CPNE1

Summary

CPNE1 (copine 1, HGNC:2314) is a protein-coding gene on chromosome 20q11.22, encoding Copine-1 (Q99829). Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes.

Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a calcium-dependent protein that also contains two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. However, the encoded protein does not contain a predicted signal sequence or transmembrane domains. This protein has a broad tissue distribution and it may function in membrane trafficking. This gene and the gene for RNA binding motif protein 12 overlap at map location 20q11.21. Alternate splicing results in multiple transcript variants encoding different proteins.

Source: NCBI Gene 8904 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 251 total — 2 pathogenic
• MANE Select transcript: NM_152925

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2314
Approved symbol	CPNE1
Name	copine 1
Location	20q11.22
Locus type	gene with protein product
Status	Approved
Aliases	CPN1
Ensembl gene	ENSG00000214078
Ensembl biotype	protein_coding
OMIM	604205
Entrez	8904

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 20 protein_coding, 4 protein_coding_CDS_not_defined, 4 retained_intron, 2 nonsense_mediated_decay

ENST00000317677, ENST00000352393, ENST00000397442, ENST00000397443, ENST00000401607, ENST00000412056, ENST00000414664, ENST00000414711, ENST00000415920, ENST00000416778, ENST00000420363, ENST00000430570, ENST00000434795, ENST00000435747, ENST00000437100, ENST00000437340, ENST00000439669, ENST00000439806, ENST00000440240, ENST00000458038, ENST00000462352, ENST00000473373, ENST00000475146, ENST00000483359, ENST00000483495, ENST00000486021, ENST00000498056, ENST00000498814, ENST00000879751, ENST00000879752

RefSeq mRNA: 6 — MANE Select: NM_152925 NM_001198863, NM_003915, NM_152925, NM_152926, NM_152927, NM_152928

CCDS: CCDS13260, CCDS46595

Canonical transcript exons

ENST00000397443 — 16 exons

Exon	Start	End
ENSE00003489600	35626567	35626803
ENSE00003492556	35631945	35632025
ENSE00003520856	35632517	35632696
ENSE00003586883	35630439	35630490
ENSE00003613375	35626044	35626381
ENSE00003633735	35631268	35631354
ENSE00003636943	35632311	35632385
ENSE00003637171	35630901	35631034
ENSE00003651778	35664760	35664900
ENSE00003688084	35627280	35627413
ENSE00003690090	35630741	35630795
ENSE00003692205	35631492	35631578
ENSE00003693092	35631114	35631173
ENSE00003757349	35632795	35632923
ENSE00003786502	35631688	35631777
ENSE00003788127	35632163	35632234

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 99.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.5939 / max 28.6943, expressed in 965 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
187075	71.4815	1823
187076	11.8743	1804
187069	0.8557	553
187070	0.6913	443
187068	0.0469	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	99.01	gold quality
endocervix	UBERON:0000458	98.98	gold quality
right lobe of thyroid gland	UBERON:0001119	98.97	gold quality
adenohypophysis	UBERON:0002196	98.95	gold quality
left lobe of thyroid gland	UBERON:0001120	98.94	gold quality
right uterine tube	UBERON:0001302	98.86	gold quality
body of uterus	UBERON:0009853	98.84	gold quality
right ovary	UBERON:0002118	98.82	gold quality
left ovary	UBERON:0002119	98.78	gold quality
lower esophagus mucosa	UBERON:0035834	98.74	gold quality
ectocervix	UBERON:0012249	98.72	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.72	gold quality
mucosa of stomach	UBERON:0001199	98.68	gold quality
metanephros cortex	UBERON:0010533	98.64	gold quality
tibial nerve	UBERON:0001323	98.63	gold quality
stromal cell of endometrium	CL:0002255	98.62	gold quality
skin of leg	UBERON:0001511	98.58	gold quality
cerebellar hemisphere	UBERON:0002245	98.58	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.57	gold quality
left uterine tube	UBERON:0001303	98.56	gold quality
right coronary artery	UBERON:0001625	98.50	gold quality
skin of abdomen	UBERON:0001416	98.47	gold quality
tibial artery	UBERON:0007610	98.47	gold quality
popliteal artery	UBERON:0002250	98.46	gold quality
descending thoracic aorta	UBERON:0002345	98.45	gold quality
upper lobe of left lung	UBERON:0008952	98.45	gold quality
cerebellar cortex	UBERON:0002129	98.42	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.40	gold quality
ascending aorta	UBERON:0001496	98.39	gold quality
thoracic aorta	UBERON:0001515	98.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6386	no	633.06
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
RELA	Repression

Upstream regulators (CollecTRI, top): NFKB

Literature-anchored findings (GeneRIF, showing 15)

• Copine I regulates tumour necrosis factor-alpha receptor signaling pathways. (PMID:14674885)
• Copine1 is upregulated in plasma membranes of TM cells in individuals with primary open-angle glaucoma. (PMID:18523666)
• CPNE1 shares a promoter and 5’UTR exons with RBM12. This genomic structure is conserved among multiple species. (PMID:18831769)
• CPNE1 overexpression can upregulate TRAF2 expression in prostate cancer DU-145 cells as determined by Western blotting and immunofluorescence assays. (PMID:29151113)
• Results demonstrated that CPNE1 was highly expressed in the osteosarcoma (OS) tissues and cell lines. Its knockdown significantly inhibited cell proliferation, colony formation, invasion and metastasis in OS cell lines. (PMID:29207139)
• Collectively, our findings suggest that JAB1 activates the neuronal differentiation ability of CPNE1 through the binding of C2A domain in CPNE1 with MPN domain in JAB1. (PMID:29448099)
• We observed that knockdown of CPNE1 and increased expression of miR-335-5p inhibits cell proliferation and motility in NSCLC cells, and found that CPNE1 was a target of miR-335-5p. (PMID:29970127)
• Study find that CPNE1 expression is upregulated in non-small cell lung cancer (NSCLC) and associated with advanced TNM stage, lymph node and distant metastasis. Furthermore, its knockdown inhibits the cell cycle in NSCLC cells. These data strongly suggest that CPNE1 is an oncogene in NSCLC and serves an important role in tumorigenesis of NSCLC progression. (PMID:30221693)
• High CPNE1 expression is associated with tumorigenesis and radioresistance via the AKT singling pathway in triple-negative breast cancer. (PMID:32181526)
• Prognostic Value of Copine 1 in Patients With Renal Cell Carcinoma. (PMID:34969745)
• CPNE1 promotes non-small cell lung cancer progression by interacting with RACK1 via the MET signaling pathway. (PMID:35101055)
• Up-regulation of CPNE1 Appears to Enhance Cancer Progression in HER2-positive and Luminal A Breast Cancer Cells. (PMID:35790271)
• Overexpression of Copines-1 is associated with clinicopathological parameters and poor outcome in gastric cancer. (PMID:36310511)
• Silencing of CPNE1-TRAF2 Axis Restrains the Development of Pancreatic Cancer. (PMID:38062811)
• CPNE1, A Potential Therapeutic Target in Nasopharyngeal Carcinoma, Affects Cell Growth and Radiation Resistance. (PMID:38355101)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	cpne1	ENSDARG00000075536

Paralogs (8): CPNE3 (ENSG00000085719), CPNE6 (ENSG00000100884), CPNE5 (ENSG00000124772), CPNE8 (ENSG00000139117), CPNE2 (ENSG00000140848), CPNE9 (ENSG00000144550), CPNE7 (ENSG00000178773), CPNE4 (ENSG00000196353)

Protein

Protein identifiers

Copine-1 — Q99829 (reviewed: Q99829)

Alternative names: Chromobindin 17, Copine I

All UniProt accessions (19): A6PVH9, B0QZ18, E7ENH5, E7EV27, Q99829, F2Z2V0, H0Y524, Q5JX44, Q5JX45, Q5JX52, Q5JX53, Q5JX54, Q5JX55, Q5JX56, Q5JX57, Q5JX58, Q5JX59, Q5JX60, Q5JX61

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes. Involved in the TNF receptor signaling pathway in a calcium-dependent manner. Exhibits calcium-dependent phospholipid binding properties. Plays a role in neuronal progenitor cell differentiation; induces neurite outgrowth via a AKT-dependent signaling cascade and calcium-independent manner. May recruit target proteins to the cell membrane in a calcium-dependent manner. May function in membrane trafficking. Involved in TNF-induced NF-kappa-B transcriptional repression by inducing endoprotease processing of the transcription factor NF-kappa-B p65/RELA subunit. Also induces endoprotease processing of NF-kappa-B p50/NFKB1, p52/NFKB2, RELB and REL.

Subunit / interactions. Homodimer; homodimerizes via its C2 domains. Interacts with p65/RELA (via N-terminus); this interaction induces proteolytic cleavage of p65/RELA subunit and inhibition of NF-kappa-B transcriptional activity. Interacts (via VWFA domain) with ACTB, CCDC22, MYCBP2, PPP5C, RDX and UBE2O.

Subcellular location. Nucleus. Cytoplasm. Cell membrane.

Tissue specificity. Expressed in neutrophils (at protein level). Widely expressed. Expressed in the brain. Expressed in neutrophil precursors from bone marrow and peripheral blood.

Domain organisation. C2 domains are necessary for calcium-dependent cell membrane association. C2 domains are necessary for neuronal progenitor cell differentiation in a calcium-independent manner.

Induction. Up-regulated by the inflammatory cytokine TNF. Up-regulated during neuronal progenitor cell differentiation.

Similarity. Belongs to the copine family.

RefSeq proteins (6): NP_001185792, NP_003906, NP_690902, NP_690903, NP_690904, NP_690905 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000008	C2_dom	Domain
IPR002035	VWF_A	Domain
IPR010734	Copine_C	Domain
IPR035892	C2_domain_sf	Homologous_superfamily
IPR036465	vWFA_dom_sf	Homologous_superfamily
IPR037768	C2B_Copine	Domain
IPR045052	Copine	Family

Pfam: PF00168, PF07002

UniProt features (30 total): binding site 16, mutagenesis site 4, domain 3, sequence variant 3, sequence conflict 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99829-F1	92.23	0.82

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 (16): 82; 92; 153; 153; 159; 214; 214; 216; 216; 222; 21; 21 …

Post-translational modifications (1): 171

Mutagenesis-validated functional residues (4):

Position	Phenotype
21	inhibits translocation to the cell membrane in a calcium-dependent manner and does not inhibit neuronal progenitor cell
90	inhibits translocation to the cell membrane in a calcium-dependent manner and does not inhibit neuronal progenitor cell
216	inhibits translocation to the cell membrane in a calcium-dependent manner and does not inhibit neuronal progenitor cell
222	inhibits translocation to the cell membrane in a calcium-dependent manner and does not inhibit neuronal progenitor cell

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1483206	Glycerophospholipid biosynthesis
R-HSA-6798695	Neutrophil degranulation

MSigDB gene sets: 406 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, MODULE_172, SHEPARD_BMYB_MORPHOLINO_UP, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, FREAC2_01, REACTOME_INNATE_IMMUNE_SYSTEM, WWTAAGGC_UNKNOWN, PAX4_01, GOBP_NEURON_PROJECTION_EXTENSION, CCAWYNNGAAR_UNKNOWN, GOMF_METALLOPEPTIDASE_ACTIVITY, GOBP_RESPONSE_TO_PEPTIDE, GOCC_VACUOLAR_MEMBRANE, PAL_PRMT5_TARGETS_UP, GOCC_SECRETORY_GRANULE

GO Biological Process (14): proteolysis (GO:0006508), lipid metabolic process (GO:0006629), negative regulation of gene expression (GO:0010629), vesicle-mediated transport (GO:0016192), regulation of canonical NF-kappaB signal transduction (GO:0043122), negative regulation of DNA binding (GO:0043392), positive regulation of neuron differentiation (GO:0045666), glycerophospholipid biosynthetic process (GO:0046474), positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051897), cellular response to calcium ion (GO:0071277), negative regulation of non-canonical NF-kappaB signal transduction (GO:1901223), positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265), neuron projection extension (GO:1990138), cell differentiation (GO:0030154)

GO Molecular Function (9): phosphatidylserine binding (GO:0001786), endopeptidase activity (GO:0004175), calcium ion binding (GO:0005509), phospholipid binding (GO:0005543), calcium-dependent phospholipid binding (GO:0005544), identical protein binding (GO:0042802), NF-kappaB binding (GO:0051059), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), nuclear membrane (GO:0031965), azurophil granule membrane (GO:0035577), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Phospholipid metabolism	1
Innate Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
phospholipid binding	2
protein metabolic process	1
primary metabolic process	1
gene expression	1
regulation of gene expression	1
negative regulation of macromolecule biosynthetic process	1
transport	1
cellular process	1
canonical NF-kappaB signal transduction	1
regulation of intracellular signal transduction	1
DNA binding	1
negative regulation of binding	1
regulation of DNA binding	1
neuron differentiation	1
positive regulation of cell differentiation	1
regulation of neuron differentiation	1
glycerophospholipid metabolic process	1
phospholipid biosynthetic process	1
glycerolipid biosynthetic process	1
phosphatidylinositol 3-kinase/protein kinase B signal transduction	1
regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	1
positive regulation of intracellular signal transduction	1
response to calcium ion	1
cellular response to metal ion	1
non-canonical NF-kappaB signal transduction	1
regulation of non-canonical NF-kappaB signal transduction	1
negative regulation of intracellular signal transduction	1
positive regulation of cytokine-mediated signaling pathway	1
regulation of tumor necrosis factor-mediated signaling pathway	1
tumor necrosis factor-mediated signaling pathway	1
developmental cell growth	1
neuron projection morphogenesis	1
developmental growth involved in morphogenesis	1
cellular developmental process	1
anion binding	1
modified amino acid binding	1
peptidase activity	1
metal ion binding	1
lipid binding	1

Protein interactions and networks

STRING

684 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPNE1	REPS1	Q96D71	569
CPNE1	ADISSP	Q9GZN8	528
CPNE1	AFTPH	Q6ULP2	527
CPNE1	TOR4A	Q9NXH8	508
CPNE1	IRGQ	Q8WZA9	505
CPNE1	AP1G2	O75843	502
CPNE1	AATF	Q9NY61	490
CPNE1	ADPGK	Q9BRR6	455
CPNE1	SWAP70	Q9UH65	447
CPNE1	JCAD	Q9P266	442
CPNE1	CD81	P18582	439
CPNE1	STXBP2	Q15833	439
CPNE1	PCYT2	Q99447	439
CPNE1	BRK1	Q8WUW1	432
CPNE1	SEC24C	P53992	420

IntAct

39 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
KLK5	DENND11	psi-mi:“MI:0914”(association)	0.640
CD27	TCAF2	psi-mi:“MI:0914”(association)	0.640
CPNE1	LHX6	psi-mi:“MI:0915”(physical association)	0.560
SORBS3	CPNE1	psi-mi:“MI:0915”(physical association)	0.560
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
	AP3D1	psi-mi:“MI:0914”(association)	0.460
YWHAZ	CPNE1	psi-mi:“MI:0915”(physical association)	0.400
STK3	CPNE1	psi-mi:“MI:0915”(physical association)	0.370
CPNE1	BUB3	psi-mi:“MI:0915”(physical association)	0.370
PLEKHA7	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ARRB2		psi-mi:“MI:0914”(association)	0.350
UIMC1	PYCR3	psi-mi:“MI:0914”(association)	0.350
NEK7	SUPT5H	psi-mi:“MI:0914”(association)	0.350
	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CDKN2A	NHERF1	psi-mi:“MI:0914”(association)	0.350
VCP	FAM171A2	psi-mi:“MI:0914”(association)	0.350
DDX28	UBA6	psi-mi:“MI:0914”(association)	0.350
MRPL49	UBA6	psi-mi:“MI:0914”(association)	0.350
PEX7	UBA6	psi-mi:“MI:0914”(association)	0.350
FN1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (115): CPNE1 (Affinity Capture-MS), CPNE1 (Co-fractionation), CPNE1 (Co-fractionation), CPNE1 (Affinity Capture-MS), CPNE1 (Reconstituted Complex), CPNE1 (Affinity Capture-MS), CPNE1 (Affinity Capture-RNA), CPNE1 (Affinity Capture-MS), COPS5 (Two-hybrid), CPNE1 (Two-hybrid), COPS5 (Reconstituted Complex), CPNE1 (Affinity Capture-Western), COPS5 (Co-localization), COPS5 (Affinity Capture-Western), Ppp5c (Two-hybrid)

ESM2 similar proteins: A0JNU3, A1A4L8, A2APY7, A2AV36, A5GFY8, A5GFZ6, A6H791, A7MBC0, A7YW45, B2GV71, B5DPF1, D4A1R8, O14744, O88202, O95396, O95571, P19623, P31754, P43353, Q28HC6, Q3KRD0, Q3T094, Q4QR99, Q4R5M3, Q5BJY6, Q5R698, Q5ZKI2, Q64674, Q66JK4, Q6AY46, Q6NS21, Q6NUA1, Q7SYK1, Q80XC2, Q86U10, Q8C166, Q8CIG8, Q8GWT4, Q8JZV7, Q96FX7

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

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	203
Likely benign	15
Benign	6

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
433195	NM_006047.6(RBM12):c.2377G>T (p.Gly793Ter)	Pathogenic
433196	NM_006047.6(RBM12):c.2532del (p.Gly845fs)	Pathogenic

SpliceAI

2612 predictions. Top by Δscore:

Variant	Effect	Δscore
20:35626561:A:AC	donor_gain	1.0000
20:35626562:C:CC	donor_gain	1.0000
20:35626562:CTCA:C	donor_gain	1.0000
20:35626565:A:AC	donor_gain	1.0000
20:35626566:C:CC	donor_gain	1.0000
20:35627409:GATGC:G	acceptor_gain	1.0000
20:35627411:TGC:T	acceptor_gain	1.0000
20:35627412:GC:G	acceptor_gain	1.0000
20:35627413:CC:C	acceptor_gain	1.0000
20:35627414:C:A	acceptor_loss	1.0000
20:35627414:C:CC	acceptor_gain	1.0000
20:35627415:T:A	acceptor_loss	1.0000
20:35627417:C:CT	acceptor_gain	1.0000
20:35627418:A:T	acceptor_gain	1.0000
20:35630899:A:AC	donor_gain	1.0000
20:35630900:C:CA	donor_gain	1.0000
20:35630900:CG:C	donor_gain	1.0000
20:35630900:CGA:C	donor_gain	1.0000
20:35630900:CGAG:C	donor_gain	1.0000
20:35630900:CGAGT:C	donor_gain	1.0000
20:35631035:C:CA	acceptor_loss	1.0000
20:35631036:T:A	acceptor_loss	1.0000
20:35631112:A:AC	donor_gain	1.0000
20:35631113:C:CC	donor_gain	1.0000
20:35631113:CA:C	donor_gain	1.0000
20:35631170:CTAC:C	acceptor_gain	1.0000
20:35631263:CTCA:C	donor_loss	1.0000
20:35631264:TCA:T	donor_loss	1.0000
20:35631265:CACCC:C	donor_loss	1.0000
20:35631266:ACCCG:A	donor_loss	1.0000

AlphaMissense

3498 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:35626591:A:C	F483L	0.998
20:35626591:A:T	F483L	0.998
20:35626593:A:G	F483L	0.998
20:35630768:A:C	F341L	0.997
20:35630768:A:T	F341L	0.997
20:35630770:A:G	F341L	0.997
20:35630476:A:C	F355L	0.996
20:35630476:A:T	F355L	0.996
20:35630478:A:G	F355L	0.996
20:35631293:C:T	G259E	0.996
20:35632652:G:C	F58L	0.996
20:35632652:G:T	F58L	0.996
20:35632654:A:G	F58L	0.996
20:35630950:A:G	Y316H	0.994
20:35631750:A:G	W189R	0.994
20:35631750:A:T	W189R	0.994
20:35631023:G:C	D291E	0.993
20:35631023:G:T	D291E	0.993
20:35631572:A:G	C212R	0.992
20:35631748:C:A	W189C	0.992
20:35631748:C:G	W189C	0.992
20:35632233:A:T	V129D	0.992
20:35632622:A:C	F68L	0.992
20:35632622:A:T	F68L	0.992
20:35632624:A:G	F68L	0.992
20:35631532:C:T	G225D	0.991
20:35631999:A:C	F161L	0.991
20:35631999:A:T	F161L	0.991
20:35632001:A:G	F161L	0.991
20:35626675:A:C	F455L	0.990

dbSNP variants (sampled 300 via entrez): RS1000003448 (20:35661115 A>C,G), RS1000250538 (20:35646283 C>A,G,T), RS1000337280 (20:35641368 A>C,T), RS1000535882 (20:35641586 T>C), RS1000539674 (20:35660860 T>C), RS1000562170 (20:35637861 T>G), RS1000593006 (20:35637546 C>T), RS1000685977 (20:35629027 C>A), RS1000805847 (20:35665805 G>A), RS1000830963 (20:35643727 G>A), RS1000897702 (20:35657499 A>C), RS1000929258 (20:35650133 C>T), RS1000950982 (20:35664238 G>A,C), RS1001142723 (20:35659486 A>T), RS1001153578 (20:35635738 G>T)

Disease associations

OMIM: gene MIM:604205 | disease phenotypes: MIM:617629

GenCC curated gene-disease

Mondo (1): schizophrenia 19 (MONDO:0033312)

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST005956_31	Waist-to-hip ratio adjusted for BMI	8.000000e-08
GCST005958_16	Waist-to-hip ratio adjusted for BMI (age >50)	6.000000e-06
GCST005962_40	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	3.000000e-08
GCST006585_1183	Blood protein levels	5.000000e-157
GCST010002_66	Refractive error	2.000000e-20
GCST012227_1139	Hip circumference adjusted for BMI	4.000000e-08
GCST012227_1144	Hip circumference adjusted for BMI	5.000000e-29

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases expression	3
aristolochic acid I	increases expression	1
beauvericin	decreases expression	1
triphenyl phosphate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, decreases expression, increases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
ochratoxin A	increases expression	1
cupric chloride	decreases expression	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
2-amino-14,16-dimethyloctadecan-3-ol	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression	1
hexabrominated diphenyl ether 153	increases expression	1
LDN 193189	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Aspirin	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects expression	1
Clozapine	decreases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Furaldehyde	affects cotreatment, affects localization, decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2V4	Abcam HEK293T CPNE1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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