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): 10 total
• GTEx eGene: eQTL in 8 tissues, sQTL in 0 (q < 0.05)
• Cancer dependency (DepMap): dependent in 22.0% of screened cell lines
• Constraint (gnomAD): pLI 0.99 (loss-of-function intolerant), LOEUF 0.25 (highly constrained)
• 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: 6 — 6 protein_coding

MANE Select: ENST00000298316

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1

ENST00000298316, ENST00000692608, ENST00000693319, ENST00000895811, ENST00000895812, ENST00001133251

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.

Highest expression (Bgee): esophagus squamous epithelium, epithelium of esophagus, gingiva, gingival epithelium, oral cavity.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ARF6 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 8 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

8 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	eqtl	1.9e-11	-0.11	14:49982986:C:A
Lung	eqtl	2.8e-04	-0.16	14:49889141:T:C
Skin Not Sun Exposed Suprapubic	eqtl	1.9e-03	-0.08	14:50038493:T:C
Brain Cerebellum	eqtl	1.3e-02	+0.19	14:50849873:C:T
Nerve Tibial	eqtl	1.4e-02	-0.18	14:49492473:C:A
Cells EBV-transformed lymphocytes	eqtl	1.9e-02	-0.62	14:49317803:T:C
Breast Mammary Tissue	eqtl	2.4e-02	-0.12	14:49989012:A:G
Skin Sun Exposed Lower leg	eqtl	4.4e-02	+0.16	14:49974061:C:T

FANTOM5 promoters

showing 10 of 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

showing 100 of 303 tissues 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
lower esophagus mucosa	UBERON:0035834	97.56	gold quality
eye	UBERON:0000970	97.55	gold quality
parotid gland	UBERON:0001831	97.47	gold quality
tendon of biceps brachii	UBERON:0008188	97.46	gold quality
superficial temporal artery	UBERON:0001614	97.43	gold quality
corpus epididymis	UBERON:0004359	97.43	gold quality
tongue squamous epithelium	UBERON:0006919	97.33	gold quality
body of tongue	UBERON:0011876	97.16	gold quality
monocyte	CL:0000576	97.04	gold quality
leukocyte	CL:0000738	97.04	gold quality
caput epididymis	UBERON:0004358	97.04	gold quality
mononuclear cell	CL:0000842	97.03	gold quality
esophagus mucosa	UBERON:0002469	97.02	gold quality
epithelium of mammary gland	UBERON:0003244	96.98	gold quality
oviduct epithelium	UBERON:0004804	96.95	gold quality
tongue	UBERON:0001723	96.91	gold quality
superior surface of tongue	UBERON:0007371	96.89	gold quality
nipple	UBERON:0002030	96.70	gold quality
vena cava	UBERON:0004087	96.70	gold quality
cartilage tissue	UBERON:0002418	96.64	gold quality
jejunum	UBERON:0002115	96.50	gold quality
bone element	UBERON:0001474	96.47	gold quality
granulocyte	CL:0000094	96.45	gold quality
urethra	UBERON:0000057	96.36	gold quality
pericardium	UBERON:0002407	96.18	gold quality
upper arm skin	UBERON:0004263	96.18	gold quality
cervix epithelium	UBERON:0004801	96.14	gold quality
saphenous vein	UBERON:0007318	96.10	gold quality
duodenum	UBERON:0002114	96.08	gold quality
seminal vesicle	UBERON:0000998	96.06	gold quality
cauda epididymis	UBERON:0004360	96.01	gold quality
endometrium	UBERON:0001295	95.96	gold quality
pylorus	UBERON:0001166	95.95	gold quality
endothelial cell	CL:0000115	95.93	silver quality
bone marrow	UBERON:0002371	95.65	gold quality
lymph node	UBERON:0000029	95.62	gold quality
rectum	UBERON:0001052	95.60	gold quality
placenta	UBERON:0001987	95.53	gold quality
bronchial epithelial cell	CL:0002328	95.48	gold quality
cardia of stomach	UBERON:0001162	95.42	gold quality
nasal cavity epithelium	UBERON:0005384	95.40	gold quality
mammary gland	UBERON:0001911	95.38	gold quality
mucosa of transverse colon	UBERON:0004991	95.35	gold quality
thoracic mammary gland	UBERON:0005200	95.35	gold quality
cervix squamous epithelium	UBERON:0006922	95.35	gold quality
nasal cavity mucosa	UBERON:0001826	95.32	gold quality
zone of skin	UBERON:0000014	95.30	gold quality
skin of abdomen	UBERON:0001416	95.16	gold quality
tonsil	UBERON:0002372	94.97	gold quality
skin of leg	UBERON:0001511	94.95	gold quality
caecum	UBERON:0001153	94.71	gold quality
renal medulla	UBERON:0000362	94.65	gold quality
fallopian tube	UBERON:0003889	94.59	gold quality
pigmented layer of retina	UBERON:0001782	94.43	gold quality
retina	UBERON:0000966	94.40	gold quality
bronchus	UBERON:0002185	94.36	gold quality
epithelium of bronchus	UBERON:0002031	94.29	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.26	gold quality
blood	UBERON:0000178	94.08	gold quality
vagina	UBERON:0000996	94.07	gold quality
vermiform appendix	UBERON:0001154	94.06	gold quality
bone marrow cell	CL:0002092	94.00	gold quality
medial globus pallidus	UBERON:0002477	93.87	gold quality
secondary oocyte	CL:0000655	93.82	gold quality
globus pallidus	UBERON:0001875	93.53	gold quality
decidua	UBERON:0002450	93.53	gold quality
periodontal ligament	UBERON:0008266	93.44	gold quality
trigeminal ganglion	UBERON:0001675	93.35	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.28	gold quality
colonic epithelium	UBERON:0000397	93.26	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Esophagus	tissue	81.9	low
Bone marrow	tissue	78.0	not detected
Tonsil	tissue	64.2	medium
Lymph node	tissue	57.9	low
Skin 1	tissue	50.6	low
Rectum	tissue	50.6	medium
Colon	tissue	50.4	medium
Superior colliculi	tissue	48.2
Small intestine	tissue	48.2	medium
Spleen	tissue	47.5	low
Spinal cord	tissue	46.7
Pons	tissue	46.6
Thalamus	tissue	45.7
Liver	tissue	45.4	medium
Stomach 1	tissue	44.4	medium
Medulla oblongata	tissue	43.8
Urinary bladder	tissue	43.6	medium
Midbrain	tissue	43.6
Duodenum	tissue	43.6	medium
Substantia nigra	tissue	42.4
Thymus	tissue	41.8
Vagina	tissue	41.6	not detected
Cerebellum	tissue	41.2	low
Appendix	tissue	41.0	medium
Hypothalamus	tissue	39.7
Corpus callosum	tissue	39.2
Periaqueductal gray	tissue	39.2
Hippocampal formation	tissue	35.9
Septum	tissue	35.1
Placenta	tissue	34.8	medium
Putamen	tissue	34.6
Cerebral cortex	tissue	34.5	low
Occipital cortex	tissue	34.5
Motor cortex	tissue	34.3
Salivary gland	tissue	33.7	medium
Somatosensory cortex	tissue	33.6
Ventral forebrain	tissue	32.3
Prefrontal cortex	tissue	32.1
Breast	tissue	31.6	medium
Olfactory bulb	tissue	31.3
Entorhinal cortex	tissue	30.9
Gallbladder	tissue	30.6	medium
Prostate	tissue	30.5	low
Temporal cortex	tissue	30.1
Adipose tissue	tissue	30.0	low
Retrosplenial and cingulate cortex	tissue	30.0
Lung	tissue	29.7	medium
Kidney	tissue	29.7	medium
Retrosplenial cortex	tissue	29.6
Basal ganglia	tissue	28.7	low
Amygdala	tissue	28.1
Insular cortex	tissue	27.8
Epididymis	tissue	27.6	medium
Choroid plexus	tissue	27.0
Fallopian tube	tissue	26.6	medium
Cervix	tissue	25.2	low
Frontal cortex	tissue	25.2
Adrenal gland	tissue	24.5	medium
Pancreas	tissue	23.2	low
Smooth muscle	tissue	22.2	not detected

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Dorsal spinal cord (46.7), Ventral spinal cord (46.2), White matter (39.2), Dorsal hippocampus (35.9), Ventral hippocampus (32.4).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1

miRNA regulators (miRDB)

Targeting ARF6 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 170 miRNAs:

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

gnomAD constraint: pLI 0.995, LOEUF 0.251, missense Z 4.04 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000298316 — one region, missense o/e 0.32. DepMap (CRISPR cell-line fitness): dependent in 22.0% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): JAR (-1.656), HuNS1 (-1.495), COLO 824 (-1.493), SU-DHL-5 (-1.479), RL (-1.384), MDST8 (-1.384), SNU-503 (-1.31), MM253 (-1.289), OCI-LY-19 (-1.272), TT1TKB (-1.125), HCC2429 (-1.118), SU-DHL-10 (-1.111), SNU-1327 (-1.108), M-07e (-1.101), GSS (-1.101).

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)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:99435) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 11 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal liver development	1
abnormal liver morphology	1
liver hypoplasia	1
pale liver	1
anemia	1
hemorrhage	1
hydrops fetalis	1
decreased liver weight	1
perinatal lethality, incomplete penetrance	1
lethality throughout fetal growth and development, incomplete penetrance	1
abnormal hepatic cord morphology	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Cryptococcus deneoformans JEC21	P0CM16	100.0%	Diamond
Cryptococcus deneoformans B-3501A	P0CM17	100.0%	Diamond
Arabidopsis thaliana	P0DH91	100.0%	Diamond
Takifugu rubripes	P61207	100.0%	Diamond
Locusta migratoria	P61210	100.0%	Diamond
Bos taurus	P84080	100.0%	Diamond
Sus scrofa	Q007T5	100.0%	Diamond
Macaca fascicularis	Q4R5P2	100.0%	Diamond
Pongo abelii	Q5R548	100.0%	Diamond
Plasmodium falciparum 3D7	Q7KQL3	100.0%	Diamond
Plasmodium falciparum	Q94650	100.0%	Diamond
Brassica rapa subsp. pekinensis	Q96361	99.5%	Diamond
Cricetulus griseus	Q9QVY3	99.5%	Diamond
Gallus gallus	P26990	99.4%	Diamond
Xenopus laevis	P51643	99.4%	Diamond
Oryza sativa Japonica Group	P51823	99.4%	Diamond
Caenorhabditis elegans	Q10943	99.4%	Diamond
Plasmodium falciparum NF54	Q25761	99.4%	Diamond
Caenorhabditis briggsae	Q61LA8	99.4%	Diamond
Vigna unguiculata	O48920	98.9%	Diamond
Daucus carota	P51822	98.9%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
MIR6076	ncRNA	102464828
LINC01588	ncRNA	283551
RN7SL2	scRNA	378706
RN7SL3	scRNA	378707
NEMF	protein-coding	9147
KLHDC2	protein-coding	23588

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; the interaction leads to suppression of ARF6 activity which promotes dendritic spine maintenance. 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)

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

UniProt features (34 total): helix 12, strand 7, binding site 5, mutagenesis site 4, turn 2, lipid moiety-binding region 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

20 structures by resolution:

PDB	Title	Method	Resolution (Å)
2A5D	Structural basis for the activation of cholera toxin by human ARF6-GTP	X-RAY DIFFRACTION	1.8
3N5C	Crystal Structure of Arf6DELTA13 complexed with GDP	X-RAY DIFFRACTION	1.82
4KAX	Crystal structure of the Grp1 PH domain in complex with Arf6-GTP	X-RAY DIFFRACTION	1.85
2W83	Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4	X-RAY DIFFRACTION	1.93
6PAU	Structure of Human NMT2 with myristoyl-lysine peptide and CoA products	X-RAY DIFFRACTION	1.93
2A5F	Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator …	X-RAY DIFFRACTION	2.02
7RK3	Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to …	X-RAY DIFFRACTION	2.05
1E0S	small G protein Arf6-GDP	X-RAY DIFFRACTION	2.28
3PCR	Structure of EspG-Arf6 complex	X-RAY DIFFRACTION	2.5
6PAV	Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated …	X-RAY DIFFRACTION	2.52
2A5G	Cholera toxin A1 subunit bound to ARF6(Q67L)	X-RAY DIFFRACTION	2.66
2J5X	STRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS	X-RAY DIFFRACTION	2.8
3LVQ	The crystal structure of ASAP3 in complex with Arf6 in transition state	X-RAY DIFFRACTION	3.38
3LVR	The crystal structure of ASAP3 in complex with Arf6 in transition state soaked with …	X-RAY DIFFRACTION	3.38
7XRD	Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane	ELECTRON MICROSCOPY	3.9
4FME	EspG-Rab1-Arf6 complex	X-RAY DIFFRACTION	4.1
6BBP	Model for compact volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) …	ELECTRON MICROSCOPY	35
6BBQ	Model for extended volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) …	ELECTRON MICROSCOPY	35
2BAO	Solution NMR structure of the myristoylated N-terminal fragment of Arf6	SOLUTION NMR
2BAU	Solution NMR structure of the micelle-bound myristoylated N-terminal Arf6	SOLUTION NMR

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Hydrolases, Predicted intracellular proteins, RAS pathway related proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol

Antibody reliability (HPA): IH approved · IF supported

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)

Position	Role
23–28	GTP
41–44	GTP
63–67	GTP
122–125	GTP
155–156	GTP

Post-translational modifications (2)

Type	Positions
N-myristoyl glycine	2
N6-myristoyl lysine	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

3 curated (TAS) of 9; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

9 pathways:

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

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 (32): 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), ruffle assembly (GO:0097178), maintenance of postsynaptic density structure (GO:0099562), positive regulation of focal adhesion disassembly (GO:0120183), 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), regulation of neuron projection development (GO:0010975), protein transport (GO:0015031)

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), lysosomal membrane (GO:0005765), early endosome (GO:0005769), endosome membrane (GO:0010008), recycling endosome (GO:0055037)

Reactome top-level categories

6 top-level categories:

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

showing 60 of 74 GO namespaces:

Category	Terms
cellular anatomical structure	7
cellular process	3
cytoplasm	3
synapse	3
intracellular protein localization	2
guanyl ribonucleotide binding	2
anion binding	2
endomembrane system	2
cytoplasmic vesicle	2
cell periphery	2
endosome membrane	2
protein transport	1
intracellular transport	1
system development	1
animal gross anatomical part developmental process	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
positive regulation of secretion by cell	1
filopodium assembly	1
regulation of plasma membrane bounded cell projection assembly	1
positive regulation of epithelial cell migration	1
keratinocyte migration	1
regulation of keratinocyte migration	1
regulation of developmental process	1
dendritic spine development	1
protein localization to membrane	1
protein localization to cell periphery	1
ribonucleoside triphosphate phosphatase activity	1
GTPase activity	1
molecular function regulator activity	1
purine ribonucleoside triphosphate binding	1
enzyme binding	1
protein-macromolecule adaptor activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 32 of 65 annotations. The rest are phylogenetic / computational / electronic (IEA).

32 experimentally-supported GO terms:

GO term	NS	Evidence
cortical actin cytoskeleton organization	BP	direct assay
endocytic recycling	BP	direct assay
positive regulation of actin filament polymerization	BP	mutant phenotype
positive regulation of mitotic cytokinetic process	BP	mutant phenotype
positive regulation of neuron projection development	BP	direct assay
positive regulation of protein secretion	BP	mutant phenotype
protein localization to cleavage furrow	BP	mutant phenotype
protein localization to endosome	BP	mutant phenotype
protein localization to plasma membrane	BP	direct assay
regulation of Rac protein signal transduction	BP	direct assay
regulation of filopodium assembly	BP	direct assay
ruffle assembly	BP	direct assay
Flemming body	CC	direct assay
Golgi apparatus	CC	direct assay
cell cortex	CC	direct assay
cleavage furrow	CC	direct assay
cytosol	CC	direct assay
endocytic vesicle	CC	direct assay
endosome	CC	direct assay
extracellular exosome	CC	high-throughput assay
filopodium membrane	CC	direct assay
focal adhesion	CC	high-throughput assay
membrane	CC	direct assay
midbody	CC	mutant phenotype
plasma membrane	CC	direct assay
recycling endosome membrane	CC	direct assay
ruffle	CC	direct assay
G protein activity	MF	direct assay
GDP binding	MF	direct assay
GTP binding	MF	direct assay
signaling adaptor activity	MF	direct assay
thioesterase binding	MF	physical interaction

Protein interactions and networks

IntAct

Human interaction partners of ARF6 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 127 partners by confidence:

Partner	Interaction type	MIscore	Records
KIF23	colocalization	0.670	23
APBB1	physical association	0.630	9
SPAG9	direct interaction	0.620	8
CYTH3	direct interaction	0.620	4
GGA3	physical association	0.590	3
ARFIP2	physical association	0.570	4
MEOX2	physical association	0.560	3
MYADM	physical association	0.560	1
EGFR	physical association	0.550	2
ATP6V1C1	physical association	0.520	4
CYTH2	direct interaction	0.440	3
IQSEC1	direct interaction	0.440	2
CYTH1	direct interaction	0.440	1
PSD4	direct interaction	0.440	1
TBC1D24	physical association	0.400	3
GGA1	physical association	0.400	1
MICALL1	physical association	0.400	1
RAB11FIP3	physical association	0.400	1
RAB11FIP4	physical association	0.400	1
RAB1A	physical association	0.400	1
NMT2	association	0.350	1
USP6NL	association	0.350	1
PSD	colocalization	0.270	3
RAB8A	colocalization	0.270	1
EIF6	physical association	0.000	2
AAR2	physical association	0.000	1
ACLY	physical association	0.000	1
AIMP1	physical association	0.000	1
ANXA2	physical association	0.000	1
APEX1	physical association	0.000	1

BioGRID (718 interactions; top human partners by supporting records in a sample of 600 records): APBB1 (Affinity Capture-Western; 5 records), CLTC (Affinity Capture-Western; 5 records), ARFIP2 (Two-hybrid; 4 records), SPAG9 (Co-crystal Structure; 4 records), AGAP1 (Biochemical Activity; 3 records), AP2B1 (Proximity Label-MS; 3 records), EXOC5 (Two-hybrid; 3 records), HTR2A (Reconstituted Complex; 3 records), KIF23 (Affinity Capture-Western; 3 records), KRAS (Proximity Label-MS; 3 records), LAMTOR1 (Proximity Label-MS; 3 records), MYADM (Affinity Capture-MS; 3 records), TGOLN2 (Affinity Capture-MS; 3 records), ACAP1 (Reconstituted Complex; 2 records), ARHGAP10 (Reconstituted Complex; 2 records)

SIGNOR signaling

12 signaling 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 127 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
Regulation of CDH1 posttranslational processing and trafficking to plasma membrane	5	16.8×	2e-03
TBC/RABGAPs	5	13.0×	5e-03
Maturation of DENV proteins	5	10.6×	7e-03
Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha	5	9.8×	9e-03
Translation initiation complex formation	5	9.5×	9e-03
Ribosomal scanning and start codon recognition	5	9.5×	9e-03
SRP-dependent cotranslational protein targeting to membrane	8	8.0×	2e-03
Translation	11	6.8×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
regulation of ARF protein signal transduction	6	42.6×	3e-06

Disease & clinical

Genetic variants

Variant evidence for ARF6: 10 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	2

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 20 predictions of 44):

Position(s)	Effect	Δscore	Sites
14:49893158–49893159	donor_loss	0.9400	6
14:49893254–49893255	acceptor_loss	0.9400	6
14:49893157	donor_loss	0.9100
14:49893160	donor_loss	0.9100
14:49893160	donor_loss	0.9000
14:49893157	donor_loss	0.8800
14:49893157	donor_loss	0.8500
14:49893253	acceptor_loss	0.8200
14:49893156	donor_loss	0.7900
14:49893243	acceptor_loss	0.7900

AlphaMissense

772 missense substitutions predicted likely pathogenic (of 1,145 scored), across 161 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M18	9	0.866	0.998
D63	8	0.999	1.000
D22	8	0.997	0.999
D89	8	0.996	0.999
F47	8	0.993	1.000
D125	8	0.986	0.993
N48	8	0.983	0.999
H76	8	0.980	0.999
D92	8	0.979	0.995
N122	8	0.968	0.999
F59	8	0.911	0.996
D109	8	0.901	0.981
D68	8	0.872	0.973
W62	7	0.999	1.000
W74	7	0.998	1.000
K26	7	0.997	1.000
E50	7	0.995	0.998
F86	7	0.995	0.998
W168	7	0.990	0.997
K123	7	0.981	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

Cancer	Prognostic	p-value
Pancreatic Adenocarcinoma (TCGA)	unfavorable	5.66e-05
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	7.64e-05
Kidney Chromophobe (TCGA)	unfavorable	0.00091

Disease associations

OMIM: gene MIM:600464 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST002380_4	Erythema nodosum in inflammatory bowel disease	7e-6
GCST012145_8	Ferritin levels	1e-5

EFO canonical traits (from GWAS)

1 canonical traits:

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 (CPIC guideline: no)

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)

140 measured of 140 human assays (140 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
3-(3,4-dichlorophenyl)-5-(3-pyridin-3-ylphenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.25 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(3,4-dichlorophenyl)-5-[3-(3,5-difluorophenoxy)phenyl]-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.33 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(3,4-dichlorophenyl)-5-(3-phenoxyphenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.46 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
N-[4-[3-(4-chlorophenyl)-7-oxo-2-(trifluoromethyl)-6H-pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]benzamide	IC50	0.5 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-(4-hydroxy-3-methoxy-5-nitrophenyl)-7-(2-methylbutan-2-yl)-2,3,5,6,7,8-hexahydro-1H-[1]benzothiolo[2,3-d]pyrimidin-4-one	IC50	0.56 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(3,4-dichlorophenyl)-5-(4-nitrophenyl)-2-phenyl-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.58 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(3,4-dichlorophenyl)-5-(4-phenoxyphenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.66 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(3,4-dichlorophenyl)-5-(4-nitrophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.66 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-[4-chloro-3-(trifluoromethyl)phenyl]-5-(4-nitrophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.67 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
5-benzyl-3-(3,4-dichlorophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.84 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
6-chloro-3-(4-chlorophenyl)-5-(4-nitrophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.88 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-(4-nitrophenyl)-2-phenyl-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.96 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-[3-(6-methyl-3-pyridinyl)phenyl]-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.96 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
6-chloro-3-(4-chlorophenyl)-5-phenyl-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	0.98 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-cyclopropyl-3-(3,4-dichlorophenyl)-5-(3-phenoxyphenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
N-[4-[3-(4-chlorophenyl)-7-oxo-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]propanamide	IC50	1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
rhodanine, 1-2	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
5-(4-bromophenyl)-3-(4-chlorophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-(4-pyridin-3-ylphenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-methyl-5-(4-nitrophenyl)-3-(4-phenylphenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-[3-[6-(dimethylamino)-3-pyridinyl]phenyl]-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-benzyl-3-naphthalen-1-yl-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
7-amino-6-(2-chlorophenyl)-2-(4-chlorophenyl)-3,8-dioxopyrido[3,4-c]pyridazine-4-carbonitrile	IC50	1.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-(3-nitrophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.2 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-cyclopropyl-3-(3,4-dichlorophenyl)-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.2 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-benzyl-3-(3,4-dichlorophenyl)-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.2 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
4-[4-(4-fluorophenyl)-3,6-dihydro-2H-pyridin-1-yl]-2-pyridin-4-yl-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidine	IC50	1.2 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-benzyl-6-chloro-3-(4-chlorophenyl)-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.3 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3,5-bis(4-chlorophenyl)-2-(trifluoromethyl)-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-chloro-3-methoxyphenyl)-2-methyl-5-(4-nitrophenyl)-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-(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-[(5Z)-5-[[3-(4-ethoxy-3-methylphenyl)-1-phenylpyrazol-4-yl]methylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]propanoic acid	IC50	1.4 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-benzyl-3-(4-chlorophenyl)-5-(4-nitrophenyl)-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.4 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-benzyl-3-(4-chlorophenyl)-5-phenyl-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.5 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-methyl-5-(4-nitrophenyl)-3-(4-phenoxyphenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.5 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-[3-(6-methoxy-3-pyridinyl)phenyl]-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.5 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-[2-tert-butyl-3-(4-chlorophenyl)-7-oxo-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-5-yl]benzonitrile	IC50	1.5 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
(7E)-7-benzylidene-2-[(2,6-dioxo-1,3-diazinan-4-yl)methylsulfanyl]-4-phenyl-5,6-dihydrocyclopenta[b]pyridine-3-carbonitrile	IC50	1.5 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-5-(4-nitrophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.6 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
5-(3-bromophenyl)-3-(4-chlorophenyl)-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.6 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
N-[4-[3-(4-chlorophenyl)-7-oxo-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]-3-methylbutanamide	IC50	1.7 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(2,4-dichlorophenyl)-2-methyl-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.7 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
2-benzyl-3-(4-chlorophenyl)-5-(2-hydroxy-4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.7 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
(5E)-1-(3-chlorophenyl)-5-[[1-(4-chlorophenyl)pyrrol-2-yl]methylidene]-2-sulfanylidene-1,3-diazinane-4,6-dione	IC50	1.8 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(4-chlorophenyl)-2-methyl-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	1.9 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
4-[3-(4-chlorophenyl)-7-oxo-2-(trifluoromethyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-5-yl]benzonitrile	IC50	1.9 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
N-[4-[3-(4-chlorophenyl)-2-methyl-7-oxo-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]-2-phenylacetamide	IC50	1.9 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
1-benzyl-3-[4-[3-(4-chlorophenyl)-2-methyl-7-oxo-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]urea	IC50	2.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-(3,5-dichlorophenyl)-2-methyl-5-(4-nitrophenyl)-2,3,3a,4-tetrahydro-1H-pyrazolo[1,5-a]pyrimidin-7-one	IC50	2.1 nM	US-10849901: Arf6 inhibitors and methods of synthesis and use thereof
3-bromo-5-chloro-N-(3,5-dichloro-4-quinolin-8-ylphenyl)-2-hydroxybenzamide	IC50	2.1 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 cotreatment, affects localization, decreases expression	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	affects cotreatment, affects localization, decreases expression	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)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for ARF6 across ~30M SureChEMBL compounds — explore on Sugi Predict.