ARRDC4

gene
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Also known as FLJ36045

Summary

ARRDC4 (arrestin domain containing 4, HGNC:28087) is a protein-coding gene on chromosome 15q26.2, encoding Arrestin domain-containing protein 4 (Q8NCT1). Functions as an adapter recruiting ubiquitin-protein ligases to their specific substrates.

Enables ubiquitin-like ligase-substrate adaptor activity. Involved in positive regulation of interferon-beta production and protein K63-linked ubiquitination. Acts upstream of or within positive regulation of ubiquitin-protein transferase activity. Located in endosome and plasma membrane.

Source: NCBI Gene 91947 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 92 total — 1 pathogenic
  • MANE Select transcript: NM_183376

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28087
Approved symbolARRDC4
Namearrestin domain containing 4
Location15q26.2
Locus typegene with protein product
StatusApproved
AliasesFLJ36045
Ensembl geneENSG00000140450
Ensembl biotypeprotein_coding
OMIM619788
Entrez91947

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000268042, ENST00000885035, ENST00000885036, ENST00000885037, ENST00000946276

RefSeq mRNA: 1 — MANE Select: NM_183376 NM_183376

CCDS: CCDS10377

Canonical transcript exons

ENST00000268042 — 8 exons

ExonStartEnd
ENSE000009431139796589597966042
ENSE000009431149796801497968116
ENSE000009431159796912397969379
ENSE000009431169796988397970045
ENSE000011639909797058997970743
ENSE000012804119796560097965666
ENSE000012804429796070397961168
ENSE000013657829797113197973833

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 97.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.1661 / max 338.8246, expressed in 1670 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
14878719.16611670

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
upper leg skinUBERON:000426297.61gold quality
upper arm skinUBERON:000426397.04gold quality
skin of hipUBERON:000155496.79gold quality
ileal mucosaUBERON:000033196.23gold quality
spinal cordUBERON:000224095.51gold quality
mucosa of sigmoid colonUBERON:000499395.34gold quality
deciduaUBERON:000245095.24gold quality
kidney epitheliumUBERON:000481995.23gold quality
C1 segment of cervical spinal cordUBERON:000646995.22gold quality
colonic mucosaUBERON:000031794.45gold quality
corpus callosumUBERON:000233694.13gold quality
germinal epithelium of ovaryUBERON:000130494.12gold quality
cardia of stomachUBERON:000116293.38gold quality
cardiac muscle of right atriumUBERON:000337993.03gold quality
nippleUBERON:000203092.70gold quality
cauda epididymisUBERON:000436092.67gold quality
amniotic fluidUBERON:000017392.60gold quality
epithelial cell of pancreasCL:000008392.44gold quality
muscle layer of sigmoid colonUBERON:003580592.42gold quality
caput epididymisUBERON:000435892.20gold quality
colonUBERON:000115591.74gold quality
parietal pleuraUBERON:000240091.66gold quality
right uterine tubeUBERON:000130291.60gold quality
large intestineUBERON:000005991.59gold quality
transverse colonUBERON:000115791.29gold quality
tibialis anteriorUBERON:000138591.23gold quality
medulla oblongataUBERON:000189690.90gold quality
intestineUBERON:000016090.61gold quality
lower esophagus muscularis layerUBERON:003583390.56gold quality
lower esophagusUBERON:001347390.53gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-GEOD-81608yes427.94
E-GEOD-83139yes318.61
E-ENAD-27yes8.94
E-ANND-3yes4.44
E-GEOD-75367no1693.80

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GATA2

miRNA regulators (miRDB)

196 targeting ARRDC4, 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-4262100.0073.263931
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3646100.0073.565283
HSA-MIR-4533100.0069.482758
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-5692A100.0074.406850
HSA-MIR-8485100.0077.574731
HSA-MIR-450099.9972.722367
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548AW99.9972.573559
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-477599.9875.006394
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-LET-7A-5P99.9872.291790

Literature-anchored findings (GeneRIF, showing 4)

  • identification of variants in the ARRDC4 coding region; seven variants were identified; fifteen haplotypes were inferred; haplotypes form two clades (PMID:18307387)
  • Txnip regulates cellular metabolism independent of its binding to thioredoxin and the arrestin domains are crucial structural elements in metabolic functions of alpha-arrestin proteins (PMID:19605364)
  • data highlight new function of ARRDC4 in innate immunity, contributing to the better understanding about regulation of MDA5 activation after EV71 infection, and also suggest ARRDC4 may serve as a potential target for intervention of EV71-induced inflammatory response. (PMID:28594402)
  • Identification of HDAC9 and ARRDC4 as potential biomarkers and targets for treatment of type 2 diabetes. (PMID:38528189)

Cross-species orthologs

13 orthologs

OrganismSymbolGene ID
mus_musculusArrdc4ENSMUSG00000042659
rattus_norvegicusArrdc4ENSRNOG00000010775
caenorhabditis_elegansWBGENE00008843
caenorhabditis_elegansWBGENE00009852
caenorhabditis_elegansWBGENE00011052
caenorhabditis_elegansWBGENE00011053
caenorhabditis_elegansWBGENE00011054
caenorhabditis_elegansWBGENE00012464
caenorhabditis_elegansWBGENE00013043
caenorhabditis_elegansWBGENE00014161
caenorhabditis_elegansWBGENE00018060
caenorhabditis_elegansWBGENE00018061
caenorhabditis_elegansWBGENE00020612

Paralogs (5): ARRDC2 (ENSG00000105643), ARRDC3 (ENSG00000113369), ARRDC1 (ENSG00000197070), ARRDC5 (ENSG00000205784), TXNIP (ENSG00000265972)

Protein

Protein identifiers

Arrestin domain-containing protein 4Q8NCT1 (reviewed: Q8NCT1)

All UniProt accessions (1): Q8NCT1

UniProt curated annotations — full annotation on UniProt →

Function. Functions as an adapter recruiting ubiquitin-protein ligases to their specific substrates. Plays a role in endocytosis of activated G protein-coupled receptors (GPCRs). Through an ubiquitination-dependent mechanism also plays a role in the incorporation of SLC11A2 into extracellular vesicles. May play a role in glucose uptake. Participates in innate immune response by promoting IFIH1/MDA5 activation through interaction with TRIM65.

Subunit / interactions. Interacts with ADRB2. Interacts (via PPxY motifs) with ITCH, NEDD4L and WWP2. Interacts with AVPR2. Identified in a complex containing at least ARRDC4, AVPR2 and HGS. Interacts with SLC11A2; controls the incorporation of SLC11A2 into extracellular vesicles through an ubiquitination-dependent mechanism. Interacts with TRIM65.

Subcellular location. Early endosome. Cell membrane. Cytoplasmic vesicle.

Similarity. Belongs to the arrestin family.

RefSeq proteins (1): NP_899232* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011021Arrestin-like_NDomain
IPR011022Arrestin-like_CDomain
IPR014752Arrestin-like_C_sfHomologous_superfamily
IPR014756Ig_E-setHomologous_superfamily
IPR050357Arrestin_domain-proteinFamily

Pfam: PF00339, PF02752

UniProt features (6 total): sequence variant 3, short sequence motif 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NCT1-F180.380.55

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 255 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_POSITIVE_REGULATION_OF_TYPE_I_INTERFERON_PRODUCTION, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, MARTINEZ_RB1_TARGETS_DN, GOBP_POSITIVE_REGULATION_OF_INTERFERON_BETA_PRODUCTION, ROZANOV_MMP14_TARGETS_UP, GOBP_CYTOKINE_PRODUCTION, WTGAAAT_UNKNOWN, NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON

GO Biological Process (6): protein transport (GO:0015031), protein ubiquitination (GO:0016567), positive regulation of interferon-beta production (GO:0032728), positive regulation of ubiquitin-protein transferase activity (GO:0051443), protein K63-linked ubiquitination (GO:0070534), extracellular vesicle biogenesis (GO:0140112)

GO Molecular Function (2): ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (7): cytoplasm (GO:0005737), endosome (GO:0005768), early endosome (GO:0005769), plasma membrane (GO:0005886), extracellular vesicle (GO:1903561), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
transport1
intracellular protein localization1
establishment of protein localization1
protein modification by small protein conjugation1
positive regulation of type I interferon production1
interferon-beta production1
regulation of interferon-beta production1
ubiquitin-protein transferase activity1
positive regulation of protein ubiquitination1
positive regulation of catalytic activity1
regulation of ubiquitin-protein transferase activity1
protein polyubiquitination1
cellular component biogenesis1
enzyme-substrate adaptor activity1
binding1
intracellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1
endosome1
membrane1
cell periphery1
extracellular region1
vesicle1
extracellular membrane-bounded organelle1
cytoplasm1
intracellular vesicle1

Protein interactions and networks

STRING

778 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARRDC4MLXIPQ9HAP2659
ARRDC4TRIM65Q6PJ69585
ARRDC4IFIH1Q9BYX4527
ARRDC4SAGP10523520
ARRDC4TRAPPC2LQ9UL33447
ARRDC4PGPEP1LA6NFU8441
ARRDC4WWP1Q9H0M0405
ARRDC4IAPPP10997401
ARRDC4NEDD4P46934401
ARRDC4TMEM132BQ14DG7401
ARRDC4ERO1BQ86YB8385
ARRDC4DNAJB5O75953383
ARRDC4ENO4A6NNW6381
ARRDC4WWP2O00308379
ARRDC4TXN2Q99757375
ARRDC4FOXO1Q12778375

IntAct

7 interactions, top by confidence:

ABTypeScore
ARRDC4WWP2psi-mi:“MI:0914”(association)0.530
ARRDC4AVPR2psi-mi:“MI:0915”(physical association)0.400
WWP1TP73psi-mi:“MI:0914”(association)0.350
SLC2A3NRP2psi-mi:“MI:0914”(association)0.350

BioGRID (92): ADRB2 (Affinity Capture-Western), ARRDC4 (Affinity Capture-Western), AVPR2 (Affinity Capture-Western), ARRDC4 (Affinity Capture-Western), IFIH1 (Affinity Capture-Western), ARRDC4 (Affinity Capture-Western), TRIM65 (Affinity Capture-Western), ARRDC4 (Affinity Capture-MS), ARRDC4 (Affinity Capture-MS), XPOT (Affinity Capture-MS), PSMD13 (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), NDFIP1 (Affinity Capture-MS), SVIL (Affinity Capture-MS), PJA2 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4J1F4, A0A0G2JXN2, A2AWP8, A2RRH5, C9J798, O43374, O70277, O95294, P04629, P59926, Q0GA42, Q13368, Q14318, Q16512, Q29RM4, Q2HY40, Q2T9P3, Q2TBA3, Q5BIM1, Q5M7W1, Q5R5M3, Q5R811, Q5T7P8, Q5XIS9, Q62746, Q6PFQ7, Q6PFY8, Q7TNM2, Q7TP90, Q7Z4K8, Q8BG60, Q8BHT7, Q8BQC3, Q8C6N3, Q8CIW5, Q8IZ69, Q8NCT1, Q920N2, Q92546, Q925B4

Diamond homologs: A0A0B4J1F4, Q0VCA2, Q2HY40, Q5M7W1, Q5R5L7, Q5R811, Q6TXF1, Q7TP90, Q7TPQ9, Q8BG60, Q8NCT1, Q8TBH0, Q96B67, Q9D668, Q9H3M7, O45782, Q99KN1, B0BNL6, Q8N5I2, Q02805

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance70
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
395722GRCh37/hg19 15q26.2-26.3(chr15:95202449-98779894)Pathogenic

SpliceAI

733 predictions. Top by Δscore:

VariantEffectΔscore
15:97965665:GA:Gdonor_gain1.0000
15:97965667:G:GGdonor_gain1.0000
15:97965886:T:Aacceptor_gain1.0000
15:97965892:CA:Cacceptor_loss1.0000
15:97965893:A:AGacceptor_gain1.0000
15:97965893:AGACC:Aacceptor_loss1.0000
15:97965894:G:GAacceptor_gain1.0000
15:97965894:GA:Gacceptor_gain1.0000
15:97965894:GAC:Gacceptor_gain1.0000
15:97965894:GACC:Gacceptor_gain1.0000
15:97965894:GACCT:Gacceptor_gain1.0000
15:97966038:TATTA:Tdonor_gain1.0000
15:97966039:ATTA:Adonor_gain1.0000
15:97966040:TTA:Tdonor_gain1.0000
15:97966041:TA:Tdonor_gain1.0000
15:97966042:AG:Adonor_loss1.0000
15:97966043:G:GGdonor_gain1.0000
15:97966044:T:Gdonor_loss1.0000
15:97968001:T:TAacceptor_gain1.0000
15:97968011:A:AGacceptor_gain1.0000
15:97968012:A:AGacceptor_gain1.0000
15:97968013:G:GGacceptor_gain1.0000
15:97969118:TTTA:Tacceptor_loss1.0000
15:97969120:TA:Tacceptor_loss1.0000
15:97969121:A:AGacceptor_gain1.0000
15:97969121:A:ATacceptor_loss1.0000
15:97969122:G:GTacceptor_gain1.0000
15:97969122:GGA:Gacceptor_gain1.0000
15:97969122:GGAGA:Gacceptor_gain1.0000
15:97969375:TAGCT:Tdonor_gain1.0000

AlphaMissense

2700 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:97968075:T:AV195D1.000
15:97969157:T:AN220K1.000
15:97969157:T:GN220K1.000
15:97969296:T:AW267R1.000
15:97969296:T:CW267R1.000
15:97965644:T:CF118L0.999
15:97965645:T:CF118S0.999
15:97965646:T:AF118L0.999
15:97965646:T:GF118L0.999
15:97965927:G:AG136E0.999
15:97965938:T:GY140D0.999
15:97968087:C:AA199D0.999
15:97969138:T:AI214N0.999
15:97969143:G:CA216P0.999
15:97969144:C:AA216E0.999
15:97969180:C:AP228Q0.999
15:97969185:G:CA230P0.999
15:97969186:C:AA230D0.999
15:97969188:G:CA231P0.999
15:97969192:T:AI232N0.999
15:97969298:G:CW267C0.999
15:97969298:G:TW267C0.999
15:97960980:G:AG40E0.998
15:97965651:T:CF120S0.998
15:97965911:T:CF131L0.998
15:97965913:T:AF131L0.998
15:97965913:T:GF131L0.998
15:97965939:A:CY140S0.998
15:97968081:T:CL197P0.998
15:97968104:G:AG205R0.998

dbSNP variants (sampled 300 via entrez): RS1000098529 (15:97968961 G>C), RS1000359411 (15:97966661 A>G), RS1000711304 (15:97965424 GAC>G,GACAC,GACACAC,GACACACAC), RS1000797766 (15:97963437 T>A), RS1001107014 (15:97970378 T>C), RS1001227368 (15:97968536 C>A), RS1001523307 (15:97960494 A>G), RS1001558092 (15:97970658 C>G,T), RS1002016975 (15:97962988 T>A,C), RS1002261569 (15:97959320 T>C), RS1002316302 (15:97970511 T>G), RS1002428679 (15:97964260 C>T), RS1002451286 (15:97963348 A>G), RS1002680994 (15:97960733 C>G,T), RS1002902952 (15:97966843 T>C)

Disease associations

OMIM: gene MIM:619788 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST001343_13Fat distribution (HIV)8.000000e-07
GCST004569_2Neuroticism1.000000e-06
GCST009276_8Response to placebo treatment in childhood asthma (FVC change)7.000000e-06
GCST011696_10Alzheimer’s disease2.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004341body fat distribution
EFO:0008344response to placebo
EFO:0010339FVC change measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression5
Valproic Acidaffects expression, increases expression5
Benzo(a)pyreneincreases expression4
Cyclosporineincreases expression4
Cadmium Chloridedecreases expression, increases abundance, increases expression4
(+)-JQ1 compounddecreases expression, increases expression3
Air Pollutantsdecreases expression, increases abundance, increases expression3
Cisplatinaffects cotreatment, decreases expression, increases expression3
Estradiolincreases expression3
Aflatoxin B1increases expression, affects expression, decreases expression, decreases methylation3
methylmercuric chloridedecreases expression2
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression, decreases expression2
entinostataffects cotreatment, decreases expression2
Acetaminophendecreases expression, increases expression2
Rotenonedecreases expression2
Silicon Dioxidedecreases expression, increases expression2
Particulate Matterincreases abundance, increases expression, decreases expression2
aristolochic acid Idecreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
OTX015increases expression1
mivebresibincreases expression1
Esketaminedecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
lead acetateincreases expression1
trichostatin Aincreases expression1
thallium sulfatedecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chlorideincreases expression1
butyraldehydeincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_F1P1HyCyte HCT 116 KO-hARRDC4Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): neurotic disorder