ARL4A

gene
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Summary

ARL4A (ARF like GTPase 4A, HGNC:695) is a protein-coding gene on chromosome 7p21.3, encoding ADP-ribosylation factor-like protein 4A (P40617). Small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP).

ADP-ribosylation factor-like 4A is a member of the ADP-ribosylation factor family of GTP-binding proteins. ARL4A is similar to ARL4C and ARL4D and each has a nuclear localization signal and an unusually high guaninine nucleotide exchange rate. ARL4A is located in both the nuclear and extranuclear cell compartments. Multiple transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 10124 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 30 total
  • MANE Select transcript: NM_005738

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:695
Approved symbolARL4A
NameARF like GTPase 4A
Location7p21.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000122644
Ensembl biotypeprotein_coding
OMIM604786
Entrez10124

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000356797, ENST00000396662, ENST00000396663, ENST00000396664, ENST00000404894, ENST00000439721, ENST00000651779, ENST00000891906, ENST00000931767, ENST00000931768, ENST00000931769, ENST00000931770

RefSeq mRNA: 4 — MANE Select: NM_005738 NM_001037164, NM_001195396, NM_005738, NM_212460

CCDS: CCDS5359

Canonical transcript exons

ENST00000651779 — 2 exons

ExonStartEnd
ENSE000038424221268763312687728
ENSE000038482071268816612690958

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 98.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.1052 / max 1751.5879, expressed in 1764 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
7729121.69331637
772887.99261619
772890.226276
772900.138547
772870.054512

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453398.72gold quality
right testisUBERON:000453498.47gold quality
testisUBERON:000047397.83gold quality
skin of abdomenUBERON:000141695.81gold quality
olfactory segment of nasal mucosaUBERON:000538695.53gold quality
mucosa of transverse colonUBERON:000499195.38gold quality
zone of skinUBERON:000001495.19gold quality
skin of legUBERON:000151194.68gold quality
lower esophagus mucosaUBERON:003583494.30gold quality
vaginaUBERON:000099694.14gold quality
esophagus mucosaUBERON:000246994.02gold quality
calcaneal tendonUBERON:000370193.29gold quality
rectumUBERON:000105293.23gold quality
small intestine Peyer’s patchUBERON:000345492.46gold quality
transverse colonUBERON:000115792.34gold quality
small intestineUBERON:000210892.21gold quality
bone marrowUBERON:000237192.19gold quality
esophagusUBERON:000104392.00gold quality
smooth muscle tissueUBERON:000113591.71gold quality
thoracic mammary glandUBERON:000520091.66gold quality
ectocervixUBERON:001224991.65gold quality
duodenumUBERON:000211491.40gold quality
intestineUBERON:000016091.17gold quality
monocyteCL:000057691.02gold quality
tonsilUBERON:000237290.74gold quality
colonUBERON:000115590.70gold quality
leukocyteCL:000073890.46gold quality
omental fat padUBERON:001041490.32gold quality
adipose tissueUBERON:000101390.17gold quality
subcutaneous adipose tissueUBERON:000219090.06gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 12.

ExperimentMarker?Max mean expression
E-MTAB-9841yes1334.51
E-CURD-98yes1210.25
E-MTAB-10855yes1106.02
E-MTAB-10885yes900.11
E-MTAB-8142yes96.68
E-MTAB-10287yes67.14
E-HCAD-1yes23.40
E-MTAB-8410yes23.31
E-GEOD-135922yes12.68
E-CURD-46yes10.56
E-CURD-114yes9.79
E-MTAB-10042no470.28
E-MTAB-6108no363.77
E-HCAD-5no2.25
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTNNB1

miRNA regulators (miRDB)

109 targeting ARL4A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-188-3P100.0068.761240
HSA-MIR-340-5P100.0072.504437
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-1213699.9872.815713
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-365899.9673.874379
HSA-MIR-9-3P99.9670.882068
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-545-3P99.9570.742783
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-335-3P99.9373.364958
HSA-MIR-314399.9371.963104
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872

Literature-anchored findings (GeneRIF, showing 6)

  • Study shows that three related Arf-like GTPases Arl4a, Arl4c, and Arl4d, are able to recruit ARNO and other cytohesins to the plasma membrane by binding to their PH domains irrespective of whether they are in the diglycine or triglycine form. (PMID:17398095)
  • The loss of PTEN was shown to lead to increased levels of ARF4L protein but no change in transcript levels. The ARF4L transcript preferentially localized to the polysomal compartment after PTEN loss in glioma. (PMID:18240926)
  • membrane targeting of ELMO via Arl4A promotes cytoskeletal reorganization including membrane ruffling and stress fiber disassembly via an ELMO-DOCK1800-Rac signaling pathway. (PMID:21930703)
  • Deletion of the ARL4A-interacting region of GCC185 results in inability to maintain Golgi structure and modulate endosome-to-Golgi transport. (PMID:22159419)
  • Arl4A participates in Slit2/Robo1 signaling to modulate cell motility by regulating Cdc42 activity. (PMID:30427759)
  • Phosphorylation of Arl4A/D promotes their binding by the HYPK chaperone for their stable recruitment to the plasma membrane. (PMID:35857868)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioarl4aaENSDARG00000099918
mus_musculusArl4aENSMUSG00000047446
rattus_norvegicusArl4aENSRNOG00000069300

Paralogs (30): ARF5 (ENSG00000004059), SAR1A (ENSG00000079332), ARFRP1 (ENSG00000101246), TRIM23 (ENSG00000113595), ARL6 (ENSG00000113966), ARL1 (ENSG00000120805), ARL8B (ENSG00000134108), ARF3 (ENSG00000134287), ARL3 (ENSG00000138175), ARL5C (ENSG00000141748), ARF1 (ENSG00000143761), ARL8A (ENSG00000143862), ARL11 (ENSG00000152213), SAR1B (ENSG00000152700), ARL5A (ENSG00000162980), ARF6 (ENSG00000165527), 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-like protein 4AP40617 (reviewed: P40617)

All UniProt accessions (2): C9J7Q9, P40617

UniProt curated annotations — full annotation on UniProt →

Function. Small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). GTP-binding protein that does not act as an allosteric activator of the cholera toxin catalytic subunit. Recruits CYTH1, CYTH2, CYTH3 and CYTH4 to the plasma membrane in GDP-bound form.

Subunit / interactions. Interacts with CYTH2. Interacts with KPNA2; the interaction is direct. Does not interact with ARL4A.

Subcellular location. Cell membrane. Cytoplasm. Nucleus. Nucleolus.

Post-translational modifications. Myristoylated.

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

RefSeq proteins (4): NP_001032241, NP_001182325, NP_005729, NP_997625 (=MANE)

Domains & families (InterPro)

IDNameType
IPR005225Small_GTP-bdDomain
IPR006689Small_GTPase_ARF/SARFamily
IPR024156Small_GTPase_ARFFamily
IPR027417P-loop_NTPaseHomologous_superfamily

Pfam: PF00025

UniProt features (8 total): binding site 3, mutagenesis site 2, initiator methionine 1, chain 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P40617-F191.870.85

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 (3): 27–34; 75–79; 134–137

Post-translational modifications (1): 2

Mutagenesis-validated functional residues (2):

PositionPhenotype
34inhibits relocalization of cyth2 to the plasma membrane. strongly localized in the nucleolus.
79localized in the nucleus and nucleolus.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 363 (showing top): RNGTGGGC_UNKNOWN, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP, BECKER_TAMOXIFEN_RESISTANCE_UP, TTTGTAG_MIR520D, GOZGIT_ESR1_TARGETS_DN, HALMOS_CEBPA_TARGETS_UP, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, BROWNE_HCMV_INFECTION_16HR_UP, KANNAN_TP53_TARGETS_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, TAL1ALPHAE47_01, CTATGCA_MIR153, EFC_Q6

GO Biological Process (3): intracellular protein transport (GO:0006886), vesicle-mediated transport (GO:0016192), brown fat cell differentiation (GO:0050873)

GO Molecular Function (4): GTPase activity (GO:0003924), GTP binding (GO:0005525), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
nuclear lumen2
intracellular protein localization1
protein transport1
intracellular transport1
transport1
cellular process1
fat cell differentiation1
ribonucleoside triphosphate phosphatase activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
intracellular anatomical structure1
cytoplasm1
membrane1
cell periphery1

Protein interactions and networks

STRING

1769 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARL4ACYTH2Q99418822
ARL4AGCC2Q8IWJ2740
ARL4ACYTH3O43739718
ARL4ASOS2Q07890685
ARL4AELMO1Q92556677
ARL4ACDKN2AP42771657
ARL4ACYTH4Q9UIA0643
ARL4AKPNA2P52292623
ARL4ACYTH1Q15438611
ARL4ALAMB1P07942596
ARL4AFHOD1Q9Y613507
ARL4AARL16Q0P5N6507
ARL4AGOLGA2Q08379491
ARL4AJDP2Q8WYK2477
ARL4ASUMF2Q8NBJ7441

IntAct

30 interactions, top by confidence:

ABTypeScore
ARL4AGOLGA2psi-mi:“MI:0915”(physical association)0.720
GOLGA2ARL4Apsi-mi:“MI:0915”(physical association)0.720
ARL4ACCDC102Bpsi-mi:“MI:0915”(physical association)0.560
ARL4ACCDC57psi-mi:“MI:0915”(physical association)0.560
ARL4ASPATC1Lpsi-mi:“MI:0915”(physical association)0.560
CCDC57ARL4Apsi-mi:“MI:0915”(physical association)0.560
SPATC1LARL4Apsi-mi:“MI:0915”(physical association)0.560
KRT19ARL4Apsi-mi:“MI:0915”(physical association)0.560
ARL4AMTUS2psi-mi:“MI:0915”(physical association)0.560
ARL4APOF1Bpsi-mi:“MI:0915”(physical association)0.560
EVI5ARL4Apsi-mi:“MI:0915”(physical association)0.560
FCN1ARL4Apsi-mi:“MI:0915”(physical association)0.370
ARL4AKRT19psi-mi:“MI:0915”(physical association)0.000
ARL4AEVI5psi-mi:“MI:0915”(physical association)0.000
ARL4AMTUS2psi-mi:“MI:0915”(physical association)0.000
ARL4APOF1Bpsi-mi:“MI:0915”(physical association)0.000
ARL4AGOLGA2psi-mi:“MI:0915”(physical association)0.000
ARL4Apsi-mi:“MI:0915”(physical association)0.000

BioGRID (22): ARL4A (Two-hybrid), CCDC102B (Two-hybrid), SPATC1L (Two-hybrid), CCDC57 (Two-hybrid), ARL4A (Synthetic Lethality), ARL4A (Two-hybrid), ARL4A (Affinity Capture-Western), ARL4A (Affinity Capture-Western), ARL4A (Affinity Capture-Western), ELMO1 (Co-localization), RAC1 (Co-localization), ARL4A (Affinity Capture-Western), ARL4A (Two-hybrid), GCC2 (Two-hybrid), GCC2 (Affinity Capture-Western)

ESM2 similar proteins: A8ISN6, B5FYQ0, F4IZ82, O00909, O14966, O45379, P11076, P25160, P36405, P37996, P38116, P40616, P40617, P40940, P49702, P51646, P56559, P61208, P61211, P61212, P61213, P61214, Q13795, Q19705, Q1MTE5, Q2KJ96, Q2TBW6, Q2YDM1, Q32LJ2, Q3T0M9, Q52NJ4, Q54R04, Q54UF1, Q5R579, Q5R7A4, Q5RCQ6, Q627K4, Q63055, Q80ZU0, Q8BXL7

Diamond homologs: O00909, O08697, O23778, O48649, O48920, P0CM16, P0CM17, P0DH91, P11076, P18085, P19146, P22274, P25160, P26990, P26991, P34212, P34727, P36397, P36404, P36406, P36407, P36579, P38116, P40616, P40617, P40940, P40945, P40946, P40994, P49076, P49702, P51643, P51644, P51645, P51646, P51821, P51822, P51823, P51824, P61204

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance23
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

263 predictions. Top by Δscore:

VariantEffectΔscore
7:12687041:CAG:Cdonor_loss1.0000
7:12687042:AG:Adonor_loss1.0000
7:12687044:GTG:Gdonor_loss1.0000
7:12687045:T:Adonor_loss1.0000
7:12688165:GCA:Gacceptor_gain1.0000
7:12687027:G:Tdonor_gain0.9900
7:12688163:CAGCA:Cacceptor_gain0.9900
7:12688164:AGCAG:Aacceptor_gain0.9900
7:12688165:GCAGT:Gacceptor_gain0.9900
7:12687031:G:GTdonor_gain0.9800
7:12687039:GTCAG:Gdonor_gain0.9800
7:12688160:TCCCA:Tacceptor_loss0.9800
7:12688161:CCCA:Cacceptor_loss0.9800
7:12688162:CCAGC:Cacceptor_loss0.9800
7:12688163:CA:Cacceptor_loss0.9800
7:12688164:A:AGacceptor_gain0.9800
7:12688165:G:GGacceptor_gain0.9800
7:12688167:A:AGacceptor_gain0.9800
7:12688168:G:GGacceptor_gain0.9800
7:12688168:GTCTT:Gacceptor_gain0.9800
7:12687027:G:GTdonor_gain0.9700
7:12688165:GC:Gacceptor_gain0.9700
7:12687506:G:GTdonor_gain0.9600
7:12688156:C:Aacceptor_loss0.9600
7:12688168:GT:Gacceptor_gain0.9600
7:12688168:GTC:Gacceptor_gain0.9600
7:12687030:GGACG:Gdonor_gain0.9400
7:12687437:T:TAdonor_gain0.9400
7:12687438:G:GAdonor_gain0.9400
7:12688166:CAGTC:Cacceptor_loss0.9400

AlphaMissense

1297 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:12688355:C:TT34I1.000
7:12688510:T:AW86R1.000
7:12688510:T:CW86R1.000
7:12688643:T:CL130P1.000
7:12688658:A:TK135I1.000
7:12688659:A:CK135N1.000
7:12688659:A:TK135N1.000
7:12688333:G:CG27R0.999
7:12688348:G:AG32R0.999
7:12688348:G:CG32R0.999
7:12688349:G:AG32E0.999
7:12688349:G:TG32V0.999
7:12688351:A:CK33Q0.999
7:12688353:G:CK33N0.999
7:12688353:G:TK33N0.999
7:12688414:T:CF54L0.999
7:12688416:T:AF54L0.999
7:12688416:T:GF54L0.999
7:12688477:G:CD75H0.999
7:12688478:A:CD75A0.999
7:12688478:A:GD75G0.999
7:12688502:G:CR83T0.999
7:12688503:G:CR83S0.999
7:12688503:G:TR83S0.999
7:12688512:G:CW86C0.999
7:12688512:G:TW86C0.999
7:12688537:G:CG95R0.999
7:12688538:G:AG95D0.999
7:12688550:T:AV99D0.999
7:12688555:G:CD101H0.999

dbSNP variants (sampled 300 via entrez): RS1000324874 (7:12690015 A>C), RS1001298906 (7:12686843 G>A), RS1001548547 (7:12685775 C>G), RS1002062919 (7:12690732 T>G), RS1002498737 (7:12690444 G>A), RS1002553098 (7:12686823 C>G,T), RS1002606957 (7:12686680 GC>G), RS1003561713 (7:12687650 T>C), RS1003613876 (7:12687466 C>T), RS1004804317 (7:12686993 C>T), RS1006298456 (7:12690911 A>G), RS1006390776 (7:12685158 T>C), RS1006461517 (7:12689320 C>G), RS1007384901 (7:12686579 T>A), RS1007694256 (7:12684925 T>C)

Disease associations

OMIM: gene MIM:604786 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002875_54Diisocyanate-induced asthma1.000000e-06
GCST007847_97Type 2 diabetes3.000000e-09
GCST008053_80Height4.000000e-09
GCST008529_41Tea consumption2.000000e-07
GCST010276_9Renal underexcretion gout3.000000e-07
GCST011742_29Triglyceride levels in HIV infection9.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate
EFO:0010091tea consumption measurement
EFO:0004530triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects methylation, decreases expression, increases abundance4
Cadmium Chlorideincreases abundance, increases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
methylselenic acidincreases expression1
methylparabendecreases expression1
butyraldehydeincreases expression1
perfluorooctanoic acidincreases expression1
S-(1,2-dichlorovinyl)cysteinedecreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
perfluorooctane sulfonic acidincreases expression1
ICG 001decreases expression1
abrineincreases expression1
jinfukangdecreases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Leflunomideaffects expression1
Air Pollutantsdecreases expression, increases abundance1
Air Pollutants, Occupationalincreases expression1
Ethanoldecreases expression, increases abundance, affects cotreatment1
Arsenicdecreases expression, increases abundance1
Vehicle Emissionsdecreases methylation1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases abundance, increases expression1
Calcitrioldecreases expression1
Estradioldecreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.