ARF6

Summary

ARF6 (ARF GTPase 6, HGNC:659) is a protein-coding gene on chromosome 14q21.3, encoding ADP-ribosylation factor 6 (P62330). GTP-binding protein involved in protein trafficking that regulates endocytic recycling and cytoskeleton remodeling. It is a selective cancer dependency (DepMap: 22.0% of cell lines).

This gene encodes a member of the human ARF gene family, which is part of the RAS superfamily. The ARF genes encode small guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin and play a role in vesicular trafficking and as activators of phospholipase D. The product of this gene is localized to the plasma membrane, and regulates vesicular trafficking, remodelling of membrane lipids, and signaling pathways that lead to actin remodeling. A pseudogene of this gene is located on chromosome 7.

Source: NCBI Gene 382 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 8 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 22.0% of screened cell lines
• MANE Select transcript: NM_001663

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:659
Approved symbol	ARF6
Name	ARF GTPase 6
Location	14q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000165527
Ensembl biotype	protein_coding
OMIM	600464
Entrez	382

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000298316, ENST00000692608, ENST00000693319, ENST00000895811, ENST00000895812

RefSeq mRNA: 1 — MANE Select: NM_001663 NM_001663

CCDS: CCDS9695

Canonical transcript exons

ENST00000298316 — 2 exons

Exon	Start	End
ENSE00001093803	49893256	49897054
ENSE00001093805	49893082	49893157

Expression profiles

Bgee: expression breadth ubiquitous, 296 present calls, max score 99.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 75.5754 / max 651.2898, expressed in 1824 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
139458	46.7387	1823
139466	15.4555	1776
139456	4.4949	1567
139461	2.1253	930
139457	1.8480	1082
139467	1.0490	534
139464	0.9787	554
139465	0.6465	383
139463	0.5683	269
139460	0.4726	247

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
esophagus squamous epithelium	UBERON:0006920	99.60	gold quality
epithelium of esophagus	UBERON:0001976	99.25	gold quality
gingiva	UBERON:0001828	99.24	gold quality
gingival epithelium	UBERON:0001949	99.24	gold quality
oral cavity	UBERON:0000167	99.22	gold quality
amniotic fluid	UBERON:0000173	99.01	gold quality
buccal mucosa cell	CL:0002336	98.98	gold quality
penis	UBERON:0000989	98.97	gold quality
mammalian vulva	UBERON:0000997	98.79	gold quality
squamous epithelium	UBERON:0006914	98.79	gold quality
germinal epithelium of ovary	UBERON:0001304	98.76	gold quality
trabecular bone tissue	UBERON:0002483	98.75	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.74	gold quality
parietal pleura	UBERON:0002400	98.71	gold quality
epithelium of nasopharynx	UBERON:0001951	98.70	gold quality
nasopharynx	UBERON:0001728	98.68	gold quality
visceral pleura	UBERON:0002401	98.67	gold quality
upper leg skin	UBERON:0004262	98.67	gold quality
colonic mucosa	UBERON:0000317	98.64	gold quality
palpebral conjunctiva	UBERON:0001812	98.60	gold quality
skin of hip	UBERON:0001554	98.52	gold quality
pharyngeal mucosa	UBERON:0000355	98.45	gold quality
pleura	UBERON:0000977	98.40	gold quality
jejunal mucosa	UBERON:0000399	98.35	gold quality
mammary duct	UBERON:0001765	97.88	gold quality
tibia	UBERON:0000979	97.82	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.82	gold quality
synovial joint	UBERON:0002217	97.64	gold quality
lower lobe of lung	UBERON:0008949	97.60	gold quality
ileal mucosa	UBERON:0000331	97.59	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	101.02
E-GEOD-135922	yes	10.02
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1

miRNA regulators (miRDB)

170 targeting ARF6, 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-4262	100.00	73.26	3931
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-340-5P	100.00	72.50	4437
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-607	99.97	73.62	5593

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 22.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• We conclude that the ARF6-mediated mechanism to release a pool of membrane-delimited arrestin to bind GPCRs may be a widespread mechanism to deliver arrestin to GPCRs for receptor desensitization. (PMID:11867621)
• endogenous ARF6 redistributes during mitosis and concentrates near the cleavage furrow during telophase (PMID:12016212)
• A tubular EHD1-containing compartment involved in the recycling of major histocompatibility complex class I molecules to the plasma membrane (PMID:12032069)
• ARF6 is a part of the pathway affected by PACS-1 and HIV-1 nef as HIV-1 escapes immune surveillance (PMID:12526811)
• ARF6 has a role in phospholipase D activation by the M3 muscarinic receptor (PMID:12799371)
• Localization of the GTP-bound form of ARF6 at the plasma membrane makes it a candidate marker for the identification of anergic T cells; T cells with distinct membrane localization of ARF6 are detected in peripheral blood of healthy individuals. (PMID:12902467)
• Arf6 has roles in epithelial cell adhesion and migration, and also in cancer cell invasion (review) (PMID:14607973)
• ARF6 activity is regulated by centaurin-alpha1 (PMID:14625293)
• ARF6 gene is expressed in all tissues; although higher levels of expression were observed in heart, substantia nigra, and kidney. ARF6 gene (class III) structure is quite distinct from the class I and class II ARF genes. (PMID:14659046)
• Data show that stimulation-dependent recycling of integrin beta1 is regulated by ARF6 and Rab11, and also requires the actin cytoskeleton in an ARF6-dependent manner. (PMID:14675422)
• appears to be an integral component of breast cancer invasive activities (PMID:15087504)
• role for ARF6 in melanoma cell invasion and a link between ARF6-mediated signaling and ERK activation (PMID:15210957)
• role of AMAP2 in cellular function of GTP-Arf6 (PMID:15231847)
• ADP-ribosylation factor 6 (ARF6) is essential for the endocytosis of a broad variety of G protein coupled receptors (PMID:15590645)
• Arf6 plays a major role in clathrin-mediated endocytosis by directly controlling the assembly of the AP-2/clathrin coat (PMID:15802264)
• Arf6 plays a crucial role in the generation of a phosphatidylinositol4,5-bisphosphate (PIP2) plasma membrane pool required for cytolytic granule-mediated target cell killing. (PMID:15817676)
• ARF6 activation was necessary for extensive actin reorganization at the bacteria invasion sites. (PMID:15897187)
• Crystal structures of a cholera toxin A1 subunit (CTA1):ARF6-GTP (guanosine triphosphate) complex reveal that binding of the human activator elicits dramatic changes in CTA1 subunit loop regions that allow NAD+ to bind to the active site (PMID:16099990)
• ARNO and ARF6 coordinate with the Dock180/Elmo complex to promote Rac activation at the leading edge of migrating cells. (PMID:16213822)
• Arf6 regulates both endocytosis and recycling of beta1 integrins and BRAG2 functions selectively to activate Arf6 during integrin internalization. (PMID:16461286)
• The transport and regulation of ARNO in polartized epithelial cells, and its interactions with ARF6 in endocytosis are reported. (PMID:16484220)
• the Arf6 GDP/GTP cycle and Arf6 GTPase-activating proteins have roles in actin remodeling and intracellular transport (PMID:16527809)
• N376 to D mutation in the conserved NPxxY motif within the carboxy terminal tail domain (CT) of the 5-HT2A receptor alters the binding preference of GST-fusion protein constructs of the CT domain from ARF1 to an alternative isoform, ARF6. (PMID:16545942)
• A phosphatidylinositol-3-kinase-dependent signal transition defines the sequence of ARF6 activation during phagocytosis. (PMID:16669702)
• ACAP4 is involved in ARF6-mediated cell migration. (PMID:16737952)
• ARAP2 is an Arf6GAP that functions downstream of RhoA to regulate focal adhesion dynamics. (PMID:17077126)
• These results suggest that ARF6 depletion or Ang II treatment are functionally equivalent and point to a role for endogenous ARF6 as an inhibitor of Rac1 activity. (PMID:17122362)
• Rab 11 and Arf6 function synergistically in the switch from furrowing to abscission, as well as in the terminal stage of abscission. (PMID:17157409)
• BRAG2 is a guanine nucleotide exchange factor for the GTPase Arf6 that cycles between the cytoplasm and the nucleus. Its nuclear functions are now described. (PMID:17461797)
• ARF6 and ELMO, two proteins known to couple ARNO to the cytoskeleton, were required for calcium-sensing receptor -dependent morphological changes and translocated to the plasma membrane ruffles (PMID:17623778)
• FIP3 is a scaffolding protein that, in addition to regulating endosome targeting to the cleavage furrow, also is required for Arf6 recruitment to the midbody during late telophase. (PMID:17628206)
• ARF6 recruits KALRN to the cell membrane facilitating Rac activation. (PMID:17640372)
• These results suggest that the cycling of ARF6 between its GDP-and GTP-bound states coordinates the recruitment of AP-2 and clathrin to activated receptors during the endocytic process. (PMID:17719203)
• Mutations in ARF6 is not associated with familial hemophagocytic lymphohistiocytosis (PMID:18000860)
• Results indicate that GEP100 links EGFR signalling to Arf6 activation to induce invasive activities of some breast cancer cells, and hence may contribute to their metastasis and malignancy. (PMID:18084281)
• Fbx8, an F-box protein bearing the Sec7 domain, mediates ubiquitination of Arf6. (PMID:18094045)
• This study demonstrates that the nucleotide state of Arf6 in platelets is regulated during the initial phases of activation and during the later stages of aggregation. (PMID:18326492)
• Arf1 and Arf6 were shown to load GTP in a membrane-curvature-dependent manner and stabilize, or further facilitate, changes in membrane curvature through the insertion of an amphipathic helix. (PMID:18597672)
• ARF6 is central in regulating focal adhesion turnover in endothelial cells and depletion of ARF6 impairs the ability of GIT1 protein to form an agonist promoted complex with Focal Adhesion Kinase, thereby preventing disassembly of focal adhesions. (PMID:18814847)
• These studies indicate a role for AP-2 in maintaining normal post-endocytic trafficking through the Arf6-regulated, non-clathrin pathway, and reveal pervasive effects of clathrin and AP-2 depletion on the endosomal and lysosomal system. (PMID:19033387)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	arf6a	ENSDARG00000101626
mus_musculus	Arf6	ENSMUSG00000044147
rattus_norvegicus	Arf6	ENSRNOG00000070951
drosophila_melanogaster	Arf6	FBGN0013750

Paralogs (30): ARF5 (ENSG00000004059), SAR1A (ENSG00000079332), ARFRP1 (ENSG00000101246), TRIM23 (ENSG00000113595), ARL6 (ENSG00000113966), ARL1 (ENSG00000120805), ARL4A (ENSG00000122644), ARL8B (ENSG00000134108), ARF3 (ENSG00000134287), ARL3 (ENSG00000138175), ARL5C (ENSG00000141748), ARF1 (ENSG00000143761), ARL8A (ENSG00000143862), ARL11 (ENSG00000152213), SAR1B (ENSG00000152700), ARL5A (ENSG00000162980), ARL5B (ENSG00000165997), ARF4 (ENSG00000168374), ARL13B (ENSG00000169379), ARL13A (ENSG00000174225), ARL10 (ENSG00000175414), ARL4D (ENSG00000175906), ARL14 (ENSG00000179674), ARL15 (ENSG00000185305), ARL17A (ENSG00000185829), ARL4C (ENSG00000188042), ARL9 (ENSG00000196503), ARL2 (ENSG00000213465), ARL16 (ENSG00000214087), ARL17B (ENSG00000228696)

Protein

Protein identifiers

ADP-ribosylation factor 6 — P62330 (reviewed: P62330)

All UniProt accessions (2): A0A8I5QJX7, P62330

UniProt curated annotations — full annotation on UniProt →

Function. GTP-binding protein involved in protein trafficking that regulates endocytic recycling and cytoskeleton remodeling. GTP-bound form plays an important role in the transport of multiple palmitoylated proteins form the Golgi to the plasma membrane. Required for normal completion of mitotic cytokinesis. Plays a role in the reorganization of the actin cytoskeleton and the formation of stress fibers. Involved in the regulation of dendritic spine development, contributing to the regulation of dendritic branching and filopodia extension. Potentiates the neurite outgrowth in primary neurons by interacting with the molecular adapter APBB1. Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization. Regulates surface levels of adherens junction proteins such as CDH1. Required for NTRK1 sorting to the recycling pathway from early endosomes. (Microbial infection) Functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP-ribosyltransferase. (Microbial infection) Plays a key role in the endocytosis of enterovirus 71 and thus viral entry into brain microvascular endothelial cells.

Subunit / interactions. Interacts (when activated) with GGA1, GGA2 and GGA3; the interaction is required for proper subcellular location of GGA1, GGA2 and GGA3. Interacts with PIP5K1C. Interacts with USP6 (via Rab-GAP TBC domain). Interacts with RAB11FIP3 and RAB11FIP4. Interacts with HERC1. Interacts with ARHGAP21. Interacts with ASAP3; the interaction is stabilized by calcium ions. Interacts with NCS1/FREQ at the plasma membrane. Interacts with TBC1D24. Interacts with ECPAS. Interacts with MICALL1. Interacts with SPAG9 homodimers, forming heterotetramers. Interacts with CYTH3. Interacts with ASAP2. Interacts with UACA. Interacts with KIF23, forming heterodimers and heterotetramers. Interacts with C9orf72. Interacts (GTP-bound form) with TJAP1/PILT. Interacts with PRKAA2. Interacts with CD36 (when palmitoylated); this interaction mediates CD36 transport from the Golgi to the plasma membrane. Interacts with APBB1. (Microbial infection) Interacts with the V.cholerae enterotoxin subunit A1; this causes a conformation change so that the toxin can bind NAD and catalyze the ADP-ribosylation of Gs alpha. (Microbial infection) Interacts with EspG from enteropathogenic E.coli. (Microbial infection) Identified in a complex with RAB1A and EspG from enteropathogenic E.coli. (Microbial infection) Interacts with human enterovirus 71 protein VP1.

Subcellular location. Cytoplasm. Cytosol. Cell membrane. Endosome membrane. Recycling endosome membrane. Cell projection. Filopodium membrane. Ruffle. Cleavage furrow. Midbody. Midbody ring. Early endosome membrane. Golgi apparatus. trans-Golgi network membrane.

Tissue specificity. Ubiquitous, with higher levels in heart, substantia nigra, and kidney.

Post-translational modifications. GTP-bound form is myristoylated on Lys-3 by NMT1 and NMT2, allowing ARF6 to remain on membranes during the GTPase cycle, thereby promoting its activity. GDP-bound inactive form is demyristoylated on Lys-3 by SIRT2 at early endosomes or endocytic recycling compartment to allow its efficient activation by a guanine exchange factor (GEF) after GDP release.

Activity regulation. Activation is generally mediated by a guanine exchange factor (GEF), while inactivation through hydrolysis of bound GTP is catalyzed by a GTPase activating protein (GAP). Activated by ASAP3. Inactivated by ACAP1 and ACAP2. Activated by NGF via NTRK1. Activated by PRKAA2 through its C-terminal regulatory domain.

Similarity. Belongs to the small GTPase superfamily. Arf family.

RefSeq proteins (1): NP_001654* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005225	Small_GTP-bd	Domain
IPR006689	Small_GTPase_ARF/SAR	Family
IPR024156	Small_GTPase_ARF	Family
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR041838	Arf6	Family

Pfam: PF00025

Enzyme classification (BRENDA):

• EC 3.6.5.2 — small monomeric GTPase (BRENDA: 49 organisms, 138 substrates, 55 inhibitors, 5 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
GTP	—	0

Catalyzed reactions (Rhea), 1 shown:

• GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (33 total): helix 10, strand 8, binding site 5, mutagenesis site 4, turn 2, lipid moiety-binding region 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

20 structures.

PDB	Method	Resolution (Å)
2A5D	X-RAY DIFFRACTION	1.8
3N5C	X-RAY DIFFRACTION	1.82
4KAX	X-RAY DIFFRACTION	1.85
2W83	X-RAY DIFFRACTION	1.93
6PAU	X-RAY DIFFRACTION	1.93
2A5F	X-RAY DIFFRACTION	2.02
7RK3	X-RAY DIFFRACTION	2.05
1E0S	X-RAY DIFFRACTION	2.28
3PCR	X-RAY DIFFRACTION	2.5
6PAV	X-RAY DIFFRACTION	2.52
2A5G	X-RAY DIFFRACTION	2.66
2J5X	X-RAY DIFFRACTION	2.8
3LVQ	X-RAY DIFFRACTION	3.38
3LVR	X-RAY DIFFRACTION	3.38
7XRD	ELECTRON MICROSCOPY	3.9
4FME	X-RAY DIFFRACTION	4.1
6BBP	ELECTRON MICROSCOPY	35
6BBQ	ELECTRON MICROSCOPY	35
2BAO	SOLUTION NMR
2BAU	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62330-F1	94.24	0.88

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 (5): 23–28; 41–44; 63–67; 122–125; 155–156

Post-translational modifications (2): 2, 3

Mutagenesis-validated functional residues (4):

Position	Phenotype
3	abolished lysine-myristoylation, leading to decreased localization to membranes.
27	constitutively inactivated. fails to associate with membranes. does not inhibit filopodia formation.
67	constitutively active. inhibits filopodia formation and dendritic branching.
2	fails to associate with membranes.

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-8854214	TBC/RABGAPs
R-HSA-8856828	Clathrin-mediated endocytosis
R-HSA-8875656	MET receptor recycling
R-HSA-162582	Signal Transduction
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6806834	Signaling by MET
R-HSA-9006934	Signaling by Receptor Tyrosine Kinases
R-HSA-9007101	Rab regulation of trafficking

MSigDB gene sets: 540 (showing top): GOBP_MITOTIC_CYTOKINESIS, GOBP_DENDRITE_DEVELOPMENT, FXR_IR1_Q6, GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, HORIUCHI_WTAP_TARGETS_DN, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, TAATAAT_MIR126, WWTAAGGC_UNKNOWN, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, PAX4_01, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_SYNAPSE_ASSEMBLY, RORA1_01, GOBP_ESTABLISHMENT_OF_EPITHELIAL_CELL_POLARITY

GO Biological Process (39): liver development (GO:0001889), intracellular protein transport (GO:0006886), cell adhesion (GO:0007155), nervous system development (GO:0007399), positive regulation of neuron projection development (GO:0010976), vesicle-mediated transport (GO:0016192), cell differentiation (GO:0030154), positive regulation of actin filament polymerization (GO:0030838), cortical actin cytoskeleton organization (GO:0030866), endocytic recycling (GO:0032456), protein localization to cell surface (GO:0034394), regulation of Rac protein signal transduction (GO:0035020), protein localization to endosome (GO:0036010), negative regulation of receptor-mediated endocytosis (GO:0048261), synaptic vesicle endocytosis (GO:0048488), positive regulation of protein secretion (GO:0050714), cell division (GO:0051301), regulation of filopodium assembly (GO:0051489), positive regulation of keratinocyte migration (GO:0051549), regulation of dendritic spine development (GO:0060998), protein localization to plasma membrane (GO:0072659), establishment of epithelial cell polarity (GO:0090162), ruffle assembly (GO:0097178), hepatocyte apoptotic process (GO:0097284), maintenance of postsynaptic density structure (GO:0099562), positive regulation of focal adhesion disassembly (GO:0120183), erythrocyte apoptotic process (GO:1902217), positive regulation of protein localization to plasma membrane (GO:1903078), positive regulation of mitotic cytokinetic process (GO:1903438), protein localization to cleavage furrow (GO:1905345), regulation of presynapse assembly (GO:1905606), cellular response to nerve growth factor stimulus (GO:1990090), negative regulation of protein localization to cell surface (GO:2000009), negative regulation of dendrite development (GO:2000171), mitotic cytokinesis (GO:0000281), obsolete vesicle docking involved in exocytosis (GO:0006904), regulation of neuron projection development (GO:0010975), protein transport (GO:0015031), cellular response to diacyl bacterial lipopeptide (GO:0071726)

GO Molecular Function (9): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), GDP binding (GO:0019003), thioesterase binding (GO:0031996), signaling adaptor activity (GO:0035591), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (24): ruffle (GO:0001726), cytoplasm (GO:0005737), endosome (GO:0005768), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), focal adhesion (GO:0005925), cell cortex (GO:0005938), membrane (GO:0016020), endocytic vesicle (GO:0030139), midbody (GO:0030496), filopodium membrane (GO:0031527), early endosome membrane (GO:0031901), cleavage furrow (GO:0032154), recycling endosome membrane (GO:0055038), extracellular exosome (GO:0070062), Flemming body (GO:0090543), presynapse (GO:0098793), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), early endosome (GO:0005769), endosome membrane (GO:0010008), cell projection (GO:0042995), recycling endosome (GO:0055037)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Membrane Trafficking	2
Rab regulation of trafficking	1
Signaling by MET	1
Vesicle-mediated transport	1
Signaling by Receptor Tyrosine Kinases	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	7
cellular process	3
cytoplasm	3
synapse	3
intracellular protein localization	2
guanyl ribonucleotide binding	2
endomembrane system	2
cytoplasmic vesicle	2
cell periphery	2
endosome membrane	2
gland development	1
hepaticobiliary system development	1
protein transport	1
intracellular transport	1
system development	1
regulation of neuron projection development	1
neuron projection development	1
positive regulation of cell projection organization	1
transport	1
cellular developmental process	1
actin filament polymerization	1
regulation of actin filament polymerization	1
positive regulation of protein polymerization	1
positive regulation of cytoskeleton organization	1
positive regulation of supramolecular fiber organization	1
actin cytoskeleton organization	1
cortical cytoskeleton organization	1
endosomal transport	1
vesicle-mediated transport to the plasma membrane	1
Rac protein signal transduction	1
regulation of small GTPase mediated signal transduction	1
protein localization to organelle	1
receptor-mediated endocytosis	1
negative regulation of endocytosis	1
regulation of receptor-mediated endocytosis	1
synaptic vesicle recycling	1
presynaptic endocytosis	1
protein secretion	1
regulation of protein secretion	1
positive regulation of protein transport	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

259 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
ARF6	rep	psi-mi:“MI:0915”(physical association)	0.660
YAF2	E2F6	psi-mi:“MI:0914”(association)	0.640
APBB1	ARF6	psi-mi:“MI:0915”(physical association)	0.630
ARF6	APBB1	psi-mi:“MI:0915”(physical association)	0.630
APBB1	ARF6	psi-mi:“MI:0407”(direct interaction)	0.630
ARF6	CYTH3	psi-mi:“MI:0407”(direct interaction)	0.620
ARF6	CYTH3	psi-mi:“MI:2252”(guanine nucleotide exchange factor reaction)	0.620
GGA3	ARF6	psi-mi:“MI:0915”(physical association)	0.590
ARF6	GGA3	psi-mi:“MI:0915”(physical association)	0.590
MYADM	ARF6	psi-mi:“MI:0915”(physical association)	0.560
ARF6	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
EGFR	ARF6	psi-mi:“MI:0915”(physical association)	0.550
ARF6	EGFR	psi-mi:“MI:0915”(physical association)	0.550
SNRNP27	UBA6	psi-mi:“MI:0914”(association)	0.530
THTPA	RTL8C	psi-mi:“MI:0914”(association)	0.530
TBC1D22B	A2ML1	psi-mi:“MI:0914”(association)	0.530

BioGRID (714): ARF6 (Reconstituted Complex), ARF6 (Two-hybrid), ARF6 (Affinity Capture-Western), ARF6 (Affinity Capture-MS), ARF6 (Affinity Capture-MS), ARF6 (Co-fractionation), TBCE (Co-fractionation), ARF6 (Reconstituted Complex), ARF6 (Reconstituted Complex), ARF6 (Two-hybrid), ARF6 (Affinity Capture-Western), ARF6 (Biochemical Activity), ARF6 (Co-fractionation), ARF6 (Affinity Capture-MS), ARF6 (Affinity Capture-MS)

ESM2 similar proteins: O48920, P0CM16, P0CM17, P0DH91, P18085, P19146, P22274, P26990, P34727, P36397, P40945, P40946, P49076, P51643, P51644, P51645, P51821, P51822, P51823, P61204, P61205, P61206, P61207, P61209, P61210, P62330, P62331, P62332, P84077, P84078, P84079, P84080, P84081, P84082, P91924, Q007T5, Q06396, Q10943, Q25761, Q3SZF2

Diamond homologs: A6NH57, B5FYQ0, O00909, O23778, O48649, O48920, P0CM16, P0CM17, P0DH91, P11076, P18085, P19146, P22274, P25160, P26990, P26991, P34212, P34727, P36397, P36405, P36406, P36407, P36579, P37996, P38116, P40616, P40940, P40945, P40946, P40994, P49076, P49702, P51643, P51644, P51645, P51646, P51821, P51822, P51823, P51824

SIGNOR signaling

12 interactions.

A	Effect	B	Mechanism
USP6	up-regulates	ARF6	relocalization
GIT1	“up-regulates activity”	ARF6	“guanine nucleotide exchange factor”
ARF6	up-regulates	“Macropinosomes recycle”
IQSEC2	“up-regulates activity”	ARF6	“guanine nucleotide exchange factor”
ARF6	up-regulates	Neurite_outgrowth
CYTH2	“up-regulates activity”	ARF6	“guanine nucleotide exchange factor”
ARF6	“up-regulates activity”	PIP4K2A
ASAP2	“up-regulates activity”	ARF6	“gtpase-activating protein”
FBXO8	“down-regulates quantity by destabilization”	ARF6	binding
“Cullin 1-RBX1-Skp1”	“down-regulates quantity by destabilization”	ARF6
ARF6	up-regulates	Vesicle_transport
ARF6	up-regulates	Endocytosis

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 168 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
Interleukin-12 family signaling	5	18.6×	6e-04
Regulation of CDH1 posttranslational processing and trafficking to plasma membrane	6	15.7×	3e-04
Maturation of spike protein	5	10.4×	3e-03
Maturation of DENV proteins	6	9.9×	2e-03
Regulation of RAS by GAPs	6	9.1×	2e-03
Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha	5	7.7×	8e-03
Translation initiation complex formation	5	7.4×	8e-03
Ribosomal scanning and start codon recognition	5	7.4×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
regulation of ARF protein signal transduction	5	28.4×	7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

79 predictions. Top by Δscore:

Variant	Effect	Δscore
14:49893155:G:GT	donor_gain	0.9800
14:49893153:TGGAG:T	donor_loss	0.9100
14:49893154:GGAG:G	donor_loss	0.9100
14:49893156:AGG:A	donor_loss	0.9100
14:49893157:GG:G	donor_loss	0.9100
14:49893158:GTAA:G	donor_loss	0.9100
14:49893159:T:G	donor_loss	0.9100
14:49893129:G:GT	donor_gain	0.8900
14:49893251:TGCA:T	acceptor_loss	0.8900
14:49893252:GCA:G	acceptor_loss	0.8900
14:49893255:G:C	acceptor_loss	0.8900
14:49893255:GGCA:G	acceptor_gain	0.8900
14:49893160:A:C	donor_loss	0.8800
14:49893254:A:AG	acceptor_gain	0.8500
14:49893255:G:GG	acceptor_gain	0.8500
14:49893243:T:TA	acceptor_loss	0.8400
14:49893255:GGC:G	acceptor_gain	0.8300
14:49893152:CTGGA:C	donor_loss	0.7700
14:49893110:G:GT	donor_gain	0.7500
14:49893254:AG:A	acceptor_gain	0.7500
14:49893255:GG:G	acceptor_gain	0.7500
14:49893251:TGCAG:T	acceptor_gain	0.7400
14:49893252:GCAGG:G	acceptor_gain	0.7400
14:49893253:CAGGC:C	acceptor_gain	0.7400
14:49893254:AGGCA:A	acceptor_gain	0.7400
14:49893255:GGCAG:G	acceptor_gain	0.7400
14:49893251:T:TA	acceptor_gain	0.6800
14:49893224:A:AG	donor_gain	0.5600
14:49893225:G:GG	donor_gain	0.5600
14:49893250:CTGCA:C	acceptor_gain	0.5500

AlphaMissense

1145 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:49893794:G:C	G20R	1.000
14:49893809:G:C	G25R	1.000
14:49893810:G:A	G25D	1.000
14:49893810:G:T	G25V	1.000
14:49893812:A:C	K26Q	1.000
14:49893813:A:T	K26M	1.000
14:49893814:G:C	K26N	1.000
14:49893814:G:T	K26N	1.000
14:49893816:C:T	T27I	1.000
14:49893872:G:C	G46R	1.000
14:49893873:G:A	G46D	1.000
14:49893875:T:C	F47L	1.000
14:49893876:T:C	F47S	1.000
14:49893877:C:A	F47L	1.000
14:49893877:C:G	F47L	1.000
14:49893920:T:A	W62R	1.000
14:49893920:T:C	W62R	1.000
14:49893922:G:C	W62C	1.000
14:49893922:G:T	W62C	1.000
14:49893923:G:C	D63H	1.000
14:49893924:A:C	D63A	1.000
14:49893924:A:T	D63V	1.000
14:49893929:G:C	G65R	1.000
14:49893930:G:A	G65D	1.000
14:49893932:G:C	G66R	1.000
14:49893933:G:A	G66D	1.000
14:49893956:T:A	W74R	1.000
14:49893956:T:C	W74R	1.000
14:49893958:G:C	W74C	1.000
14:49893958:G:T	W74C	1.000

dbSNP variants (sampled 300 via entrez): RS1000010581 (14:49895287 T>C), RS1000557537 (14:49892643 T>G), RS1000920801 (14:49891491 G>C), RS1001431881 (14:49891772 C>A), RS1001473822 (14:49895892 T>C), RS1001821249 (14:49896166 C>T), RS1002035019 (14:49892848 C>G), RS1002320565 (14:49892682 A>G), RS1002420982 (14:49894716 C>T), RS1002975803 (14:49892259 T>C), RS1003874953 (14:49894381 AGTTACT>A), RS1004826188 (14:49893415 C>G,T), RS1004878622 (14:49893193 C>T), RS1004994871 (14:49893165 C>G,T), RS1005026477 (14:49893404 A>C,G)

Disease associations

OMIM: gene MIM:600464 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002380_4	Erythema nodosum in inflammatory bowel disease	7.000000e-06
GCST012145_13	Ferritin levels	1.000000e-05

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004459	ferritin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5987 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — RAS subfamily

Most potent curated ligand interactions (1 total), top 1:

Ligand	Action	Affinity	Parameter
NAV2729	Inhibition	6.0	pIC50

Binding affinities (BindingDB)

2 measured of 2 human assays (2 total across all organisms); most potent 2 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
3-(4-chlorophenyl)-5-(4-nitrophenyl)-2-(1-phenylethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.4 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-(1-phenylethyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	2.3 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof

ChEMBL bioactivities

31 potent at pChembl≥5 of 38 total, top 31 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.00	IC50	1000	nM	CHEMBL5082039
5.85	IC50	1400	nM	CHEMBL5081334
5.80	IC50	1600	nM	CHEMBL5086155
5.72	IC50	1900	nM	CHEMBL5087149
5.72	IC50	1900	nM	CHEMBL5085035
5.72	IC50	1900	nM	CHEMBL5083555
5.72	IC50	1900	nM	CHEMBL5076054
5.70	IC50	2000	nM	CHEMBL5091538
5.64	IC50	2300	nM	CHEMBL5075447
5.62	IC50	2400	nM	CHEMBL5072181
5.62	IC50	2400	nM	CHEMBL5093546
5.58	IC50	2600	nM	CHEMBL5079647
5.57	IC50	2700	nM	CHEMBL5079718
5.55	IC50	2800	nM	CHEMBL5075101
5.54	IC50	2900	nM	CHEMBL5088506
5.50	IC50	3200	nM	CHEMBL5087352
5.48	IC50	3300	nM	CHEMBL5093094
5.48	IC50	3300	nM	CHEMBL5082145
5.38	IC50	4200	nM	CHEMBL5086919
5.37	IC50	4250	nM	CHEMBL5079439
5.34	IC50	4600	nM	CHEMBL5092638
5.34	IC50	4600	nM	CHEMBL5078813
5.31	IC50	4900	nM	CHEMBL5089704
5.29	IC50	5100	nM	CHEMBL5076162
5.21	IC50	6200	nM	CHEMBL5075074
5.21	IC50	6200	nM	CHEMBL5075126
5.17	IC50	6700	nM	CHEMBL5093553
5.14	IC50	7200	nM	CHEMBL5089883
5.04	IC50	9200	nM	CHEMBL5093207
5.04	IC50	9200	nM	CHEMBL5086167
5.00	IC50	1e+04	nM	CHEMBL5094049

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases methylation	3
bisphenol A	decreases expression, increases expression, decreases reaction	2
Estradiol	affects binding, increases reaction, increases expression	2
Tetradecanoylphorbol Acetate	affects localization	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects localization, decreases expression, affects cotreatment	1
decabromobiphenyl ether	decreases expression	1
sodium arsenite	increases expression	1
aluminum fluoride	increases activity	1
tamibarotene	affects expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
Bortezomib	increases expression	1
Acetaminophen	decreases expression	1
Glyphosate	increases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects response to substance	1
Diethylstilbestrol	increases expression	1
Doxorubicin	decreases expression	1
Furaldehyde	decreases expression, affects cotreatment, affects localization	1
Ivermectin	decreases expression	1
N-Formylmethionine Leucyl-Phenylalanine	affects reaction, decreases reaction, increases abundance, increases reaction, affects localization	1
Phenobarbital	affects expression	1
Propranolol	affects localization	1
Smoke	decreases expression	1
Sodium Chloride	affects cotreatment, affects localization, decreases expression	1
Superoxides	increases abundance, increases reaction, affects reaction, decreases reaction	1
Tobacco Smoke Pollution	affects expression	1
Tretinoin	affects expression	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5052979	Binding	Inhibition of ARF6 (unknown origin)	Arf6 inhibitors and related methods

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D1VD	Abcam A-549 ARF6 KO	Cancer cell line	Male
CVCL_SD30	HAP1 ARF6 (-) 1	Cancer cell line	Male
CVCL_SD31	HAP1 ARF6 (-) 2	Cancer cell line	Male
CVCL_SD32	HAP1 ARF6 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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