PLEKHG3

gene
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Also known as ARHGEF43

Summary

PLEKHG3 (pleckstrin homology and RhoGEF domain containing G3, HGNC:20364) is a protein-coding gene on chromosome 14q23.3, encoding Pleckstrin homology domain-containing family G member 3 (A1L390). Plays a role in controlling cell polarity and cell motility by selectively binding newly polymerized actin and activating RAC1 and CDC42 to enhance local actin polymerization.

Enables actin binding activity. Involved in regulation of cell migration and regulation of establishment of cell polarity. Predicted to be located in cytosol.

Source: NCBI Gene 26030 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 314 total — 1 pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_001308147

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20364
Approved symbolPLEKHG3
Namepleckstrin homology and RhoGEF domain containing G3
Location14q23.3
Locus typegene with protein product
StatusApproved
AliasesARHGEF43
Ensembl geneENSG00000126822
Ensembl biotypeprotein_coding
OMIM617940
Entrez26030

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000247226, ENST00000394691, ENST00000471182, ENST00000484731, ENST00000490180, ENST00000492928, ENST00000554499, ENST00000555982, ENST00000556801, ENST00000634379, ENST00000864150, ENST00000864151, ENST00000864152, ENST00000864153, ENST00000967516, ENST00000967517

RefSeq mRNA: 1 — MANE Select: NM_001308147 NM_001308147

CCDS: CCDS76690

Canonical transcript exons

ENST00000247226 — 17 exons

ExonStartEnd
ENSE000015192346473024364730312
ENSE000015192396470442464704704
ENSE000016311226473735664737375
ENSE000017418946473136164731543
ENSE000017440146473171464731806
ENSE000018016536473685364736891
ENSE000019551116474298264750249
ENSE000024298296472759364727982
ENSE000034647906474103664742455
ENSE000034794996473209564732181
ENSE000035688646473079964730949
ENSE000035909526473280364732901
ENSE000036320446473874264738855
ENSE000036320976473242764732460
ENSE000036688926473103864731169
ENSE000036859606472899664729093
ENSE000037842086473064264730688

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 96.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.4821 / max 338.7218, expressed in 1540 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
14012918.28351519
1401301.1018532
1401260.250881
1401310.243690
1401250.197174
1401270.185365
1401240.112653
1401320.062534
1401280.044920

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548896.22gold quality
popliteal arteryUBERON:000225096.15gold quality
tibial arteryUBERON:000761096.14gold quality
right coronary arteryUBERON:000162594.94gold quality
corpus callosumUBERON:000233694.81gold quality
granulocyteCL:000009494.71gold quality
body of uterusUBERON:000985393.72gold quality
aortaUBERON:000094793.35gold quality
C1 segment of cervical spinal cordUBERON:000646992.41gold quality
left uterine tubeUBERON:000130392.30gold quality
left coronary arteryUBERON:000162692.28gold quality
metanephros cortexUBERON:001053392.22gold quality
coronary arteryUBERON:000162192.09gold quality
spinal cordUBERON:000224091.29gold quality
nerveUBERON:000102191.11gold quality
tibial nerveUBERON:000132391.11gold quality
bloodUBERON:000017890.88gold quality
ectocervixUBERON:001224990.67gold quality
muscle layer of sigmoid colonUBERON:003580590.67gold quality
lower esophagus mucosaUBERON:003583490.63gold quality
olfactory bulbUBERON:000226490.61silver quality
skin of legUBERON:000151190.52gold quality
esophagus mucosaUBERON:000246990.44gold quality
right ovaryUBERON:000211890.06gold quality
skin of abdomenUBERON:000141690.02gold quality
ascending aortaUBERON:000149689.88gold quality
descending thoracic aortaUBERON:000234589.88gold quality
thoracic aortaUBERON:000151589.84gold quality
mucosa of stomachUBERON:000119989.71gold quality
smooth muscle tissueUBERON:000113589.26gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

  • This is the first implication of chr14q23.2-23.3 in the etiology of autism and points to MTHFD1, PLEKHG3, and CHURC1 as potential candidate genes contributing to autism risk. (PMID:21360829)
  • PLEKHG3 enhances polarized cell migration by activating actin filaments at the cell front. (PMID:27555588)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosi:ch73-212j7.3ENSDARG00000058835
danio_reriosi:ch73-212j7.3ENSDARG00000096613
mus_musculusPlekhg3ENSMUSG00000052609
rattus_norvegicusPlekhg3ENSRNOG00000006570

Protein

Protein identifiers

Pleckstrin homology domain-containing family G member 3A1L390 (reviewed: A1L390)

All UniProt accessions (7): A1L390, A0A0U1RR71, A0A2X0SFH4, A0A8C8NWT4, G3V278, G3V311, G3V3I3

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in controlling cell polarity and cell motility by selectively binding newly polymerized actin and activating RAC1 and CDC42 to enhance local actin polymerization.

Subcellular location. Cytoplasm. Cytoskeleton.

Isoforms (3)

UniProt IDNamesCanonical?
A1L390-11yes
A1L390-22
A1L390-33

RefSeq proteins (1): NP_001295076* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000219DH_domDomain
IPR001849PH_domainDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR035899DBL_dom_sfHomologous_superfamily
IPR043324PH_PLEKHG1_G2_G3Domain
IPR055251SOS1_NGEF_PHDomain

Pfam: PF00621, PF22697

UniProt features (50 total): modified residue 19, compositionally biased region 11, region of interest 8, sequence conflict 4, splice variant 3, domain 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A1L390-F155.280.15

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 (19): 76, 433, 576, 577, 618, 631, 640, 643, 647, 741, 779, 827, 962, 1011, 1023, 1037, 1040, 1081, 1107

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-8980692RHOA GTPase cycle
R-HSA-9013148CDC42 GTPase cycle
R-HSA-9013149RAC1 GTPase cycle
R-HSA-9013406RHOQ GTPase cycle
R-HSA-9013408RHOG GTPase cycle

MSigDB gene sets: 153 (showing top): GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOMF_GTPASE_BINDING, GOBP_ESTABLISHMENT_OF_CELL_POLARITY, CATTTCA_MIR203, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, chr14q23, GOMF_ACTIN_BINDING, GOBP_REGULATION_OF_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, MULLIGHAN_NPM1_SIGNATURE_3_DN, MORF_PDPK1, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, LEIN_OLIGODENDROCYTE_MARKERS, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY, BOCHKIS_FOXA2_TARGETS

GO Biological Process (3): regulation of cell migration (GO:0030334), regulation of small GTPase mediated signal transduction (GO:0051056), regulation of establishment of cell polarity (GO:2000114)

GO Molecular Function (3): actin binding (GO:0003779), guanyl-nucleotide exchange factor activity (GO:0005085), small GTPase binding (GO:0031267)

GO Cellular Component (3): cytosol (GO:0005829), cytoskeleton (GO:0005856), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RHO GTPase cycle5

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cell migration1
regulation of cell motility1
small GTPase-mediated signal transduction1
regulation of intracellular signal transduction1
establishment of cell polarity1
regulation of establishment or maintenance of cell polarity1
cytoskeletal protein binding1
GTP binding1
GDP binding1
GTPase regulator activity1
GTPase binding1
cytoplasm1
intracellular membraneless organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

626 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PLEKHG3GRIFINA4D1Z8512
PLEKHG3PPP1R36Q96LQ0439
PLEKHG3PLEKHG7Q6ZR37393
PLEKHG3SGSM1Q2NKQ1385
PLEKHG3ARHGEF33A8MVX0370
PLEKHG3CHURC1Q8WUH1369
PLEKHG3SERPINE3A8MV23367
PLEKHG3TET1Q8NFU7353
PLEKHG3NOS1APO75052352
PLEKHG3PRMT2IPQ6ZRI6348
PLEKHG3PPIL1Q9Y3C6348
PLEKHG3DNMT3AQ9Y6K1348
PLEKHG3ARL11Q969Q4331
PLEKHG3SYDE1Q6ZW31328
PLEKHG3RGPD1P0C839324

IntAct

103 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
YWHABBLTP3Bpsi-mi:“MI:2364”(proximity)0.610
PLEKHG3YWHAGpsi-mi:“MI:0914”(association)0.610
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
YWHABPLEKHG3psi-mi:“MI:0914”(association)0.480
YWHAQPLEKHG3psi-mi:“MI:0914”(association)0.480
MYH9PLEKHG3psi-mi:“MI:0914”(association)0.350
Bmpr1aPLEKHG3psi-mi:“MI:0914”(association)0.350
ANLNPLEKHG3psi-mi:“MI:0914”(association)0.350
Flot1PLEKHG3psi-mi:“MI:0914”(association)0.350
MYO18APLEKHG3psi-mi:“MI:0914”(association)0.350
MYO1CPLEKHG3psi-mi:“MI:0914”(association)0.350
MYO19PLEKHG3psi-mi:“MI:0914”(association)0.350
FLNAPLEKHG3psi-mi:“MI:0914”(association)0.350
Lima1PLEKHG3psi-mi:“MI:0914”(association)0.350
LIMA1PLEKHG3psi-mi:“MI:0914”(association)0.350
Calml3PLEKHG3psi-mi:“MI:0914”(association)0.350
Tmod3PLEKHG3psi-mi:“MI:0914”(association)0.350
Tpm1PLEKHG3psi-mi:“MI:0914”(association)0.350
Coro1cPLEKHG3psi-mi:“MI:0914”(association)0.350
Ppp6cPLEKHG3psi-mi:“MI:0914”(association)0.350
DBN1PLEKHG3psi-mi:“MI:0914”(association)0.350

BioGRID (126): PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS), PLEKHG3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2JUG7, A1L390, E9Q0S6, O08774, O14924, O15085, O43182, O54834, O54960, O60307, O75052, P57095, Q13009, Q3U1V8, Q3U214, Q3UHC7, Q4VAC9, Q5DU25, Q5JU85, Q5RBI7, Q5SXA9, Q5VWQ8, Q60610, Q64512, Q6AX33, Q6DN90, Q6NXJ0, Q6P0Q8, Q6P1I6, Q6ZMN7, Q76G19, Q76LL6, Q76M68, Q7T2V3, Q810W7, Q8CGE9, Q8IX03, Q8R0S2, Q8R4H2, Q8WYP3

Diamond homologs: A1L390, F1M0Z1, O43307, O75962, P91620, P91621, Q0KL02, Q13009, Q1ZXH8, Q3UTH8, Q4VAC9, Q58DL7, Q58EX7, Q5DU57, Q5RDK0, Q60610, Q6KAU7, Q6P720, Q6ZPF3, Q7TNR9, Q96N96, Q9H7P9, Q9NR80, Q9QX73, Q9ULL1, A0JNJ1, A4RF61, A6H8I2, A6NI72, A8MVU1, O15068, O43125, O75886, O89100, O93436, P07751, P10569, P14598, P16086, P16546

SIGNOR signaling

1 interactions.

AEffectBMechanism
PLEKHG3“up-regulates activity”CDC42“guanine nucleotide exchange factor”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 86 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
Activation of BAD and translocation to mitochondria796.9×6e-11
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex673.3×8e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways673.3×8e-09
Activation of BH3-only proteins763.2×1e-09
RHO GTPases activate PAKs549.4×1e-06
RHO GTPases activate PKNs846.1×8e-10
Intrinsic Pathway for Apoptosis737.3×3e-08
FOXO-mediated transcription530.5×1e-05

GO biological processes:

GO termPartnersFoldFDR
substantia nigra development527.8×3e-04
actin filament organization610.8×2e-03
intracellular protein localization69.5×3e-03
actin cytoskeleton organization78.4×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance242
Likely benign37
Benign11

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3772398NM_001355436.2(SPTB):c.6640G>T (p.Glu2214Ter)Pathogenic

SpliceAI

3971 predictions. Top by Δscore:

VariantEffectΔscore
14:64704700:GCTCG:Gdonor_gain1.0000
14:64704701:CTCGG:Cdonor_loss1.0000
14:64704703:CGGT:Cdonor_loss1.0000
14:64704705:G:GGdonor_gain1.0000
14:64727592:GA:Gacceptor_gain1.0000
14:64727592:GAAT:Gacceptor_gain1.0000
14:64727981:AGG:Adonor_loss1.0000
14:64727983:G:GAdonor_loss1.0000
14:64728992:GCAG:Gacceptor_loss1.0000
14:64728993:CAGG:Cacceptor_loss1.0000
14:64730689:G:GGdonor_gain1.0000
14:64730794:CCCAG:Cacceptor_loss1.0000
14:64730796:CA:Cacceptor_loss1.0000
14:64730797:A:AGacceptor_gain1.0000
14:64730797:AGCTC:Aacceptor_loss1.0000
14:64730798:G:GTacceptor_gain1.0000
14:64730798:GC:Gacceptor_gain1.0000
14:64730798:GCT:Gacceptor_gain1.0000
14:64730798:GCTCC:Gacceptor_gain1.0000
14:64730931:G:GGdonor_gain1.0000
14:64730946:CCAG:Cdonor_loss1.0000
14:64730947:CAGGT:Cdonor_loss1.0000
14:64730948:AG:Adonor_loss1.0000
14:64730949:GGTAG:Gdonor_loss1.0000
14:64730951:T:Adonor_loss1.0000
14:64731031:T:Aacceptor_gain1.0000
14:64731033:C:CAacceptor_gain1.0000
14:64731036:A:AGacceptor_gain1.0000
14:64731036:AG:Aacceptor_gain1.0000
14:64731037:G:Aacceptor_loss1.0000

AlphaMissense

8007 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:64727945:A:TE105V1.000
14:64727966:T:CL112P1.000
14:64730260:T:CL156P1.000
14:64730293:C:AA167D1.000
14:64730302:T:CF170S1.000
14:64730903:T:CL224P1.000
14:64730906:T:CL225P1.000
14:64730912:C:AP227Q1.000
14:64730912:C:GP227R1.000
14:64730915:T:AV228D1.000
14:64730919:G:CQ229H1.000
14:64730919:G:TQ229H1.000
14:64730920:C:AR230S1.000
14:64730921:G:CR230P1.000
14:64730927:T:AL232H1.000
14:64730927:T:CL232P1.000
14:64730929:A:GK233E1.000
14:64730931:G:CK233N1.000
14:64730931:G:TK233N1.000
14:64730939:T:CL236P1.000
14:64730942:T:CL237P1.000
14:64730945:T:CL238P1.000
14:64731117:C:AA266D1.000
14:64732122:T:AW385R1.000
14:64732122:T:CW385R1.000
14:64727942:C:TT104I0.999
14:64727946:G:CE105D0.999
14:64727946:G:TE105D0.999
14:64727953:T:CY108H0.999
14:64727953:T:GY108D0.999

dbSNP variants (sampled 300 via entrez): RS1000015681 (14:64748658 C>T), RS1000035216 (14:64748857 C>A), RS1000145896 (14:64716176 C>G,T), RS1000223451 (14:64708214 C>T), RS1000253433 (14:64730556 C>A,G,T), RS1000286042 (14:64743820 G>T), RS1000334298 (14:64736503 C>G), RS1000423511 (14:64710547 C>T), RS1000481054 (14:64709996 G>T), RS1000574577 (14:64727937 G>T), RS1000590554 (14:64719659 G>A,T), RS1000630108 (14:64734264 G>A,T), RS1000680328 (14:64707907 G>A), RS1000764241 (14:64714005 A>T), RS1000807104 (14:64722095 G>A,T)

Disease associations

OMIM: gene MIM:617940 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): familial hemolytic anemia (MONDO:0003689)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST003518_66Daytime sleep phenotypes4.000000e-06
GCST009462_79Optic disc size3.000000e-16
GCST009723_89Vertical cup-disc ratio (adjusted for vertical disc diameter)2.000000e-07
GCST009724_58Vertical cup-disc ratio (multi-trait analysis)5.000000e-11
GCST90002397_351Mean spheric corpuscular volume4.000000e-14
GCST90002401_74Platelet distribution width4.000000e-11

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007828daytime rest measurement
EFO:0006939cup-to-disc ratio measurement
EFO:0007984platelet component distribution width

MeSH disease descriptors (1)

DescriptorNameTree numbers
D000745Anemia, Hemolytic, CongenitalC15.378.050.141.150; C16.320.070

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066528 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.50Kd0.315nMCHEMBL3752910
8.26ED505.534nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149913: Binding affinity to human PLEKHG3 incubated for 45 mins by Kinobead based pull down assaykd0.0003uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Arsenicaffects expression, affects methylation, affects cotreatment, decreases expression, increases abundance3
sodium arseniteaffects cotreatment, increases abundance, decreases expression2
Benzo(a)pyrenedecreases methylation, affects methylation, decreases expression2
Estradiolincreases reaction, affects cotreatment, increases expression, affects binding2
Smokedecreases expression2
aristolochic acid Iincreases expression1
GSK-J4decreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Aincreases methylation1
trichostatin Aaffects expression1
beta-lapachoneincreases expression1
coumarinaffects phosphorylation1
muconaldehydedecreases expression1
beta-methylcholineaffects expression1
avobenzoneincreases expression1
polyhexamethyleneguanidineaffects expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
abrineincreases expression1
NSC 689534affects binding, decreases expression1
(+)-JQ1 compounddecreases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Arsenic Trioxidedecreases response to substance1
Acetaminophendecreases expression1
Ethanolaffects cotreatment, increases abundance, increases expression1
Caffeineaffects phosphorylation1
Copperaffects binding, decreases expression1
Cytarabinedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652955BindingBinding affinity to human PLEKHG3 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00061568PHASE1/PHASE2UNKNOWNImproving the Results of Bone Marrow Transplantation for Patients With Severe Congenital Anemias
NCT04902833Not specifiedCOMPLETEDAcquired Pyruvate Kinase Deficiency In Clonal Myeloid Neoplasms
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): familial hemolytic anemia