CPNE7

gene
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Summary

CPNE7 (copine 7, HGNC:2320) is a protein-coding gene on chromosome 16q24.3, encoding Copine-7 (Q9UBL6). Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. It is a selective cancer dependency (DepMap: 14.0% of cell lines).

This gene encodes a member of the copine family, which is composed of calcium-dependent membrane-binding proteins. The gene product contains two N-terminal C2 domains and one von Willebrand factor A domain. The encoded protein may be involved in membrane trafficking. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 27132 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 184 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 14.0% of screened cell lines
  • MANE Select transcript: NM_153636

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2320
Approved symbolCPNE7
Namecopine 7
Location16q24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000178773
Ensembl biotypeprotein_coding
OMIM605689
Entrez27132

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000268720, ENST00000319518, ENST00000525982, ENST00000526232, ENST00000529800, ENST00000532500, ENST00000564421, ENST00000566398, ENST00000568977, ENST00000857691, ENST00000936168, ENST00000936169, ENST00000936170, ENST00000954262

RefSeq mRNA: 2 — MANE Select: NM_153636 NM_014427, NM_153636

CCDS: CCDS10980, CCDS10981

Canonical transcript exons

ENST00000319518 — 15 exons

ExonStartEnd
ENSE000011894548958867589588808
ENSE000011894698958477489584857
ENSE000011894738958402889584102
ENSE000011894838958369789583771
ENSE000011895058957753989577721
ENSE000013015268959112789591260
ENSE000013055278958989789589951
ENSE000013299348959100789591058
ENSE000015634118959648489597246
ENSE000019364558957575889576071
ENSE000034769318959536789595603
ENSE000035542958958546489585553
ENSE000035737968958667089586756
ENSE000035794538958568789585785
ENSE000036836668958704389587102

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 93.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2902 / max 151.4336, expressed in 1099 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1556095.4936989
1556101.6280661
1556110.104541
1556140.032618
1556120.03168

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lateral nuclear group of thalamusUBERON:000273693.84gold quality
triceps brachiiUBERON:000150993.22gold quality
gluteal muscleUBERON:000200093.11gold quality
stromal cell of endometriumCL:000225590.39gold quality
vena cavaUBERON:000408790.15silver quality
parotid glandUBERON:000183189.86silver quality
pituitary glandUBERON:000000789.42gold quality
type B pancreatic cellCL:000016989.34gold quality
cingulate cortexUBERON:000302789.15gold quality
anterior cingulate cortexUBERON:000983589.14gold quality
olfactory bulbUBERON:000226489.04gold quality
adenohypophysisUBERON:000219688.68gold quality
right frontal lobeUBERON:000281088.36gold quality
dorsal plus ventral thalamusUBERON:000189787.56gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451186.89gold quality
hypothalamusUBERON:000189886.43gold quality
dorsal motor nucleus of vagus nerveUBERON:000287086.39silver quality
tongue squamous epitheliumUBERON:000691986.30silver quality
heart right ventricleUBERON:000208086.29silver quality
nasal cavity epitheliumUBERON:000538486.02silver quality
Brodmann (1909) area 9UBERON:001354085.70gold quality
cerebellar vermisUBERON:000472085.68gold quality
vastus lateralisUBERON:000137985.42gold quality
dorsolateral prefrontal cortexUBERON:000983485.31gold quality
diaphragmUBERON:000110385.27gold quality
buccal mucosa cellCL:000233684.75silver quality
frontal cortexUBERON:000187084.51gold quality
superficial temporal arteryUBERON:000161484.47gold quality
amygdalaUBERON:000187684.45gold quality
prefrontal cortexUBERON:000045184.25gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-6678yes5.34
E-ANND-3no1.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting CPNE7, 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-3151-5P99.8663.831069
HSA-MIR-444799.8567.812900
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-447299.5666.081478
HSA-MIR-431899.3866.941505
HSA-MIR-1273H-3P99.2967.55980
HSA-MIR-361-3P99.1966.451381
HSA-MIR-491-5P99.1365.981468
HSA-MIR-485-5P99.1064.781889
HSA-MIR-6884-5P99.1064.501987
HSA-MIR-6846-5P98.8165.861121
HSA-MIR-6848-5P98.8165.491126
HSA-MIR-4755-3P98.7765.591915
HSA-MIR-6769B-5P98.7364.911092
HSA-MIR-3192-5P96.9865.761926
HSA-MIR-71196.6065.75528
HSA-MIR-4652-5P96.4664.22553
HSA-MIR-6742-5P96.3264.01869
HSA-MIR-1237-5P95.3862.21451
HSA-MIR-448895.3862.00443
HSA-MIR-4697-5P95.3861.72457
HSA-MIR-6796-5P95.3766.081120
HSA-MIR-6879-3P93.9364.00759

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 14.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • These results suggest Cpne7 is a diffusible signaling molecule that is secreted by preameloblasts, and regulates the differentiation of mesenchymal cells of dental or non-dental origin into odontoblasts. (PMID:25453951)
  • The Role of CPNE7 (Copine-7) in Colorectal Cancer Prognosis and Metastasis. (PMID:38069026)
  • Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression. (PMID:38526029)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriocpne7ENSDARG00000102584
mus_musculusCpne7ENSMUSG00000034796
rattus_norvegicusCpne7ENSRNOG00000015397
caenorhabditis_elegansWBGENE00001577
caenorhabditis_elegansWBGENE00006441
caenorhabditis_elegansWBGENE00012128
caenorhabditis_elegansWBGENE00015061

Paralogs (8): CPNE3 (ENSG00000085719), CPNE6 (ENSG00000100884), CPNE5 (ENSG00000124772), CPNE8 (ENSG00000139117), CPNE2 (ENSG00000140848), CPNE9 (ENSG00000144550), CPNE4 (ENSG00000196353), CPNE1 (ENSG00000214078)

Protein

Protein identifiers

Copine-7Q9UBL6 (reviewed: Q9UBL6)

Alternative names: Copine VII

All UniProt accessions (5): E9PJ31, Q9UBL6, H0YE30, H0YEH8, H3BP03

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes.

Subcellular location. Cytoplasm. Nucleus. Cell membrane.

Tissue specificity. Expressed in the brain, testis, thymus and small intestine.

Domain organisation. The C2 domain 1 is not necessary for calcium-mediated translocation and association to the plasma membrane. The C2 domain 2 is necessary for calcium-mediated translocation and association to the plasma membrane.

Similarity. Belongs to the copine family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UBL6-11yes
Q9UBL6-22

RefSeq proteins (2): NP_055242, NP_705900* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR002035VWF_ADomain
IPR010734Copine_CDomain
IPR035892C2_domain_sfHomologous_superfamily
IPR036465vWFA_dom_sfHomologous_superfamily
IPR037768C2B_CopineDomain
IPR045052CopineFamily

Pfam: PF00168, PF07002

UniProt features (17 total): binding site 8, sequence variant 4, domain 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UBL6-F178.410.47

Functional residue map

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

Ligand- & substrate-binding residues (8): 309; 315; 245; 245; 251; 307; 307; 309

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1483206Glycerophospholipid biosynthesis

MSigDB gene sets: 71 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_RESPONSE_TO_METAL_ION, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, MODULE_331, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_CELLULAR_RESPONSE_TO_CALCIUM_ION, DOUGLAS_BMI1_TARGETS_UP, CTAWWWATA_RSRFC4_Q2

GO Biological Process (3): lipid metabolic process (GO:0006629), glycerophospholipid biosynthetic process (GO:0046474), cellular response to calcium ion (GO:0071277)

GO Molecular Function (4): phospholipid binding (GO:0005543), calcium-dependent phospholipid binding (GO:0005544), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), plasma membrane (GO:0005886), synapse (GO:0045202), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Phospholipid metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
primary metabolic process1
glycerophospholipid metabolic process1
phospholipid biosynthetic process1
glycerolipid biosynthetic process1
response to calcium ion1
cellular response to metal ion1
lipid binding1
phospholipid binding1
cation binding1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
membrane1
cell periphery1
cell junction1
extracellular vesicle1

Protein interactions and networks

STRING

640 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CPNE7ZNF778Q96MU6566
CPNE7NUCLEOLINP19338495
CPNE7SPG7Q9UQ90482
CPNE7CDH15P55291467
CPNE7SRRM5B3KS81453
CPNE7SLC22A31A6NKX4414
CPNE7DBNDD1Q9H9R9408
CPNE7SPATA2LQ8IUW3406
CPNE7OR1L3Q8NH93400
CPNE7ANKRD11Q6UB99387
CPNE7ZNF276Q8N554384
CPNE7OR1L1Q8NH94376
CPNE7DSPPQ9NZW4370
CPNE7DPEP1P16444355
CPNE7STUMQ69YW2355

IntAct

39 interactions, top by confidence:

ABTypeScore
CDCA4PPP2R1Apsi-mi:“MI:0914”(association)0.790
DOCK8LRCH4psi-mi:“MI:0914”(association)0.620
ADAMTSL4CPNE7psi-mi:“MI:0915”(physical association)0.560
CPNE7ADAMTSL4psi-mi:“MI:0915”(physical association)0.560
RNF19BPIK3R2psi-mi:“MI:0914”(association)0.530
WASF3CYFIP1psi-mi:“MI:0914”(association)0.530
BRD1KAT7psi-mi:“MI:0914”(association)0.530
GSTO1CPNE7psi-mi:“MI:0915”(physical association)0.400
MS4A7CPNE7psi-mi:“MI:0915”(physical association)0.400
MTRES1CPNE7psi-mi:“MI:0915”(physical association)0.400
CPNE7CSNK2Bpsi-mi:“MI:0915”(physical association)0.370
CALCOCO2CPNE7psi-mi:“MI:0915”(physical association)0.370
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
OTUB1STAMBPpsi-mi:“MI:0914”(association)0.350
USP53ANXA2P2psi-mi:“MI:0914”(association)0.350
CSAG2CAMK2Dpsi-mi:“MI:0914”(association)0.350
UVRAGTUBAL3psi-mi:“MI:0914”(association)0.350
GEMIN8GEMIN2psi-mi:“MI:0914”(association)0.350
METTL2ANDUFS6psi-mi:“MI:0914”(association)0.350
CPNE4CPNE6psi-mi:“MI:0914”(association)0.350
CPNE7UBTFpsi-mi:“MI:0914”(association)0.350
CHMP4AHSPA2psi-mi:“MI:0914”(association)0.350
SURF6GTPBP10psi-mi:“MI:0914”(association)0.350
FOXF2POTEFpsi-mi:“MI:0914”(association)0.350
PLEKHG7MROH6psi-mi:“MI:0914”(association)0.350
KLHL14ARHGAP32psi-mi:“MI:0914”(association)0.350
OPALINFAM171A2psi-mi:“MI:0914”(association)0.350

BioGRID (90): ADAMTSL4 (Two-hybrid), CPNE7 (Two-hybrid), CPNE7 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), UBTF (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), EBF3 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), RPS27A (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), SETD2 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3NFE2, A0FGR8, A0FGR9, A2AP18, A4IJ05, O08625, O08874, O15357, O75038, P51432, P70218, P70268, Q01970, Q12851, Q3TZZ7, Q3U7R1, Q4VX76, Q5DTI8, Q5FWL4, Q5M7N9, Q5R8Q5, Q5RAG2, Q5RCK6, Q5RJH2, Q61161, Q62807, Q63433, Q6DN12, Q6XYQ8, Q7ZWU7, Q812E4, Q86SS6, Q8K394, Q8TDW5, Q920M7, Q925C0, Q92918, Q99JE6, Q99N48, Q9BSJ8

Diamond homologs: A8WMY4, D4A1R8, H1UBN0, H2KYS8, O75131, O95741, P59108, Q08DB4, Q0VE82, Q1RLL3, Q1ZXB3, Q2KHY1, Q54FY7, Q54P51, Q55GG1, Q5BJS7, Q5R4W6, Q5RAE1, Q5S1W2, Q5XQC7, Q7YXU4, Q86K21, Q86YQ8, Q8BLR2, Q8BT60, Q8C166, Q8IYJ1, Q8JZW4, Q941L3, Q96A23, Q96FN4, Q99829, Q9DC53, Q9HCH3, Q9UBL6, Q9XUB9, Q9Z140, A0JJX5, Q09219, Q12466

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance155
Likely benign7
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
267483Single allelePathogenic

SpliceAI

3394 predictions. Top by Δscore:

VariantEffectΔscore
16:89577680:G:GTdonor_gain1.0000
16:89584103:G:GGdonor_gain1.0000
16:89584103:G:Tdonor_loss1.0000
16:89584769:CCCA:Cacceptor_loss1.0000
16:89584770:CCAG:Cacceptor_loss1.0000
16:89584773:GGAC:Gacceptor_gain1.0000
16:89584851:G:GTdonor_gain1.0000
16:89584854:GGAG:Gdonor_gain1.0000
16:89584855:G:GTdonor_gain1.0000
16:89584855:GAG:Gdonor_gain1.0000
16:89584856:AGGTG:Adonor_loss1.0000
16:89584857:GGTGA:Gdonor_loss1.0000
16:89584858:G:GGdonor_gain1.0000
16:89585460:ACAGG:Aacceptor_loss1.0000
16:89585461:CAGGT:Cacceptor_loss1.0000
16:89585462:AGGT:Aacceptor_gain1.0000
16:89585463:GGTG:Gacceptor_gain1.0000
16:89585544:GCCTC:Gdonor_gain1.0000
16:89585685:A:AGacceptor_gain1.0000
16:89585686:G:GGacceptor_gain1.0000
16:89585686:GT:Gacceptor_gain1.0000
16:89585783:CAG:Cdonor_loss1.0000
16:89585784:AG:Adonor_loss1.0000
16:89585785:GGTG:Gdonor_loss1.0000
16:89585786:G:Adonor_loss1.0000
16:89585787:T:Adonor_loss1.0000
16:89588798:GAC:Gdonor_gain1.0000
16:89588807:AGGTG:Adonor_loss1.0000
16:89588809:G:GCdonor_loss1.0000
16:89588810:T:Gdonor_loss1.0000

AlphaMissense

3656 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:89588684:G:CD388H1.000
16:89588685:A:CD388A1.000
16:89588685:A:TD388V1.000
16:89588686:C:AD388E1.000
16:89588686:C:GD388E1.000
16:89588691:C:TT390I1.000
16:89588701:T:AN393K1.000
16:89588701:T:GN393K1.000
16:89588759:T:CY413H1.000
16:89588760:A:GY413C1.000
16:89589922:T:CF438L1.000
16:89589924:T:AF438L1.000
16:89589924:T:GF438L1.000
16:89595395:A:TD519V1.000
16:89595396:C:AD519E1.000
16:89595396:C:GD519E1.000
16:89595397:G:CG520R1.000
16:89595398:G:AG520D1.000
16:89595398:G:TG520V1.000
16:89595493:T:CF552L1.000
16:89595494:T:CF552S1.000
16:89595495:C:AF552L1.000
16:89595495:C:GF552L1.000
16:89595577:T:CF580L1.000
16:89595579:C:AF580L1.000
16:89595579:C:GF580L1.000
16:89585491:T:AW282R0.999
16:89585491:T:CW282R0.999
16:89588682:T:AI387N0.999
16:89588685:A:GD388G0.999

dbSNP variants (sampled 300 via entrez): RS1000031435 (16:89575514 C>T), RS1000079252 (16:89594557 C>T), RS1000186637 (16:89579483 C>T), RS1000243934 (16:89597519 C>T), RS1000326963 (16:89579303 A>T), RS1000384012 (16:89597690 T>A), RS1000411641 (16:89574953 G>A), RS1000605299 (16:89591611 G>A), RS1000702090 (16:89584244 G>A), RS1000738376 (16:89591569 G>A,T), RS1000751449 (16:89594332 C>G), RS1000867284 (16:89575245 C>T), RS1000931027 (16:89588496 G>A,C), RS1001115867 (16:89584420 C>T), RS1001116209 (16:89586507 T>A,G)

Disease associations

OMIM: gene MIM:605689 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): 16q24.3 microdeletion syndrome (MONDO:0016838)

Orphanet (1): 16q24.3 microdeletion syndrome (Orphanet:261250)

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST007335_29Age at first sexual intercourse7.000000e-10
GCST008129_27Body mass index3.000000e-08
GCST008803_14Smoking behaviour (cigarette pack-years)3.000000e-09
GCST010703_280Brain morphology (MOSTest)2.000000e-15

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0009749age at first sexual intercourse measurement
EFO:0004340body mass index
EFO:0009115tobacco smoke exposure measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, increases methylation, decreases expression2
Smokeincreases expression2
aristolochic acid Iincreases expression1
ethyl-p-hydroxybenzoatedecreases expression1
o,p’-DDTincreases expression1
aflatoxin B2increases methylation1
perfluorooctane sulfonic acidincreases expression1
jinfukangincreases expression1
3-hydroxy-4-prenyl-5-methoxystilbene-2-carboxylic acidincreases expression1
(+)-JQ1 compounddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Arsenicaffects methylation1
Benzo(a)pyrenedecreases methylation, increases methylation, affects methylation1
Dexamethasoneincreases expression1
Diazinonincreases methylation1
Drugs, Chinese Herbaldecreases expression1
Estradiolincreases expression1
Hydrogen Peroxideincreases expression1
Leadaffects expression1
Plant Extractsaffects cotreatment, decreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Triclosanincreases expression1
Cyclosporineincreases methylation1
Okadaic Acidincreases 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): 16q24.3 microdeletion syndrome