CPNE3

Summary

CPNE3 (copine 3, HGNC:2316) is a protein-coding gene on chromosome 8q21.3, encoding Copine-3 (O75131). Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation.

Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a protein which contains two type II C2 domains in the amino-terminus and an A domain-like sequence in the carboxy-terminus. The A domain mediates interactions between integrins and extracellular ligands.

Source: NCBI Gene 8895 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 100 total
• MANE Select transcript: NM_003909

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2316
Approved symbol	CPNE3
Name	copine 3
Location	8q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000085719
Ensembl biotype	protein_coding
OMIM	604207
Entrez	8895

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 25 protein_coding, 5 retained_intron

ENST00000517354, ENST00000517391, ENST00000517490, ENST00000517862, ENST00000522240, ENST00000523469, ENST00000523588, ENST00000614678, ENST00000620393, ENST00000621245, ENST00000621526, ENST00000621783, ENST00000622183, ENST00000877723, ENST00000877724, ENST00000877725, ENST00000877726, ENST00000877727, ENST00000877728, ENST00000877729, ENST00000877730, ENST00000937950, ENST00000937951, ENST00000970508, ENST00000970509, ENST00000970510, ENST00000970511, ENST00000970512, ENST00000970513, ENST00000970514

RefSeq mRNA: 1 — MANE Select: NM_003909 NM_003909

CCDS: CCDS6243

Canonical transcript exons

ENST00000517490 — 17 exons

Exon	Start	End
ENSE00000406138	86537563	86537646
ENSE00000698726	86546595	86546681
ENSE00000698734	86544740	86544838
ENSE00000698735	86540245	86540334
ENSE00001260653	86531155	86531229
ENSE00001260662	86528945	86529124
ENSE00001323802	86558288	86561498
ENSE00002099300	86515462	86515499
ENSE00002121133	86528536	86528677
ENSE00003476420	86556102	86556338
ENSE00003485227	86551046	86551100
ENSE00003524808	86554851	86554984
ENSE00003553397	86548301	86548434
ENSE00003611633	86551183	86551234
ENSE00003659308	86547711	86547770
ENSE00003730011	86514435	86514541
ENSE00003790313	86532509	86532580

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 99.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 41.5774 / max 823.4013, expressed in 1798 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89644	40.7761	1798
89647	0.5573	341
89645	0.2439	145

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tongue squamous epithelium	UBERON:0006919	99.20	gold quality
esophagus squamous epithelium	UBERON:0006920	98.52	gold quality
trabecular bone tissue	UBERON:0002483	98.48	gold quality
oral cavity	UBERON:0000167	98.39	gold quality
epithelium of esophagus	UBERON:0001976	98.25	gold quality
type B pancreatic cell	CL:0000169	97.75	gold quality
bone marrow cell	CL:0002092	97.35	gold quality
calcaneal tendon	UBERON:0003701	97.35	gold quality
bone marrow	UBERON:0002371	97.32	gold quality
islet of Langerhans	UBERON:0000006	97.30	gold quality
left ventricle myocardium	UBERON:0006566	97.21	gold quality
gingiva	UBERON:0001828	97.13	gold quality
pharyngeal mucosa	UBERON:0000355	97.03	gold quality
gingival epithelium	UBERON:0001949	96.87	gold quality
upper leg skin	UBERON:0004262	96.85	gold quality
buccal mucosa cell	CL:0002336	96.84	gold quality
caput epididymis	UBERON:0004358	96.80	gold quality
germinal epithelium of ovary	UBERON:0001304	96.71	gold quality
parietal pleura	UBERON:0002400	96.71	gold quality
mammary duct	UBERON:0001765	96.65	gold quality
seminal vesicle	UBERON:0000998	96.54	gold quality
bronchial epithelial cell	CL:0002328	96.51	gold quality
mammalian vulva	UBERON:0000997	96.51	gold quality
trigeminal ganglion	UBERON:0001675	96.41	gold quality
corpus epididymis	UBERON:0004359	96.38	gold quality
epithelium of mammary gland	UBERON:0003244	96.37	gold quality
myocardium	UBERON:0002349	96.34	gold quality
choroid plexus epithelium	UBERON:0003911	96.19	gold quality
ganglionic eminence	UBERON:0004023	96.16	gold quality
cauda epididymis	UBERON:0004360	96.10	gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 9.

Experiment	Marker?	Max mean expression
E-GEOD-89232	yes	1978.91
E-HCAD-1	yes	25.19
E-HCAD-13	yes	24.01
E-MTAB-6701	yes	18.70
E-CURD-88	yes	8.89
E-MTAB-6678	yes	8.70
E-MTAB-10042	yes	8.69
E-MTAB-9801	yes	8.12
E-MTAB-6058	no	424.56
E-MTAB-7037	no	161.66
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

184 targeting CPNE3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488

Literature-anchored findings (GeneRIF, showing 13)

• Susceptibility genes CPNE3, IL16 and CDH13 with moderate effects associated with susceptibility to prostate cancer. (PMID:18264096)
• Data suggest that Copine-III is a novel player in the regulation of ErbB2-dependent cancer cell motility. (PMID:20010870)
• This study demonistrated that dysregulation of cpne3 3’UTR in brain of patient with schizophrenia. (PMID:23062752)
• our results indicate that CPNE3 could play a critical role in NSCLC metastasis. (PMID:23713811)
• Copine3 binding to ErbB2 increases when Jab1 is overexpressed in SKBr3 breast cancer cells. Copine3 and Jab1 binding regulates the ErbB2 signaling pathway. (PMID:26719032)
• CPNE3(high) is an adverse prognostic biomarker for acute myeloid leukemia. (PMID:28670859)
• Patients who have low CPNE3 expression in peripheral blood are more likely to suffer from AMI than those with stable CAD. Low expression of CPNE3 gene serves as an potential independent risk factor of AMI. (PMID:29297177)
• upregulation of EMP1 significantly increases cancer cell migration that leads to tumor metastasis (PMID:29867202)
• Exosomal CPNE3 levels are associated with the tumor extent and may serve as a diagnostic biomarker in colorectal cancer patients. (PMID:30078189)
• Upregulation of CPNE3 suppresses invasion, migration and proliferation of glioblastoma cells through FAK pathway inactivation. (PMID:33725213)
• CPNE3 moderates the association between anxiety and working memory. (PMID:33767297)
• [High expression of CPNE3 correlates with poor long-term prognosis of gastric cancer by inhibiting cell apoptosis via activating PI3K/AKT signaling]. (PMID:38293984)
• YAP1-CPNE3 positive feedback pathway promotes gastric cancer cell progression. (PMID:38493426)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cpne3	ENSDARG00000104177
mus_musculus	Cpne3	ENSMUSG00000028228
rattus_norvegicus	Cpne3	ENSRNOG00000006298

Paralogs (8): CPNE6 (ENSG00000100884), CPNE5 (ENSG00000124772), CPNE8 (ENSG00000139117), CPNE2 (ENSG00000140848), CPNE9 (ENSG00000144550), CPNE7 (ENSG00000178773), CPNE4 (ENSG00000196353), CPNE1 (ENSG00000214078)

Protein

Protein identifiers

Copine-3 — O75131 (reviewed: O75131)

Alternative names: Copine III

All UniProt accessions (8): O75131, A0A087WUS8, A0A087WXR6, A0A087WYQ3, A0A0G2JMP5, E5RFT7, E5RHZ0, H0YB26

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation.

Subunit / interactions. Monomer. Interacts with ERBB2 (preferentially with the tyrosine phosphorylated form); this interaction occurs at the cell membrane and is increased in a growth factor heregulin-dependent manner. Interacts with SHC1; this interaction may mediate the binding of CPNE3 with ERBB2. Interacts with RACK1.

Subcellular location. Nucleus. Cytoplasm. Cell membrane. Cell junction. Focal adhesion.

Tissue specificity. Expressed in breast and weakly in prostate and ovarian tissues. Expressed in neutrophils (at protein level). Widely expressed. Expressed in the brain. Expressed in neutrophil precursors from the bone marrow and peripheral blood. Expressed in primary breast tumors and ovarian endometrioid adenocarcinoma.

Post-translational modifications. Phosphorylated on serine and threonine residues.

Similarity. Belongs to the copine family.

RefSeq proteins (1): NP_003900* (*=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 (28 total): binding site 16, domain 3, modified residue 3, sequence conflict 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75131-F1	92.38	0.81

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): 83; 93; 154; 154; 160; 216; 216; 218; 218; 224; 22; 22 …

Post-translational modifications (3): 14, 197, 243

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

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

MSigDB gene sets: 247 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, SHEPARD_BMYB_MORPHOLINO_UP, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, MATTIOLI_MGUS_VS_PCL, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, GOBP_ERBB2_SIGNALING_PATHWAY, GOBP_RESPONSE_TO_METAL_ION, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS

GO Biological Process (5): positive regulation of cell migration (GO:0030335), ERBB2 signaling pathway (GO:0038128), glycerophospholipid biosynthetic process (GO:0046474), cellular response to calcium ion (GO:0071277), cellular response to growth factor stimulus (GO:0071363)

GO Molecular Function (8): RNA binding (GO:0003723), protein serine/threonine kinase activity (GO:0004674), phospholipid binding (GO:0005543), calcium-dependent phospholipid binding (GO:0005544), receptor tyrosine kinase binding (GO:0030971), metal ion binding (GO:0046872), calcium-dependent protein binding (GO:0048306), protein binding (GO:0005515)

GO Cellular Component (13): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829), plasma membrane (GO:0005886), focal adhesion (GO:0005925), cell junction (GO:0030054), azurophil granule membrane (GO:0035577), extracellular exosome (GO:0070062), membrane (GO:0016020), anchoring junction (GO:0070161)

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	5
intracellular membrane-bounded organelle	2
nuclear lumen	2
cytoplasm	2
cell migration	1
regulation of cell migration	1
positive regulation of cell motility	1
ERBB signaling pathway	1
glycerophospholipid metabolic process	1
phospholipid biosynthetic process	1
glycerolipid biosynthetic process	1
response to calcium ion	1
cellular response to metal ion	1
response to growth factor	1
cellular response to endogenous stimulus	1
nucleic acid binding	1
protein kinase activity	1
lipid binding	1
phospholipid binding	1
signaling receptor binding	1
protein tyrosine kinase binding	1
cation binding	1
calcium ion binding	1
protein binding	1
binding	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
cell-substrate junction	1
lysosomal membrane	1
secretory granule membrane	1
azurophil granule	1
extracellular vesicle	1
cell junction	1

Protein interactions and networks

STRING

680 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPNE3	LMTK2	Q8IWU2	515
CPNE3	SLC7A13	Q8TCU3	514
CPNE3	MSMB	P08118	503
CPNE3	IL16	Q14005	496
CPNE3	JAZF1	Q86VZ6	488
CPNE3	EHBP1	Q8NDI1	486
CPNE3	AZGP1	P25311	450
CPNE3	CTBP2	P56545	450
CPNE3	SRD5A2	P31213	447
CPNE3	GNMT	Q14749	435
CPNE3	PCSK7	Q16549	429
CPNE3	ELAC2	Q9BQ52	429
CPNE3	SARDH	Q9UL12	429
CPNE3	AMACR	Q9UHK6	428
CPNE3	ZFHX3	Q15911	427

IntAct

63 interactions, top by confidence:

A	B	Type	Score
IGF1R	PIK3R2	psi-mi:“MI:2364”(proximity)	0.590
TINF2	CPNE3	psi-mi:“MI:0915”(physical association)	0.510
FEN1	CPNE3	psi-mi:“MI:0915”(physical association)	0.400
EXOC8	CPNE3	psi-mi:“MI:0915”(physical association)	0.400
HPGDS	CPNE3	psi-mi:“MI:0915”(physical association)	0.400
CCDC146	CPNE3	psi-mi:“MI:0915”(physical association)	0.400
PHF2	CPNE3	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
TERF1	CPNE3	psi-mi:“MI:0915”(physical association)	0.370
TERF2IP	CPNE3	psi-mi:“MI:0915”(physical association)	0.370
CPNE3	POT1	psi-mi:“MI:0915”(physical association)	0.370
MEP1B	CPNE3	psi-mi:“MI:0915”(physical association)	0.370
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
USP42	KPNA3	psi-mi:“MI:0914”(association)	0.350
KDM3B	CPNE3	psi-mi:“MI:0914”(association)	0.350
rep	CPNE3	psi-mi:“MI:0914”(association)	0.350
HTRA4	PSMD12	psi-mi:“MI:0914”(association)	0.350
CSAG1	NAP1L4	psi-mi:“MI:0914”(association)	0.350
CSAG2	CAMK2D	psi-mi:“MI:0914”(association)	0.350
PGR	DDX3X	psi-mi:“MI:0914”(association)	0.350
PGR	CPNE3	psi-mi:“MI:0914”(association)	0.350
	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
CSNK2A1	RPS3A	psi-mi:“MI:0914”(association)	0.350
CSNK2A2	VWA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (145): CPNE3 (Affinity Capture-MS), CPNE3 (Co-fractionation), CPNE3 (Co-fractionation), CPNE3 (Co-fractionation), HNRNPH1 (Co-fractionation), HSPA9 (Co-fractionation), CPNE3 (Affinity Capture-MS), CPNE3 (Proximity Label-MS), CPNE3 (Affinity Capture-MS), CPNE3 (Affinity Capture-MS), CPNE3 (Reconstituted Complex), CPNE3 (Affinity Capture-MS), CPNE3 (Affinity Capture-MS), CPNE3 (Affinity Capture-MS), TRAP1 (Affinity Capture-MS)

ESM2 similar proteins: A1A4Q2, A6NEY8, B2RZ27, E9QI36, O06465, O75131, O76003, O81187, P0A155, P0A156, P12081, P19480, P35340, P55143, Q28EX9, Q28ID3, Q2KI84, Q2KJD7, Q3ZCL8, Q4I963, Q58DA7, Q5FWT7, Q5R4C4, Q5R4R2, Q5RAE1, Q5RC61, Q5XJ54, Q5ZJJ8, Q61035, Q641F1, Q6DBT3, Q6DI37, Q7KLV9, Q80T18, Q80Y14, Q86SX6, Q8BGR9, Q8CI33, Q8K3X2, Q8WVY7

Diamond homologs: A0JJX5, A1CQG2, A1ZBD6, A2QQ28, A3KGK3, A4IFJ5, A6QQP7, A8KBH6, B1WAZ6, B8N7E5, G0S9J5, O14065, O14795, O43581, O75131, O75923, O94812, P04409, P05126, P05128, P05129, P05696, P05771, P05772, P0C869, P0C871, P10102, P10829, P13677, P17252, P20444, P21521, P27715, P29101, P41823, P41885, P46097, P46935, P49147, P63318

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 78 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
Removal of the Flap Intermediate from the C-strand	5	52.9×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	65
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2681 predictions. Top by Δscore:

Variant	Effect	Δscore
8:86528522:ATT:A	acceptor_gain	1.0000
8:86528524:T:A	acceptor_gain	1.0000
8:86528618:TCA:T	donor_gain	1.0000
8:86528932:C:CA	acceptor_gain	1.0000
8:86529125:G:GG	donor_gain	1.0000
8:86531145:A:G	acceptor_gain	1.0000
8:86531152:CA:C	acceptor_loss	1.0000
8:86531153:A:AG	acceptor_gain	1.0000
8:86531154:G:GG	acceptor_gain	1.0000
8:86531154:GATT:G	acceptor_gain	1.0000
8:86531219:G:GT	donor_gain	1.0000
8:86531225:TTACG:T	donor_loss	1.0000
8:86531226:TACGG:T	donor_loss	1.0000
8:86531227:ACG:A	donor_loss	1.0000
8:86531228:CGGTA:C	donor_loss	1.0000
8:86531229:GGT:G	donor_loss	1.0000
8:86531230:G:GG	donor_gain	1.0000
8:86531230:GT:G	donor_loss	1.0000
8:86531231:T:A	donor_loss	1.0000
8:86531236:A:AG	donor_gain	1.0000
8:86531241:A:G	donor_gain	1.0000
8:86532492:ACCT:A	acceptor_gain	1.0000
8:86532495:T:A	acceptor_gain	1.0000
8:86536700:A:AG	acceptor_gain	1.0000
8:86536701:A:G	acceptor_gain	1.0000
8:86537558:TGTAG:T	acceptor_loss	1.0000
8:86537559:GTAGG:G	acceptor_loss	1.0000
8:86537560:TAGGA:T	acceptor_loss	1.0000
8:86537561:AG:A	acceptor_gain	1.0000
8:86537562:G:GC	acceptor_loss	1.0000

AlphaMissense

3568 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:86540272:T:A	W191R	1.000
8:86540272:T:C	W191R	1.000
8:86551071:T:C	F347L	1.000
8:86551073:T:A	F347L	1.000
8:86551073:T:G	F347L	1.000
8:86556312:T:C	F489L	1.000
8:86556314:T:A	F489L	1.000
8:86556314:T:G	F489L	1.000
8:86537585:C:A	P161Q	0.999
8:86537591:T:C	L163P	0.999
8:86537639:G:C	R179P	0.999
8:86540273:G:C	W191S	0.999
8:86540274:G:C	W191C	0.999
8:86540274:G:T	W191C	0.999
8:86544786:G:A	G227E	0.999
8:86548305:G:A	G295E	0.999
8:86548310:G:C	D297H	0.999
8:86548311:A:C	D297A	0.999
8:86548311:A:G	D297G	0.999
8:86548311:A:T	D297V	0.999
8:86548312:C:A	D297E	0.999
8:86548312:C:G	D297E	0.999
8:86548317:C:T	T299I	0.999
8:86548327:T:A	N302K	0.999
8:86548327:T:G	N302K	0.999
8:86548385:T:C	Y322H	0.999
8:86551069:G:A	G346D	0.999
8:86551075:G:A	G348D	0.999
8:86556115:T:C	L423P	0.999
8:86556130:A:T	D428V	0.999

dbSNP variants (sampled 300 via entrez): RS1000034074 (8:86545655 T>C), RS1000045927 (8:86524396 G>A), RS1000146128 (8:86530725 C>A,T), RS1000156025 (8:86549338 C>G,T), RS1000286794 (8:86512443 T>C), RS1000290523 (8:86548683 A>G), RS1000395731 (8:86524700 T>C), RS1000499123 (8:86542149 C>G), RS1000502621 (8:86529245 A>T), RS1000608791 (8:86536178 A>C), RS1000648799 (8:86553964 T>C), RS1000662256 (8:86549109 A>G), RS1000771386 (8:86542296 A>G), RS1000804038 (8:86560038 C>A), RS1000807461 (8:86517419 C>T)

Disease associations

OMIM: gene MIM:604207 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005316_88	Intelligence (MTAG)	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	affects binding, increases reaction, decreases expression, affects cotreatment, increases abundance (+1 more)	3
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
Valproic Acid	decreases methylation, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	increases expression	1
geldanamycin	increases expression	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation, affects cotreatment	1
sodium arsenate	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
nickel sulfate	decreases expression	1
deguelin	decreases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
thifluzamide	decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Vorinostat	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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