaUBERON:000094797.14gold quality
popliteal arteryUBERON:000225097.07gold quality
tibial arteryUBERON:000761097.07gold quality
descending thoracic aortaUBERON:000234597.05gold quality
lower esophagus muscularis layerUBERON:003583396.98gold quality
stromal cell of endometriumCL:000225596.95gold quality
lower esophagusUBERON:001347396.94gold quality
tibial nerveUBERON:000132396.92gold quality
tendonUBERON:000004396.88gold quality
left coronary arteryUBERON:000162696.81gold quality
tibiaUBERON:000097996.80gold quality
coronary arteryUBERON:000162196.57gold quality
esophagogastric junction muscularis propriaUBERON:003584196.47gold quality
mucosa of stomachUBERON:000119996.15gold quality
hindlimb stylopod muscleUBERON:000425296.07gold quality
apex of heartUBERON:000209895.92gold quality
calcaneal tendonUBERON:000370195.90gold quality
gastrocnemiusUBERON:000138895.89gold quality
subcutaneous adipose tissueUBERON:000219095.84gold quality
right atrium auricular regionUBERON:000663195.74gold quality
muscle of legUBERON:000138395.68gold quality
adipose tissueUBERON:000101395.58gold quality
adipose tissue of abdominal regionUBERON:000780895.37gold quality
omental fat padUBERON:001041495.36gold quality
peritoneumUBERON:000235895.33gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-112yes15.02
E-ANND-3yes14.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting COPZ2, 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-211099.9666.681930
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-65799.4866.02848
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-429299.1665.571767
HSA-MIR-328-5P99.0864.651000
HSA-MIR-5006-5P98.7966.921246
HSA-MIR-6885-5P98.7164.33902
HSA-MIR-4700-5P98.6367.431915
HSA-MIR-450A-2-3P97.9167.561459
HSA-MIR-63797.9164.051517
HSA-MIR-808997.7466.211698
HSA-MIR-3121-5P97.3066.621146
HSA-MIR-4433B-3P97.2263.62663
HSA-MIR-1296-5P93.9467.71305

Literature-anchored findings (GeneRIF, showing 2)

  • The solution structure of a truncated form (residues 1-149; zeta-COP149) of human zeta-COP (total 177 residues), is reported. (PMID:19167404)
  • The knockdown of COPZ1, but not of COPZ2 encoding isoform coatomer protein complex zeta2, caused Golgi apparatus collapse, blocked autophagy, and induced apoptosis in both proliferating and nondividing tumor cells. (PMID:21746916)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocopz2ENSDARG00000006786
mus_musculusCopz2ENSMUSG00000018672
rattus_norvegicusCopz2ENSRNOG00000009225
drosophila_melanogasterzetaCOPFBGN0040512
caenorhabditis_elegansWBGENE00010333

Paralogs (1): COPZ1 (ENSG00000111481)

Protein

Protein identifiers

Coatomer subunit zeta-2 — Q9P299 (reviewed: Q9P299)

Alternative names: Zeta-2-coat protein

All UniProt accessions (7): Q9P299, A0A0G2JLH9, J3KRJ9, J3QL73, J3QLS7, J3QQQ5, J3QS21

UniProt curated annotations — full annotation on UniProt →

Function. The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. The zeta subunit may be involved in regulating the coat assembly and, hence, the rate of biosynthetic protein transport due to its association-dissociation properties with the coatomer complex.

Subunit / interactions. Oligomeric complex.

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

Similarity. Belongs to the adaptor complexes small subunit family.

RefSeq proteins (1): NP_057513* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011012Longin-like_dom_sfHomologous_superfamily
IPR022775AP_mu_sigma_suDomain
IPR039652Coatomer_zetaFamily

Pfam: PF01217

UniProt features (4 total): compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P299-F184.530.66

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-6807878COPI-mediated anterograde transport
R-HSA-6811434COPI-dependent Golgi-to-ER retrograde traffic

MSigDB gene sets: 166 (showing top): RNGTGGGC_UNKNOWN, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOCC_COATED_VESICLE, DELYS_THYROID_CANCER_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOCC_GOLGI_ASSOCIATED_VESICLE, GOCC_VESICLE_COAT, ZHAN_MULTIPLE_MYELOMA_LB_UP, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON

GO Biological Process (5): intracellular protein transport (GO:0006886), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), intra-Golgi vesicle-mediated transport (GO:0006891), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (0):

GO Cellular Component (12): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), cis-Golgi network (GO:0005801), cytosol (GO:0005829), COPI vesicle coat (GO:0030126), transport vesicle (GO:0030133), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), membrane (GO:0016020), COPI-coated vesicle membrane (GO:0030663), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
ER to Golgi Anterograde Transport1
Golgi-to-ER retrograde transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
Golgi apparatus3
cytoplasm3
cellular anatomical structure3
intracellular protein localization2
Golgi vesicle transport2
transport2
bounding membrane of organelle2
intracellular membrane-bounded organelle2
endomembrane system2
protein transport1
intracellular transport1
establishment of protein localization1
cellular process1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
vesicle coat1
COPI-coated vesicle membrane1
cytoplasmic vesicle1
endoplasmic reticulum-Golgi intermediate compartment1
intracellular anatomical structure1
COPI-coated vesicle1
Golgi-associated vesicle membrane1
coated vesicle membrane1
intracellular vesicle1

Protein interactions and networks

STRING

968 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COPZ2COPG1Q9Y678750
COPZ2COPG2Q9UBF2704
COPZ2COPB1P53618602
COPZ2NTAQ1Q96HA8574
COPZ2ARCN1P48444572
COPZ2COPB2P35606562
COPZ2COPEO14579562
COPZ2COPAP53621544
COPZ2NUDT22Q9BRQ3524
COPZ2TRABDQ9H4I3499
COPZ2TMED6Q8WW62491
COPZ2COPRSQ9NQ92491
COPZ2LARGE2Q8N3Y3473
COPZ2TTC7BQ86TV6468
COPZ2EFEMP2O95967465

IntAct

5 interactions, top by confidence:

ABTypeScore
COPZ2COPB2psi-mi:“MI:0914”(association)0.350
ETV3EEF1A2psi-mi:“MI:0914”(association)0.350
COPZ2COPEpsi-mi:“MI:0914”(association)0.350
SWSAP1NACApsi-mi:“MI:2364”(proximity)0.270

BioGRID (18): COPG1 (Two-hybrid), COPZ2 (Two-hybrid), COPB2 (Affinity Capture-MS), HSPA9 (Affinity Capture-MS), COPA (Affinity Capture-MS), COPB1 (Affinity Capture-MS), ARCN1 (Affinity Capture-MS), COPG1 (Affinity Capture-MS), COPZ2 (Affinity Capture-MS), SNX17 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), COPE (Affinity Capture-MS), ZMPSTE24 (Affinity Capture-MS), COPZ2 (Negative Genetic), COPZ2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: B0G185, C0HLF1, D3ZVF4, E2QV03, F1SRI0, O02173, O13732, O17901, O23685, O74891, P0DI81, P0DI82, P35181, P35604, P38334, P47064, P53600, P56377, P61923, P61924, P61966, P61967, Q00381, Q03630, Q08CN0, Q09905, Q1JQ98, Q28IG8, Q3ZBS3, Q4S4I5, Q54CA7, Q54CU7, Q54HD4, Q54RV6, Q54WW3, Q5R5F2, Q5RES6, Q5ZKP4, Q6CCU8, Q75F71

Diamond homologs: O17901, O74891, P35604, P53600, P61923, P61924, Q54HD4, Q5NA06, Q5R5F2, Q6Z844, Q84LG4, Q8H1F4, Q940S5, Q9JHH9, Q9MAX5, Q9P299, Q54CA7, P47064, B0G185, O23685, O50016, O82201, P35181, P53680, P56377, P59780, P61966, P61967, P62743, P62744, Q00381, Q09905, Q17QC5, Q1JQ98, Q1JQA3, Q2YDH6, Q3ZBB6, Q3ZBS3, Q4ICG5, Q4WS49

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1861 predictions. Top by Δscore:

VariantEffectΔscore
17:48033856:CACTT:Cdonor_loss1.0000
17:48033857:ACTT:Adonor_loss1.0000
17:48033858:CTTA:Cdonor_loss1.0000
17:48033859:TTA:Tdonor_loss1.0000
17:48033860:TACT:Tdonor_loss1.0000
17:48033861:A:ACdonor_gain1.0000
17:48033862:C:CGdonor_gain1.0000
17:48033862:CT:Cdonor_gain1.0000
17:48033862:CTCT:Cdonor_gain1.0000
17:48033940:TAATA:Tacceptor_gain1.0000
17:48033943:TA:Tacceptor_gain1.0000
17:48033945:C:CCacceptor_gain1.0000
17:48029119:TCTTA:Tdonor_loss0.9900
17:48029120:CTTA:Cdonor_loss0.9900
17:48029121:TTACC:Tdonor_loss0.9900
17:48029122:TACC:Tdonor_loss0.9900
17:48029123:A:Gdonor_loss0.9900
17:48029123:AC:Adonor_gain0.9900
17:48029124:CC:Cdonor_gain0.9900
17:48029172:TCACA:Tacceptor_gain0.9900
17:48029173:CACA:Cacceptor_gain0.9900
17:48029173:CACAC:Cacceptor_gain0.9900
17:48029175:CA:Cacceptor_gain0.9900
17:48029177:C:CCacceptor_gain0.9900
17:48032150:CCTCA:Cdonor_loss0.9900
17:48032151:CTCA:Cdonor_loss0.9900
17:48032152:TCAC:Tdonor_loss0.9900
17:48032153:CA:Cdonor_loss0.9900
17:48032154:A:ATdonor_loss0.9900
17:48032154:AC:Adonor_gain0.9900

AlphaMissense

1380 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:48026462:G:TA200D0.998
17:48036895:C:GA48P0.998
17:48032715:G:CC129W0.996
17:48033214:A:CN119K0.996
17:48033214:A:TN119K0.996
17:48033231:C:GG114R0.996
17:48033897:C:AE78D0.996
17:48033897:C:GE78D0.996
17:48032701:A:GL134P0.995
17:48033230:C:TG114D0.995
17:48033889:A:TV81D0.995
17:48026463:C:GA200P0.994
17:48032156:C:TG165D0.994
17:48032734:A:GL123P0.994
17:48033215:T:AN119I0.994
17:48036882:A:GL52P0.994
17:48032156:C:AG165V0.993
17:48032165:A:TV162E0.993
17:48032713:A:GL130P0.993
17:48032722:A:GL127P0.993
17:48032725:A:TV126D0.993
17:48033236:A:TV112E0.993
17:48036894:G:TA48D0.993
17:48026450:A:GI204T0.992
17:48033248:A:GL108P0.992
17:48033269:A:TV101D0.992
17:48033944:A:CY63D0.991
17:48036891:A:TV49D0.991
17:48032157:C:GG165R0.990
17:48029168:A:GL168P0.989

dbSNP variants (sampled 300 via entrez): RS1000093713 (17:48039897 G>A), RS1000146217 (17:48040107 G>A), RS1000230474 (17:48048334 CGGTAGCA>C), RS1000371576 (17:48026227 G>A), RS1000539225 (17:48029829 C>T), RS1000696423 (17:48027905 G>A), RS1000758274 (17:48028258 T>C), RS1000888119 (17:48046558 C>A,T), RS1001236917 (17:48046182 T>C), RS1001328303 (17:48045709 A>G), RS1001439683 (17:48041979 G>A,T), RS1001441019 (17:48045524 G>C), RS1001545898 (17:48034331 C>G), RS1001674271 (17:48039513 G>A), RS1001714778 (17:48032544 C>T)

Disease associations

OMIM: gene MIM:615526 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001662_4Generalized epilepsy9.000000e-09
GCST005951_17Body mass index3.000000e-09
GCST007576_91Chronotype5.000000e-13
GCST012227_341Hip circumference adjusted for BMI4.000000e-08
GCST90002398_278Neutrophil count8.000000e-10

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008328chronotype measurement
EFO:0008039BMI-adjusted hip circumference
EFO:0004833neutrophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression, affects cotreatment, decreases expression2
bisphenol Faffects cotreatment, increases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects cotreatment, increases expression1
ochratoxin Aincreases expression, increases acetylation1
entinostatincreases expression1
bisphenol Bincreases expression1
bis-N,N-dimethylamino-2-(N-methylpyrrolyl)methyl cyclopentadienyl titanium (IV)increases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicincreases abundance, affects cotreatment, decreases expression1
Calcitrioldecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Estradiolaffects expression1
Indomethacinaffects cotreatment, increases expression1
Valproic Aciddecreases expression1
Vitamin Eincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Antirheumatic Agentsincreases expression1
Okadaic Aciddecreases expression1
Lactic Acidincreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot