CDC42EP3

gene
On this page

Also known as CEP3UB1BORG2

Summary

CDC42EP3 (CDC42 effector protein 3, HGNC:16943) is a protein-coding gene on chromosome 2p22.2, encoding Cdc42 effector protein 3 (Q9UKI2). Probably involved in the organization of the actin cytoskeleton.

This gene encodes a member of a small family of guanosine triphosphate (GTP) metabolizing proteins that contain a CRIB (Cdc42, Rac interactive binding) domain. Members of this family of proteins act as effectors of CDC42 function. The encoded protein is involved in actin cytoskeleton re-organization during cell shape changes, including pseudopodia formation. A pseudogene of this gene is found on chromosome 19. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10602 — RefSeq curated summary.

At a glance

  • GWAS associations: 21
  • Clinical variants (ClinVar): 49 total
  • MANE Select transcript: NM_006449

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16943
Approved symbolCDC42EP3
NameCDC42 effector protein 3
Location2p22.2
Locus typegene with protein product
StatusApproved
AliasesCEP3, UB1, BORG2
Ensembl geneENSG00000163171
Ensembl biotypeprotein_coding
OMIM606133
Entrez10602

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 24 protein_coding, 1 retained_intron

ENST00000295324, ENST00000422687, ENST00000453555, ENST00000457889, ENST00000494083, ENST00000611976, ENST00000885380, ENST00000885381, ENST00000885382, ENST00000885383, ENST00000885384, ENST00000927367, ENST00000927368, ENST00000927369, ENST00000927370, ENST00000927371, ENST00000956783, ENST00000956784, ENST00000956785, ENST00000956786, ENST00000956787, ENST00000956788, ENST00000956789, ENST00000956790, ENST00000956791

RefSeq mRNA: 6 — MANE Select: NM_006449 NM_001270436, NM_001270437, NM_001270438, NM_001371569, NM_001371570, NM_006449

CCDS: CCDS1791

Canonical transcript exons

ENST00000295324 — 2 exons

ExonStartEnd
ENSE000010722813764194437646822
ENSE000013697353767142637671642

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 115.5665 / max 2412.6846, expressed in 1752 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
27822100.16971739
278238.31941532
278101.7992769
278271.4721860
278251.3741744
278161.0561575
278240.5133296
278260.3436181
278130.173661
278140.161853

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097997.86gold quality
monocyteCL:000057697.69gold quality
seminal vesicleUBERON:000099897.62gold quality
mononuclear cellCL:000084297.50gold quality
left ventricle myocardiumUBERON:000656697.49gold quality
renal glomerulusUBERON:000007497.39gold quality
leukocyteCL:000073897.37gold quality
metanephric glomerulusUBERON:000473697.08gold quality
saphenous veinUBERON:000731897.06gold quality
heart right ventricleUBERON:000208096.57gold quality
cauda epididymisUBERON:000436096.50gold quality
myometriumUBERON:000129696.26gold quality
myocardiumUBERON:000234996.15gold quality
bloodUBERON:000017895.92gold quality
smooth muscle tissueUBERON:000113595.86gold quality
cardiac muscle of right atriumUBERON:000337995.23gold quality
deciduaUBERON:000245095.11gold quality
adult organismUBERON:000702395.07gold quality
cartilage tissueUBERON:000241894.95gold quality
mucosa of paranasal sinusUBERON:000503094.82gold quality
urethraUBERON:000005794.71gold quality
body of uterusUBERON:000985394.62gold quality
pericardiumUBERON:000240794.61gold quality
ganglionic eminenceUBERON:000402394.61gold quality
granulocyteCL:000009494.22gold quality
tibialis anteriorUBERON:000138594.20gold quality
buccal mucosa cellCL:000233694.11gold quality
vena cavaUBERON:000408794.06gold quality
choroid plexus epitheliumUBERON:000391193.94gold quality
blood vessel layerUBERON:000479793.89gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-MTAB-8142yes1454.67
E-MTAB-10287yes42.22
E-MTAB-9221yes23.25
E-CURD-112yes8.60
E-GEOD-135922yes6.79
E-CURD-46yes5.10
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

129 targeting CDC42EP3, 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-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4692100.0067.322066
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-451499.9967.101870
HSA-MIR-548AW99.9972.573559
HSA-MIR-607799.9968.042299
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-548N99.9871.944170
HSA-MIR-50799.9770.111915
HSA-MIR-314899.9775.066478
HSA-MIR-55799.9670.011640
HSA-MIR-493-5P99.9672.472382
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-545-3P99.9570.742783

Literature-anchored findings (GeneRIF, showing 7)

  • The expression of CDC42EP3 mRNA was significantly increased by 19.7% in dorsal prefrontal cortex in patient with schizophrenia. (PMID:20385374)
  • Results provide evidence that Cdc42EP3 function in cancer-associated fibroblasts relies on tight regulation by Cdc42. (PMID:27248291)
  • Studies indicate some of the functional and mechanistic roles of the binder of Rho GTPases Borg1-5 proteins (Cdc42EP1-5), including cytoskeletal remodelling and signalling. (PMID:27913681)
  • Overactivated Cdc42 acts through Cdc42EP3/Borg2 and NCK to trigger DNA damage response signaling and sensitize cells to DNA-damaging agents. (PMID:32739212)
  • CDC42EP3 is a key promoter involved in the development and progression of gastric cancer. (PMID:34111280)
  • Deduction of CDC42EP3 suppress development and progression of osteosarcoma. (PMID:34998812)
  • CDC42EP3 promotes glioma progression via regulation of CCND1. (PMID:35365622)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocdc42ep3ENSDARG00000052783
mus_musculusCdc42ep3ENSMUSG00000036533
rattus_norvegicusCdc42ep3ENSRNOG00000032136

Paralogs (5): CDC42EP1 (ENSG00000128283), CDC42EP2 (ENSG00000149798), CDC42EP5 (ENSG00000167617), CDC42EP4 (ENSG00000179604), C15orf62 (ENSG00000188277)

Protein

Protein identifiers

Cdc42 effector protein 3Q9UKI2 (reviewed: Q9UKI2)

Alternative names: Binder of Rho GTPases 2, MSE55-related Cdc42-binding protein

All UniProt accessions (4): Q9UKI2, C9J7F7, C9JEZ4, C9JKW5

UniProt curated annotations — full annotation on UniProt →

Function. Probably involved in the organization of the actin cytoskeleton. May act downstream of CDC42 to induce actin filament assembly leading to cell shape changes. Induces pseudopodia formation in fibroblasts.

Subunit / interactions. Interacts with RHOQ and CDC42, in a GTP-dependent manner, and with SEPT7.

Subcellular location. Endomembrane system. Cytoplasm. Cytoskeleton.

Tissue specificity. Highly expressed in the heart and weakly in the brain.

Similarity. Belongs to the BORG/CEP family.

RefSeq proteins (6): NP_001257365, NP_001257366, NP_001257367, NP_001358498, NP_001358499, NP_006440* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000095CRIB_domDomain
IPR029273Cdc42_effect-likeDomain
IPR051296Cdc42_Effector_BORG/CEPFamily

Pfam: PF00786, PF14957

UniProt features (10 total): modified residue 4, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UKI2-F158.430.00

Functional residue map

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

Post-translational modifications (4): 63, 89, 108, 144

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-5687128MAPK6/MAPK4 signaling
R-HSA-9013148CDC42 GTPase cycle
R-HSA-9013406RHOQ GTPase cycle
R-HSA-162582Signal Transduction
R-HSA-194315Signaling by Rho GTPases
R-HSA-5683057MAPK family signaling cascades
R-HSA-9012999RHO GTPase cycle
R-HSA-9716542Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 435 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, HNF3ALPHA_Q6, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GCANCTGNY_MYOD_Q6, CHUNG_BLISTER_CYTOTOXICITY_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, TGACCTY_ERR1_Q2, GOMF_GTPASE_BINDING, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, NAGASHIMA_NRG1_SIGNALING_UP, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS

GO Biological Process (5): signal transduction (GO:0007165), Rho protein signal transduction (GO:0007266), regulation of cell shape (GO:0008360), positive regulation of actin filament polymerization (GO:0030838), positive regulation of pseudopodium assembly (GO:0031274)

GO Molecular Function (3): cytoskeletal regulatory protein binding (GO:0005519), small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (7): cytoplasm (GO:0005737), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), endomembrane system (GO:0012505), actin cytoskeleton (GO:0015629), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
RHO GTPase cycle2
Signal Transduction2
MAPK family signaling cascades1
Signaling by Rho GTPases, Miro GTPases and RHOBTB31
Signaling by Rho GTPases1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
small GTPase-mediated signal transduction1
regulation of cell morphogenesis1
regulation of biological quality1
actin filament polymerization1
regulation of actin filament polymerization1
positive regulation of protein polymerization1
positive regulation of cytoskeleton organization1
positive regulation of supramolecular fiber organization1
pseudopodium assembly1
regulation of pseudopodium assembly1
positive regulation of plasma membrane bounded cell projection assembly1
cytoskeletal protein binding1
GTPase binding1
binding1
intracellular anatomical structure1
cytoplasm1
intracellular membraneless organelle1
membrane1
cell periphery1
vacuole1
plasma membrane1
cytoskeleton1

Protein interactions and networks

STRING

750 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CDC42EP3SKP1P34991977
CDC42EP3CDC42EP5Q6NZY7955
CDC42EP3RHOQP17081954
CDC42EP3CDC42P21181724
CDC42EP3SEPTIN7Q16181662
CDC42EP3PLIN2Q99541543
CDC42EP3ISG15P05161532
CDC42EP3SEPTIN9Q9UHD8522
CDC42EP3NPLOC4Q8TAT6479
CDC42EP3CEBPZQ03701476
CDC42EP3TMEM51Q9NW97471
CDC42EP3TP53P04637467
CDC42EP3PUM2Q8TB72443
CDC42EP3ZUP1Q96AP4419
CDC42EP3UBBP02248419

IntAct

15 interactions, top by confidence:

ABTypeScore
CDC42EP3LRRK2psi-mi:“MI:0407”(direct interaction)0.620
LRRK2CDC42EP3psi-mi:“MI:0407”(direct interaction)0.620
COPECDC42EP3psi-mi:“MI:0915”(physical association)0.560
CDC42EP3DAPK1psi-mi:“MI:0407”(direct interaction)0.440
CDC42EP3MFHAS1psi-mi:“MI:0407”(direct interaction)0.440
CDC42EP3SRPK1psi-mi:“MI:0217”(phosphorylation reaction)0.440
CDC42EP3LRRK1psi-mi:“MI:0407”(direct interaction)0.440
CDC42EP3MON1Bpsi-mi:“MI:0915”(physical association)0.400
CDC42EP3CDC42EP3psi-mi:“MI:0915”(physical association)0.370
COPECDC42EP3psi-mi:“MI:0915”(physical association)0.000
ftsSCDC42EP3psi-mi:“MI:0915”(physical association)0.000
CDC42CDC42EP3psi-mi:“MI:0915”(physical association)0.000
UMPSCDC42EP3psi-mi:“MI:0915”(physical association)0.000

BioGRID (32): CDC42EP3 (Two-hybrid), CDC42EP3 (Affinity Capture-RNA), CDC42EP3 (Reconstituted Complex), CDC42EP3 (Reconstituted Complex), CDC42EP3 (Reconstituted Complex), CDC42EP3 (Reconstituted Complex), CDC42EP3 (Two-hybrid), CDC42EP3 (Two-hybrid), CDC42EP3 (Two-hybrid), SEPT7 (Reconstituted Complex), SEPT6 (Reconstituted Complex), CDC42EP3 (Reconstituted Complex), MON1B (Affinity Capture-MS), RHOQ (Reconstituted Complex), CDC42 (Reconstituted Complex)

ESM2 similar proteins: A0A140LFM6, A0A1B0GUA6, A0JMD2, A4IGV6, A6H5Y1, A6NFA0, A6NKB5, A8E653, B3DHS1, D3ZJ47, D3ZMK9, E9Q309, O14513, O60284, P0CAX8, Q1RMQ5, Q32LN6, Q3URK1, Q3UTJ2, Q3ZBS1, Q49A88, Q5DU28, Q5RDK8, Q5REU9, Q5SW75, Q5VT06, Q60664, Q62417, Q642A3, Q68D20, Q6A065, Q6DFB0, Q6NRK3, Q6NWJ0, Q6ZVD7, Q76I79, Q7TSH4, Q8K2J4, Q8K3V7, Q8VEB3

Diamond homologs: A1A5P0, Q00587, Q08DN6, Q17QW1, Q5PQP4, Q6NZY7, Q8JZX9, Q91W92, Q9CQC5, Q9H3Q1, Q9I7F7, Q9JM96, Q9UKI2, Q9Z0X0, O14613

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

670 predictions. Top by Δscore:

VariantEffectΔscore
2:37645829:A:ACdonor_gain0.9900
2:37645830:T:Cdonor_gain0.9900
2:37661746:A:Cacceptor_gain0.9900
2:37661748:G:Cacceptor_gain0.9900
2:37672088:G:Cdonor_gain0.9900
2:37645789:CCTT:Cdonor_gain0.9800
2:37646819:AAACC:Aacceptor_loss0.9800
2:37646820:AACCT:Aacceptor_loss0.9800
2:37646822:CCTG:Cacceptor_loss0.9800
2:37646823:C:Tacceptor_loss0.9800
2:37646824:T:Aacceptor_loss0.9800
2:37661746:A:ACacceptor_gain0.9800
2:37645825:A:ACdonor_gain0.9700
2:37645826:C:CCdonor_gain0.9700
2:37646818:CAAAC:Cacceptor_gain0.9700
2:37672239:C:Adonor_gain0.9700
2:37661750:A:Cacceptor_gain0.9600
2:37645934:A:ACdonor_gain0.9500
2:37646823:C:CCacceptor_gain0.9500
2:37661748:G:GCacceptor_gain0.9500
2:37672280:C:CAdonor_gain0.9500
2:37645941:C:Adonor_gain0.9400
2:37672399:G:Adonor_gain0.9400
2:37645934:AGT:Adonor_gain0.9200
2:37645940:T:Adonor_gain0.9100
2:37645935:G:Cdonor_gain0.9000
2:37645900:A:ATdonor_gain0.8900
2:37671422:TCACC:Tdonor_loss0.8900
2:37671424:A:AAdonor_loss0.8900
2:37671425:C:Gdonor_loss0.8900

AlphaMissense

1676 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:37646461:G:CH43D1.000
2:37646492:A:CS32R1.000
2:37646492:A:TS32R1.000
2:37646494:T:GS32R1.000
2:37646496:A:CI31S1.000
2:37646496:A:TI31N1.000
2:37646414:A:CF58L0.999
2:37646414:A:TF58L0.999
2:37646415:A:GF58S0.999
2:37646416:A:GF58L0.999
2:37646427:C:AG54V0.999
2:37646427:C:TG54E0.999
2:37646428:C:GG54R0.999
2:37646428:C:TG54R0.999
2:37646429:A:CF53L0.999
2:37646429:A:TF53L0.999
2:37646431:A:GF53L0.999
2:37646459:G:CH43Q0.999
2:37646459:G:TH43Q0.999
2:37646460:T:CH43R0.999
2:37646468:G:CH40Q0.999
2:37646468:G:TH40Q0.999
2:37646469:T:CH40R0.999
2:37646470:G:CH40D0.999
2:37646472:C:GR39P0.999
2:37646475:A:GF38S0.999
2:37646496:A:GI31T0.999
2:37646511:A:TL26Q0.999
2:37645848:A:GL247P0.998
2:37645873:C:GG239R0.998

dbSNP variants (sampled 300 via entrez): RS1000034337 (2:37656820 C>G), RS1000057369 (2:37658888 C>A,G,T), RS1000180105 (2:37663706 G>A), RS1000232460 (2:37663858 C>T), RS1000357113 (2:37668804 G>C), RS1000382904 (2:37674476 C>T), RS1000425580 (2:37674751 G>T), RS1000519326 (2:37662699 A>G), RS1000573118 (2:37662937 G>A), RS1000715474 (2:37673017 A>G), RS1000758365 (2:37671373 GACAGAC>G), RS1000768093 (2:37673308 C>T), RS1001109106 (2:37660543 C>A,T), RS1001152568 (2:37648610 G>A,C), RS1001254147 (2:37674696 A>C)

Disease associations

OMIM: gene MIM:606133 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

StudyTraitp-value
GCST000817_70Height2.000000e-18
GCST000892_1Total ventricular volume (Alzheimer’s disease interaction)2.000000e-06
GCST001956_44Height2.000000e-08
GCST003542_12Night sleep phenotypes1.000000e-06
GCST007822_1Facial attractiveness (male raters)2.000000e-08
GCST007843_3Rheumatoid arthritis1.000000e-09
GCST008163_388Height2.000000e-06
GCST008839_226Height5.000000e-08
GCST008839_513Height2.000000e-28
GCST008839_521Height1.000000e-09
GCST010697_38Cortical surface area (min-P)3.000000e-41
GCST010698_1Subcortical volume (min-P)4.000000e-08
GCST010699_86Brain morphology (min-P)6.000000e-14
GCST010700_70Cortical thickness (MOSTest)8.000000e-09
GCST010701_81Cortical surface area (MOSTest)5.000000e-09
GCST010702_53Subcortical volume (MOSTest)2.000000e-12
GCST010703_207Brain morphology (MOSTest)2.000000e-11
GCST011011_7Youthful appearance (self-reported)7.000000e-16
GCST011616_43Cortical volume3.000000e-10
GCST011743_31HDL cholesterol levels in HIV infection3.000000e-06
GCST90020029_799Waist circumference adjusted for body mass index2.000000e-08

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0009892facial attractiveness measurement
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Tretinoinaffects cotreatment, decreases expression, increases expression4
methylmercuric chlorideincreases expression3
trichostatin Aaffects cotreatment, decreases expression3
sodium arsenitedecreases expression, affects cotreatment, increases abundance2
Panobinostataffects cotreatment, decreases expression2
Progesteroneincreases expression2
Valproic Acidaffects expression, increases expression2
Aflatoxin B1affects expression, increases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
TL8-506affects cotreatment, increases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, decreases methylation1
methylselenic acidincreases expression1
arseniteaffects binding, increases reaction1
cobaltous chloridedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
potassium chromate(VI)affects cotreatment, decreases expression1
coumarinincreases phosphorylation1
S-(1,2-dichlorovinyl)cysteinedecreases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
cylindrospermopsinincreases expression1
corosolic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
dorsomorphinincreases expression, affects cotreatment, decreases expression1
PCI 5002affects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenic Trioxideaffects cotreatment, decreases expression1
Fulvestrantdecreases methylation, affects cotreatment1

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.