CDC42SE2

gene
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Also known as FLJ21967SPEC2

Summary

CDC42SE2 (CDC42 small effector 2, HGNC:18547) is a protein-coding gene on chromosome 5q31.1, encoding CDC42 small effector protein 2 (Q9NRR3). Probably involved in the organization of the actin cytoskeleton by acting downstream of CDC42, inducing actin filament assembly.

Enables signaling adaptor activity. Involved in regulation of signal transduction. Located in plasma membrane.

Source: NCBI Gene 56990 — RefSeq curated summary.

At a glance

  • GWAS associations: 20
  • Clinical variants (ClinVar): 18 total
  • MANE Select transcript: NM_001375635

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18547
Approved symbolCDC42SE2
NameCDC42 small effector 2
Location5q31.1
Locus typegene with protein product
StatusApproved
AliasesFLJ21967, SPEC2
Ensembl geneENSG00000158985
Ensembl biotypeprotein_coding
OMIM619457
Entrez56990

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 protein_coding_CDS_not_defined, 6 protein_coding

ENST00000360515, ENST00000395246, ENST00000502582, ENST00000502639, ENST00000502840, ENST00000503291, ENST00000504701, ENST00000505065, ENST00000506419, ENST00000506929, ENST00000511432, ENST00000515533, ENST00000892403

RefSeq mRNA: 5 — MANE Select: NM_001375635 NM_001038702, NM_001375633, NM_001375634, NM_001375635, NM_020240

CCDS: CCDS34224

Canonical transcript exons

ENST00000505065 — 5 exons

ExonStartEnd
ENSE00001298120131315976131316144
ENSE00001326537131359209131359547
ENSE00002041653131390993131394672
ENSE00002045409131264053131264166
ENSE00003516888131385543131385644

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 56.7016 / max 2224.5546, expressed in 1818 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
5839949.07611813
583982.78981003
583961.1212157
584140.9491460
583950.9191147
584110.7579348
584120.5855255
584130.226992
2036810.133537
583970.128151

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033199.45gold quality
middle temporal gyrusUBERON:000277199.05gold quality
Brodmann (1909) area 23UBERON:001355498.93gold quality
Brodmann (1909) area 46UBERON:000648398.86gold quality
mucosa of sigmoid colonUBERON:000499398.78gold quality
endothelial cellCL:000011598.75gold quality
colonic mucosaUBERON:000031798.66gold quality
epithelium of nasopharynxUBERON:000195198.62gold quality
kidney epitheliumUBERON:000481998.52gold quality
oviduct epitheliumUBERON:000480498.51gold quality
palpebral conjunctivaUBERON:000181298.19gold quality
trabecular bone tissueUBERON:000248397.84gold quality
postcentral gyrusUBERON:000258197.82gold quality
parietal lobeUBERON:000187297.71gold quality
superior frontal gyrusUBERON:000266197.66gold quality
globus pallidusUBERON:000187597.52gold quality
medial globus pallidusUBERON:000247797.52gold quality
jejunal mucosaUBERON:000039997.49gold quality
entorhinal cortexUBERON:000272897.49gold quality
caput epididymisUBERON:000435897.48gold quality
upper arm skinUBERON:000426397.47gold quality
parotid glandUBERON:000183197.35gold quality
nasal cavity epitheliumUBERON:000538497.33gold quality
corpus epididymisUBERON:000435997.32gold quality
bone marrowUBERON:000237197.22gold quality
lateral globus pallidusUBERON:000247697.16gold quality
lymph nodeUBERON:000002997.15gold quality
substantia nigra pars compactaUBERON:000196597.08gold quality
substantia nigra pars reticulataUBERON:000196697.06gold quality
ponsUBERON:000098897.02gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-6678yes36.95
E-GEOD-135922yes32.69
E-ANND-3yes23.18
E-CURD-119yes4.09
E-GEOD-106540no2382.11
E-MTAB-7606no819.56

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PAX3

miRNA regulators (miRDB)

130 targeting CDC42SE2, 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-340-5P100.0072.504437
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3163100.0077.238605
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-453199.9969.703181
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-1213699.9872.815713
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-314899.9775.066478
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-570-3P99.9672.414910
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-590-3P99.9674.346478
HSA-MIR-6778-3P99.9667.292693
HSA-LET-7C-3P99.9573.422862
HSA-MIR-545-3P99.9570.742783
HSA-MIR-144-3P99.9473.982698
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-218-5P99.9372.222103
HSA-MIR-3682-5P99.9367.971163

Literature-anchored findings (GeneRIF, showing 3)

  • Recruitment of SPEC2 within Jurkat T cells to the antigen-presenting cell interface occurred following incubation with staphylococcal enterotoxin E superantigen-loaded B cells and colocalized there with F-actin and Cdc42. T cell receptor (PMID:15840583)
  • haplotypes underlying the SPEC2/PDZ-GEF2/acyl-CoA synthetase long-chain family member 6 region are associated with schizophrenia (PMID:17030554)
  • Cdc42 is an important regulator of corneal epithelial wound repair. To promote healing, Cdc42 may interact with receptor tyrosine kinase-activated signaling cascades that participate in cell migration and cell-cycle progression. (PMID:23833064)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocdc42se2ENSDARG00000094577
mus_musculusCdc42se2ENSMUSG00000052298
rattus_norvegicusCdc42se2ENSRNOG00000042449

Paralogs (1): CDC42SE1 (ENSG00000197622)

Protein

Protein identifiers

CDC42 small effector protein 2Q9NRR3 (reviewed: Q9NRR3)

Alternative names: Small effector of CDC42 protein 2

All UniProt accessions (3): Q9NRR3, D6REL0, H0Y9W5

UniProt curated annotations — full annotation on UniProt →

Function. Probably involved in the organization of the actin cytoskeleton by acting downstream of CDC42, inducing actin filament assembly. Alters CDC42-induced cell shape changes. In activated T-cells, may play a role in CDC42-mediated F-actin accumulation at the immunological synapse. May play a role in early contractile events in phagocytosis in macrophages.

Subunit / interactions. Interacts with CDC42 (in GTP-bound form). Interacts weakly with RAC1 and not at all with RHOA.

Subcellular location. Cytoplasm. Cytoskeleton. Cell membrane. Cell projection. Phagocytic cup.

Tissue specificity. Widely expressed. Expressed at higher level in T-lymphocytes. Highly expressed in CCRF-CEM T-lymphocytes, Jurkat T-lymphocytes, and Raji B-lymphocytes compared (at protein level).

Domain organisation. The CRIB domain mediates interaction with CDC42.

Miscellaneous. CDC42SE2 is mapped in the genomic region associated with schizophrenia.

Similarity. Belongs to the CDC42SE/SPEC family.

RefSeq proteins (5): NP_001033791, NP_001362562, NP_001362563, NP_001362564, NP_064625 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000095CRIB_domDomain
IPR036936CRIB_dom_sfHomologous_superfamily
IPR039056SPECFamily

Pfam: PF00786

UniProt features (6 total): modified residue 2, lipid moiety-binding region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NRR3-F168.020.00

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): 43, 52, 10, 11

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-9013148CDC42 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: 192 (showing top): GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_VESICLE_MEDIATED_TRANSPORT, GOMF_GTPASE_BINDING, MODULE_503, MODULE_195, GOBP_REGULATION_OF_RHO_PROTEIN_SIGNAL_TRANSDUCTION, MODULE_147, DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER, SENESE_HDAC1_TARGETS_UP, FUJII_YBX1_TARGETS_UP, YAMAZAKI_TCEB3_TARGETS_UP, GOBP_IMPORT_INTO_CELL, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_ENDOCYTOSIS

GO Biological Process (4): phagocytosis (GO:0006909), regulation of cell shape (GO:0008360), regulation of signal transduction (GO:0009966), regulation of Rho protein signal transduction (GO:0035023)

GO Molecular Function (3): small GTPase binding (GO:0031267), signaling adaptor activity (GO:0035591), protein binding (GO:0005515)

GO Cellular Component (6): phagocytic cup (GO:0001891), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cytoplasm (GO:0005737), membrane (GO:0016020), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
RHO GTPase cycle1
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
endocytosis1
regulation of cell morphogenesis1
regulation of biological quality1
signal transduction1
regulation of cell communication1
regulation of signaling1
regulation of response to stimulus1
Rho protein signal transduction1
regulation of small GTPase mediated signal transduction1
GTPase binding1
protein-macromolecule adaptor activity1
binding1
plasma membrane1
intracellular membraneless organelle1
membrane1
cell periphery1
intracellular anatomical structure1

Protein interactions and networks

STRING

2155 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CDC42SE2RAPGEF6Q8TEU7638
CDC42SE2ACSL6Q9UKU0599
CDC42SE2CDC42P21181554
CDC42SE2OR2B3O76000507
CDC42SE2CDR2LQ86X02476
CDC42SE2SLC35F4A4IF30471
CDC42SE2CDC42EP4Q9H3Q1450
CDC42SE2CDC42BPBQ9Y5S2439
CDC42SE2LYRM7Q5U5X0437
CDC42SE2TMEM196Q5HYL7435
CDC42SE2STPG3Q8N7X2431
CDC42SE2LMBRD2Q68DH5410
CDC42SE2BAIAP2L1Q9UHR4401
CDC42SE2KANSL1Q7Z3B3395
CDC42SE2CASS4Q9NQ75387

IntAct

19 interactions, top by confidence:

ABTypeScore
CDC42SE2CDC42psi-mi:“MI:0914”(association)0.730
CDC42BBXpsi-mi:“MI:0914”(association)0.350
MYO19PLEKHG3psi-mi:“MI:0914”(association)0.350
MAD2L2psi-mi:“MI:0914”(association)0.350
CDC42psi-mi:“MI:0914”(association)0.350
HLA-Cpsi-mi:“MI:0914”(association)0.350
CDC42SE2SSC5Dpsi-mi:“MI:0914”(association)0.350
TUBBpsi-mi:“MI:0914”(association)0.350
TUBB4BPLD2psi-mi:“MI:0914”(association)0.350
TMPRSS5CLGNpsi-mi:“MI:0914”(association)0.350
AFG2AESYT2psi-mi:“MI:0914”(association)0.350
HPNDDX39Apsi-mi:“MI:0914”(association)0.350
LY86MAP2K7psi-mi:“MI:0914”(association)0.350
MAGEA8B4GALT5psi-mi:“MI:0914”(association)0.350
UPK2IFT56psi-mi:“MI:0914”(association)0.350
SLC37A3PLXNB2psi-mi:“MI:0914”(association)0.350
SLC46A3CLGNpsi-mi:“MI:0914”(association)0.350

BioGRID (33): CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS), CDC42 (Affinity Capture-MS), TSC22D3 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-RNA), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Two-hybrid), CDC42SE2 (Two-hybrid), CDC42SE2 (Affinity Capture-MS), CDC42SE2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUI7, A1DL98, A1L1K4, A4V8B4, A6QLJ4, A6ZMG4, A6ZR60, A7NVJ4, A9JR56, B3LLZ8, C5E1C7, C7GWA2, C8ZEW0, O13916, O60153, P0C2W9, P15130, P16135, P20486, P27271, P28974, P35198, P40063, P84395, Q04438, Q28EW5, Q28GG3, Q4V853, Q5FVD7, Q5R4F8, Q5R977, Q5RD94, Q5U550, Q66657, Q68EK9, Q68FR5, Q6AX78, Q6C3T0, Q751I6, Q7T2A3

Diamond homologs: A1L1K4, A6QLJ4, A9JR56, Q28EW5, Q28GG3, Q4V853, Q5BIS3, Q5BJM7, Q5BKH3, Q5FVD7, Q5R4F8, Q5RDD6, Q5ZKB1, Q66KZ1, Q6AX78, Q6GPV4, Q6TEL3, Q8BGH7, Q8BHL7, Q9NRR3, Q9NRR8, Q9VNE7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance13
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1528 predictions. Top by Δscore:

VariantEffectΔscore
5:131264167:G:GGdonor_gain1.0000
5:131359207:A:AGacceptor_gain1.0000
5:131359208:G:GGacceptor_gain1.0000
5:131359208:GACT:Gacceptor_gain1.0000
5:131385645:G:GGdonor_gain1.0000
5:131391109:G:GGdonor_gain1.0000
5:131264163:GACG:Gdonor_gain0.9900
5:131264165:CGGT:Cdonor_loss0.9900
5:131264166:GGTG:Gdonor_loss0.9900
5:131264167:G:Adonor_loss0.9900
5:131264168:TGAG:Tdonor_loss0.9900
5:131264169:GAGT:Gdonor_loss0.9900
5:131264483:A:Tdonor_gain0.9900
5:131315975:GATA:Gacceptor_gain0.9900
5:131359205:CTAG:Cacceptor_gain0.9900
5:131359205:CTAGA:Cacceptor_loss0.9900
5:131359206:TAG:Tacceptor_loss0.9900
5:131359206:TAGA:Tacceptor_gain0.9900
5:131359207:A:Gacceptor_loss0.9900
5:131359207:AGAC:Aacceptor_gain0.9900
5:131359208:G:GCacceptor_loss0.9900
5:131359208:GA:Gacceptor_gain0.9900
5:131359208:GAC:Gacceptor_gain0.9900
5:131359208:GACTA:Gacceptor_gain0.9900
5:131359302:G:GTdonor_gain0.9900
5:131359422:A:Tdonor_gain0.9900
5:131359544:GCCT:Gdonor_gain0.9900
5:131385535:T:Gacceptor_gain0.9900
5:131385541:A:AGacceptor_gain0.9900
5:131385542:G:GGacceptor_gain0.9900

AlphaMissense

554 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:131385559:T:AI24N1.000
5:131385559:T:GI24S1.000
5:131385574:T:AI29N1.000
5:131385574:T:GI29S1.000
5:131385582:C:TP32S1.000
5:131385583:C:AP32H1.000
5:131385591:T:AF35I1.000
5:131385591:T:CF35L1.000
5:131385592:T:CF35S1.000
5:131385592:T:GF35C1.000
5:131385593:T:AF35L1.000
5:131385593:T:GF35L1.000
5:131385597:C:AH37N1.000
5:131385597:C:GH37D1.000
5:131385606:C:GH40D1.000
5:131385608:T:AH40Q1.000
5:131385608:T:GH40Q1.000
5:131391015:T:CM60T1.000
5:131391025:G:CK63N1.000
5:131391025:G:TK63N1.000
5:131385559:T:CI24T0.999
5:131385565:G:TR26I0.999
5:131385572:G:AM28I0.999
5:131385572:G:CM28I0.999
5:131385572:G:TM28I0.999
5:131385574:T:CI29T0.999
5:131385576:G:AG30R0.999
5:131385576:G:CG30R0.999
5:131385577:G:AG30E0.999
5:131385577:G:TG30V0.999

dbSNP variants (sampled 300 via entrez): RS1000013971 (5:131386949 A>G), RS1000028545 (5:131281100 G>T), RS1000048967 (5:131238821 G>A,C,T), RS1000073234 (5:131370157 T>C), RS1000073633 (5:131298709 C>T), RS1000077267 (5:131324079 C>G), RS1000120069 (5:131386643 G>C,T), RS1000130361 (5:131345972 C>A,G,T), RS1000138463 (5:131356746 A>T), RS1000147180 (5:131349951 A>G), RS1000186050 (5:131336927 A>G,T), RS1000187579 (5:131392763 C>T), RS1000194707 (5:131270945 G>C,T), RS1000207013 (5:131264952 A>G), RS1000211448 (5:131305383 G>A)

Disease associations

OMIM: gene MIM:619457 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

20 associations (top):

StudyTraitp-value
GCST002817_5Alzheimer’s disease in APOE e4- carriers2.000000e-07
GCST002875_174Diisocyanate-induced asthma1.000000e-06
GCST004131_32Inflammatory bowel disease4.000000e-27
GCST004132_10Crohn’s disease6.000000e-36
GCST004133_36Ulcerative colitis2.000000e-06
GCST004861_64Itch intensity from mosquito bite1.000000e-27
GCST004862_151Itch intensity from mosquito bite adjusted by bite size2.000000e-15
GCST004862_224Itch intensity from mosquito bite adjusted by bite size3.000000e-08
GCST004862_57Itch intensity from mosquito bite adjusted by bite size2.000000e-08
GCST004863_99Mosquito bite size2.000000e-15
GCST004864_30Perceived unattractiveness to mosquitoes5.000000e-06
GCST004865_88Itch intensity from mosquito bite adjusted by bite size5.000000e-15
GCST010241_308Apolipoprotein A1 levels2.000000e-08
GCST010242_379HDL cholesterol levels3.000000e-10
GCST010244_416Triglyceride levels7.000000e-10
GCST010701_41Cortical surface area (MOSTest)1.000000e-20
GCST010702_96Subcortical volume (MOSTest)2.000000e-08
GCST010703_160Brain morphology (MOSTest)3.000000e-09
GCST012047_19Fasting glucose1.000000e-07
GCST90002388_322Lymphocyte count4.000000e-11

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0008380perceived unattractiveness to mosquitos measurement
EFO:0004614apolipoprotein A 1 measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0004346neuroimaging measurement
EFO:0004587lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression2
Nickelincreases expression2
Cadmium Chloridedecreases reaction, increases abundance, increases palmitoylation, decreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
bufotalindecreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
jinfukangdecreases expression1
Bortezomibdecreases expression1
Sunitinibincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzoatesdecreases expression1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1
Caffeinedecreases phosphorylation1
Cycloheximideincreases expression, affects cotreatment, affects expression1
Tetrachlorodibenzodioxinaffects expression, affects cotreatment1
Thimerosalincreases expression1
Thiramdecreases expression1
Tretinoinincreases expression1
Valproic Aciddecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1
Copper Sulfatedecreases expression1

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.