CDC42EP4

gene
On this page

Also known as CEP4KAIA1777BORG4MGC3740MGC17125

Summary

CDC42EP4 (CDC42 effector protein 4, HGNC:17147) is a protein-coding gene on chromosome 17q25.1, encoding Cdc42 effector protein 4 (Q9H3Q1). Probably involved in the organization of the actin cytoskeleton.

The product of this gene is a member of the CDC42-binding protein family. Members of this family interact with Rho family GTPases and regulate the organization of the actin cytoskeleton. This protein has been shown to bind both CDC42 and TC10 GTPases in a GTP-dependent manner. When overexpressed in fibroblasts, this protein was able to induce pseudopodia formation, which suggested a role in inducing actin filament assembly and cell shape control.

Source: NCBI Gene 23580 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 85 total — 1 pathogenic
  • MANE Select transcript: NM_012121

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17147
Approved symbolCDC42EP4
NameCDC42 effector protein 4
Location17q25.1
Locus typegene with protein product
StatusApproved
AliasesCEP4, KAIA1777, BORG4, MGC3740, MGC17125
Ensembl geneENSG00000179604
Ensembl biotypeprotein_coding
OMIM605468
Entrez23580

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000335793, ENST00000439510, ENST00000578516, ENST00000579611, ENST00000580315, ENST00000581014, ENST00000581045, ENST00000582303, ENST00000858293, ENST00000858294, ENST00000858295, ENST00000858296, ENST00000858297, ENST00000858298, ENST00000943416, ENST00000943417

RefSeq mRNA: 1 — MANE Select: NM_012121 NM_012121

CCDS: CCDS11695

Canonical transcript exons

ENST00000335793 — 2 exons

ExonStartEnd
ENSE000014326037328362473286612
ENSE000027108957331189373312001

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 98.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.7125 / max 258.3081, expressed in 1750 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
16790830.12951741
1679061.2645834
1679050.6874373
1679070.5830350
1679040.028211
1679030.02009

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cranial nerve IIUBERON:000094198.82gold quality
paraflocculusUBERON:000535198.62gold quality
olfactory bulbUBERON:000226496.69gold quality
left uterine tubeUBERON:000130396.67gold quality
ventricular zoneUBERON:000305396.38gold quality
middle frontal gyrusUBERON:000270295.57gold quality
olfactory segment of nasal mucosaUBERON:000538695.53gold quality
medial globus pallidusUBERON:000247795.29gold quality
corpus epididymisUBERON:000435995.19gold quality
globus pallidusUBERON:000187595.17gold quality
lateral globus pallidusUBERON:000247695.13gold quality
right hemisphere of cerebellumUBERON:001489095.09gold quality
right ovaryUBERON:000211895.03gold quality
nippleUBERON:000203094.85gold quality
left ovaryUBERON:000211994.84gold quality
caudate nucleusUBERON:000187394.82gold quality
pericardiumUBERON:000240794.72gold quality
putamenUBERON:000187494.64gold quality
peritoneumUBERON:000235894.59gold quality
omental fat padUBERON:001041494.59gold quality
tracheaUBERON:000312694.58gold quality
cerebellar vermisUBERON:000472094.57gold quality
ganglionic eminenceUBERON:000402394.55gold quality
ovaryUBERON:000099294.46gold quality
left adrenal gland cortexUBERON:003582594.39gold quality
adipose tissue of abdominal regionUBERON:000780894.32gold quality
body of pancreasUBERON:000115094.31gold quality
type B pancreatic cellCL:000016994.27silver quality
endocervixUBERON:000045894.27gold quality
left adrenal glandUBERON:000123494.24gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-9435yes369.67
E-GEOD-137537yes34.68
E-MTAB-7316yes31.49
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting CDC42EP4, 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-4692100.0067.322066
HSA-MIR-656-3P100.0072.152788
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-451499.9967.101870
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-391999.8769.452489
HSA-MIR-444799.8567.812900
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-132199.8465.301811
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-473999.8465.251832
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-313399.8170.923506
HSA-MIR-205299.7969.372031
HSA-MIR-129999.7771.242389
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-149-3P99.7268.223963
HSA-MIR-120899.7068.281533
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-3679-3P99.6469.881599
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-182799.6368.573265
HSA-MIR-875-3P99.6369.472548
HSA-MIR-6758-3P99.5767.551078
HSA-MIR-4649-3P99.5666.901783
HSA-MIR-447299.5666.081478

Literature-anchored findings (GeneRIF, showing 3)

  • This study showed that CDC42EP4 messenger RNA levels was significantly upregulated in subjects with schizophrenia in laminar and cellular samples. (PMID:25981171)
  • 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)
  • Cell division cycle 42 effector protein 4 inhibits prostate cancer progression by suppressing ERK signaling pathway. (PMID:38153517)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocdc42ep4bENSDARG00000045036
danio_reriocdc42ep4aENSDARG00000101457
mus_musculusCdc42ep4ENSMUSG00000041598
rattus_norvegicusCdc42ep4ENSRNOG00000028946

Paralogs (5): CDC42EP1 (ENSG00000128283), CDC42EP2 (ENSG00000149798), CDC42EP3 (ENSG00000163171), CDC42EP5 (ENSG00000167617), C15orf62 (ENSG00000188277)

Protein

Protein identifiers

Cdc42 effector protein 4Q9H3Q1 (reviewed: Q9H3Q1)

Alternative names: Binder of Rho GTPases 4

All UniProt accessions (5): B2R6D8, Q9H3Q1, J3KRZ9, J3QQS6, J3QR93

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, when overexpressed in fibroblasts.

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

Subcellular location. Endomembrane system. Cytoplasm. Cytoskeleton.

Tissue specificity. Not detected in any of the adult tissues tested. May be expressed only in fetal or embryonic tissues.

Similarity. Belongs to the BORG/CEP family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H3Q1-11yes
Q9H3Q1-22

RefSeq proteins (1): NP_036253* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000095CRIB_domDomain
IPR029273Cdc42_effect-likeDomain
IPR051296Cdc42_Effector_BORG/CEPFamily

Pfam: PF00786, PF14957

UniProt features (30 total): modified residue 12, compositionally biased region 6, sequence conflict 6, region of interest 3, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H3Q1-F158.670.05

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 (12): 5, 18, 64, 105, 109, 118, 138, 140, 142, 174, 292, 295

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-9013148CDC42 GTPase cycle
R-HSA-9013149RAC1 GTPase cycle
R-HSA-9013404RAC2 GTPase cycle
R-HSA-9013406RHOQ GTPase cycle
R-HSA-162582Signal Transduction
R-HSA-194315Signaling by Rho GTPases
R-HSA-9012999RHO GTPase cycle
R-HSA-9716542Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 262 (showing top): GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_RESPONSE_TO_PEPTIDE, PEREZ_TP63_TARGETS, TAL1ALPHAE47_01, GOMF_GTPASE_BINDING, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, BLALOCK_ALZHEIMERS_DISEASE_UP

GO Biological Process (5): 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), cellular response to type II interferon (GO:0071346)

GO Molecular Function (3): RNA binding (GO:0003723), small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (10): cytoplasm (GO:0005737), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), adherens junction (GO:0005912), endomembrane system (GO:0012505), actin cytoskeleton (GO:0015629), microtubule cytoskeleton (GO:0015630), phagocytic vesicle (GO:0045335), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
RHO GTPase cycle4
Signaling by Rho GTPases, Miro GTPases and RHOBTB31
Signaling by Rho GTPases1
Signal Transduction1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cytoskeleton2
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
response to type II interferon1
cellular response to cytokine stimulus1
nucleic acid binding1
GTPase binding1
binding1
intracellular anatomical structure1
cytoplasm1
intracellular membraneless organelle1
membrane1
cell periphery1
cell-cell junction1
vacuole1
plasma membrane1
endocytic vesicle1

Protein interactions and networks

STRING

690 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CDC42EP4RHOQP17081951
CDC42EP4CDC42P21181830
CDC42EP4CDC42BPBQ9Y5S2562
CDC42EP4PROSER2Q86WR7499
CDC42EP4CCDC102AQ96A19495
CDC42EP4CDC42SE1Q9NRR8473
CDC42EP4CDC42SE2Q9NRR3450
CDC42EP4SEPTIN7Q16181435
CDC42EP4CMIPQ8IY22435
CDC42EP4WDPCPO95876423
CDC42EP4SERTAD2Q14140411
CDC42EP4WHAMMQ8TF30410
CDC42EP4BAIAP2L1Q9UHR4407
CDC42EP4SEPTIN6Q14141401
CDC42EP4ARHGEF3Q9NR81394

IntAct

48 interactions, top by confidence:

ABTypeScore
HOMER1TRAF5psi-mi:“MI:0914”(association)0.740
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
CDC42EP4FAM9Bpsi-mi:“MI:0915”(physical association)0.670
FAM9BCDC42EP4psi-mi:“MI:0915”(physical association)0.670
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
HTTCDC42EP4psi-mi:“MI:0915”(physical association)0.560
RTN4IP1HEXIM1psi-mi:“MI:0914”(association)0.530
CDC42EP4SEPTIN6psi-mi:“MI:0914”(association)0.530
RBFAMETTL15psi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
CDC42EP4SRPK2psi-mi:“MI:0217”(phosphorylation reaction)0.440
SRPK1CDC42EP4psi-mi:“MI:0217”(phosphorylation reaction)0.440
SPRY2CDC42EP4psi-mi:“MI:0915”(physical association)0.400
PCNACDC42EP4psi-mi:“MI:0915”(physical association)0.370
CDC42EP4PApsi-mi:“MI:0915”(physical association)0.370
WDR6CDC42EP4psi-mi:“MI:0915”(physical association)0.370
Kctd5psi-mi:“MI:0914”(association)0.350
Septin9SEPTIN8psi-mi:“MI:0914”(association)0.350
Septin2SEPTIN8psi-mi:“MI:0914”(association)0.350
Septin7SEPTIN8psi-mi:“MI:0914”(association)0.350
CDC42EP4SEPTIN4psi-mi:“MI:0914”(association)0.350
CDC42PPP1R12Apsi-mi:“MI:0914”(association)0.350
POLR1DBDP1psi-mi:“MI:0914”(association)0.350

BioGRID (131): FAM9B (Two-hybrid), CDC42EP4 (Affinity Capture-MS), SEPT4 (Affinity Capture-MS), SEPT2 (Affinity Capture-MS), SEPT7 (Affinity Capture-MS), SEPT5 (Affinity Capture-MS), SEPT6 (Affinity Capture-MS), SEPT8 (Affinity Capture-MS), SEPT11 (Affinity Capture-MS), SEPT9 (Affinity Capture-MS), SEPT3 (Affinity Capture-MS), KLHL15 (Affinity Capture-MS), SEPT10 (Affinity Capture-MS), YBEY (Affinity Capture-MS), FHL2 (Affinity Capture-MS)

ESM2 similar proteins: A0A098DPY0, A0A0D1DRJ3, A0A194W8T8, A0A3G1DJJ7, A4R227, A6RHW0, A7KAN7, B0XXN8, G1XLI4, G4NDR3, J9VT33, O13412, O13415, O13508, P10071, P17429, P19970, P37938, P53289, Q01115, Q01582, Q01631, Q09033, Q0U6W8, Q10060, Q1K8E7, Q2GW22, Q4I5R3, Q4P328, Q4PFA7, Q4WXK4, Q4WXY0, Q5AYT1, Q5IS56, Q6BWK6, Q6C449, Q6MW04, Q6MW50, Q6SW99, Q74ZL3

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

SIGNOR signaling

2 interactions.

AEffectBMechanism
PRKCA“down-regulates activity”CDC42EP4phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 54 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:

PathwayPartnersFoldFDR
RHO GTPase Effectors612.0×2e-04
SARS-CoV Infections58.2×2e-03
Signaling by Rho GTPases77.0×4e-04
Signaling by Rho GTPases, Miro GTPases and RHOBTB376.9×4e-04
Infectious disease75.1×2e-03

GO biological processes:

GO termPartnersFoldFDR
intracellular protein localization613.4×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance76
Likely benign7
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2685607GRCh37/hg19 17q24.3-25.1(chr17:69501527-71380722)x1Pathogenic

SpliceAI

440 predictions. Top by Δscore:

VariantEffectΔscore
17:73286608:TAAGG:Tacceptor_gain1.0000
17:73286613:C:CCacceptor_gain1.0000
17:73286610:AGG:Aacceptor_gain0.9900
17:73286611:GG:Gacceptor_gain0.9900
17:73286611:GGCTG:Gacceptor_loss0.9900
17:73286612:GCT:Gacceptor_loss0.9900
17:73286613:C:CGacceptor_loss0.9900
17:73286614:T:Aacceptor_loss0.9900
17:73286609:AAGG:Aacceptor_gain0.9800
17:73286576:A:Tacceptor_gain0.9700
17:73311888:CCTA:Cdonor_loss0.9700
17:73311889:CTAC:Cdonor_loss0.9700
17:73311890:TAC:Tdonor_loss0.9700
17:73311891:ACC:Adonor_loss0.9700
17:73311892:C:CTdonor_loss0.9700
17:73310880:CCGG:Cdonor_gain0.9600
17:73286620:C:CTacceptor_gain0.9500
17:73286621:A:Tacceptor_gain0.9500
17:73310873:GCACT:Gdonor_loss0.9400
17:73310874:CACTC:Cdonor_loss0.9400
17:73310875:ACTC:Adonor_loss0.9400
17:73310876:CT:Cdonor_loss0.9400
17:73310877:TCACC:Tdonor_loss0.9400
17:73310878:CACC:Cdonor_loss0.9400
17:73310879:A:Cdonor_loss0.9400
17:73310880:C:Gdonor_loss0.9400
17:73310872:GGCAC:Gdonor_loss0.9300
17:73311862:C:CTdonor_gain0.9300
17:73310879:A:ACdonor_gain0.9200
17:73310880:C:CCdonor_gain0.9200

AlphaMissense

2320 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:73286345:G:CF52L1.000
17:73286345:G:TF52L1.000
17:73286346:A:CF52C1.000
17:73286346:A:GF52S1.000
17:73286347:A:GF52L1.000
17:73286358:C:TG48E1.000
17:73286360:A:CF47L1.000
17:73286360:A:TF47L1.000
17:73286361:A:CF47C1.000
17:73286362:A:GF47L1.000
17:73286382:A:TV40D1.000
17:73286386:G:CH39D1.000
17:73286395:G:CH36D1.000
17:73286400:A:GF34S1.000
17:73286421:A:TI27N1.000
17:73285860:C:TG214E0.999
17:73285861:C:GG214R0.999
17:73285861:C:TG214R0.999
17:73286159:C:AK114N0.999
17:73286159:C:GK114N0.999
17:73286343:A:GL53P0.999
17:73286343:A:TL53H0.999
17:73286355:T:CD49G0.999
17:73286358:C:AG48V0.999
17:73286359:C:AG48W0.999
17:73286359:C:GG48R0.999
17:73286359:C:TG48R0.999
17:73286361:A:GF47S0.999
17:73286380:C:GG41R0.999
17:73286384:G:CH39Q0.999

dbSNP variants (sampled 300 via entrez): RS1000004200 (17:73288556 C>G,T), RS1000379924 (17:73291834 T>C), RS1000427596 (17:73308784 C>T), RS1000562866 (17:73297869 G>A), RS1000689724 (17:73303729 T>C), RS1000859444 (17:73310244 C>T), RS1000912962 (17:73297678 A>G), RS1001035948 (17:73299826 C>A), RS1001347478 (17:73293384 T>C), RS1001443245 (17:73287822 G>A), RS1001451352 (17:73287993 C>T), RS1001603712 (17:73312601 C>T), RS1001669645 (17:73297430 C>T), RS1001819156 (17:73313690 A>G), RS1001841075 (17:73293704 A>T)

Disease associations

OMIM: gene MIM:605468 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, increases expression, affects expression2
Air Pollutantsincreases oxidation, decreases expression, affects cotreatment, increases abundance2
Benzo(a)pyreneaffects methylation, decreases expression2
Valproic Aciddecreases expression, increases methylation, affects expression2
Cyclosporinedecreases expression2
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
pirinixic acidincreases expression, affects binding, increases activity1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression1
perfluorooctanoic aciddecreases expression1
coumarinaffects phosphorylation1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
chloropicrinincreases expression1
2-palmitoylglycerolincreases expression1
nutlin 3affects cotreatment, increases secretion1
Sunitinibdecreases expression1
Vorinostatdecreases expression1
Leflunomidedecreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Caffeineaffects phosphorylation1
Dactinomycinaffects cotreatment, increases secretion1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Demecolcineincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Estradiolaffects cotreatment, decreases expression1
Ethyl Methanesulfonateincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B1MXAbcam HeLa CDC42EP4 KOCancer cell lineFemale

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.