ACTR6

gene
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Also known as ARP6FLJ13433

Summary

ACTR6 (actin related protein 6, HGNC:24025) is a protein-coding gene on chromosome 12q23.1, encoding Actin-related protein 6 (Q9GZN1). Required for formation and/or maintenance of proper nucleolar structure and function. It is a selective cancer dependency (DepMap: 77.6% of cell lines).

Predicted to enable nucleosome binding activity. Involved in nucleolus organization. Located in nucleolus.

Source: NCBI Gene 64431 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 52 total — 1 pathogenic, 2 likely-pathogenic
  • Cancer dependency (DepMap): dependent in 77.6% of screened cell lines
  • MANE Select transcript: NM_022496

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24025
Approved symbolACTR6
Nameactin related protein 6
Location12q23.1
Locus typegene with protein product
StatusApproved
AliasesARP6, FLJ13433
Ensembl geneENSG00000075089
Ensembl biotypeprotein_coding
OMIM619729
Entrez64431

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 14 protein_coding, 4 nonsense_mediated_decay, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000188312, ENST00000546902, ENST00000547458, ENST00000548180, ENST00000549977, ENST00000550813, ENST00000551440, ENST00000551517, ENST00000551617, ENST00000551652, ENST00000552064, ENST00000552376, ENST00000553038, ENST00000899395, ENST00000899396, ENST00000899397, ENST00000899398, ENST00000899399, ENST00000899400, ENST00000926808, ENST00000926809, ENST00000926810

RefSeq mRNA: 1 — MANE Select: NM_022496 NM_022496

CCDS: CCDS9074

Canonical transcript exons

ENST00000188312 — 11 exons

ExonStartEnd
ENSE00001155372100200815100200919
ENSE00002419156100223786100224424
ENSE00003561595100210295100210351
ENSE00003569491100212256100212354
ENSE00003581214100205676100205744
ENSE00003591446100218415100218586
ENSE00003596784100210073100210208
ENSE00003603810100220008100220146
ENSE00003624458100204940100205057
ENSE00003689929100212450100212528
ENSE00003691303100207663100207786

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 93.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.8537 / max 315.7795, expressed in 1750 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
12756013.81701750
1275610.036819

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402393.71gold quality
cortical plateUBERON:000534393.58gold quality
ventricular zoneUBERON:000305393.03gold quality
buccal mucosa cellCL:000233692.87gold quality
Brodmann (1909) area 23UBERON:001355492.39gold quality
palpebral conjunctivaUBERON:000181292.30gold quality
choroid plexus epitheliumUBERON:000391191.94gold quality
Brodmann (1909) area 9UBERON:001354091.67gold quality
bronchial epithelial cellCL:000232891.63gold quality
prefrontal cortexUBERON:000045191.16gold quality
dorsolateral prefrontal cortexUBERON:000983491.04gold quality
monocyteCL:000057690.78gold quality
jejunal mucosaUBERON:000039990.69gold quality
calcaneal tendonUBERON:000370190.69gold quality
mononuclear cellCL:000084290.65gold quality
substantia nigra pars compactaUBERON:000196590.41gold quality
leukocyteCL:000073890.38gold quality
mucosa of paranasal sinusUBERON:000503090.37gold quality
primary visual cortexUBERON:000243690.34gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.12gold quality
anterior cingulate cortexUBERON:000983590.05gold quality
C1 segment of cervical spinal cordUBERON:000646989.96gold quality
cingulate cortexUBERON:000302789.89gold quality
hypothalamusUBERON:000189889.71gold quality
neocortexUBERON:000195089.56gold quality
pigmented layer of retinaUBERON:000178289.55gold quality
embryoUBERON:000092289.52gold quality
lateral nuclear group of thalamusUBERON:000273689.52gold quality
cerebral cortexUBERON:000095689.48gold quality
germinal epithelium of ovaryUBERON:000130489.43gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.98
E-MTAB-6142no180.41

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EHMT2, GATA3, MTA3

miRNA regulators (miRDB)

46 targeting ACTR6, 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-3646100.0073.565283
HSA-MIR-5692A100.0074.406850
HSA-MIR-4682100.0068.891258
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-56899.9869.862084
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-651-3P99.9473.485177
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-548M99.7068.871749
HSA-MIR-46699.6770.852863
HSA-MIR-426199.5970.303415
HSA-MIR-510-3P99.5470.062965
HSA-MIR-6832-3P99.5270.441726
HSA-MIR-548G-3P99.4868.672159
HSA-MIR-582-5P99.4770.792635

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Results describe the predominant nuclear localization of another Arp subfamily, Arp6, in vertebrate cells, and show its colocalization with heterochromatin protein 1 orthologs in pericentric heterochromatin. (PMID:16487625)
  • under starvation, ARP6 was required for cell survival through the repression of rDNA transcription independently of H2A.Z (PMID:26164235)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioactr6ENSDARG00000021370
mus_musculusActr6ENSMUSG00000019948
rattus_norvegicusActr6ENSRNOG00000007875
drosophila_melanogasterArp6FBGN0011741
caenorhabditis_elegansWBGENE00007434

Paralogs (26): ACTB (ENSG00000075624), ACTL6B (ENSG00000077080), ACTR5 (ENSG00000101442), ACTR3C (ENSG00000106526), ACTA2 (ENSG00000107796), ACTR8 (ENSG00000113812), ACTR1B (ENSG00000115073), ACTR3 (ENSG00000115091), ACTL8 (ENSG00000117148), ACTRT1 (ENSG00000123165), ACTR10 (ENSG00000131966), ACTR3B (ENSG00000133627), ACTL6A (ENSG00000136518), ACTR2 (ENSG00000138071), ACTR1A (ENSG00000138107), ACTA1 (ENSG00000143632), ACTL7B (ENSG00000148156), ACTC1 (ENSG00000159251), ACTG2 (ENSG00000163017), ACTBL2 (ENSG00000169067), ACTRT2 (ENSG00000169717), ACTL9 (ENSG00000181786), ACTG1 (ENSG00000184009), ACTRT3 (ENSG00000184378), ACTL7A (ENSG00000187003), ACTL10 (ENSG00000288649)

Protein

Protein identifiers

Actin-related protein 6Q9GZN1 (reviewed: Q9GZN1)

Alternative names: hARPX

All UniProt accessions (8): Q9GZN1, F8VP72, F8VRL1, F8VSD1, F8W043, F8W057, F8W0Q1, G3V1Y1

UniProt curated annotations — full annotation on UniProt →

Function. Required for formation and/or maintenance of proper nucleolar structure and function. Plays a dual role in the regulation of ribosomal DNA (rDNA) transcription. In the presence of high glucose, maintains active rDNA transcription through H2A.Z deposition and under glucose starvation, is required for the repression of rDNA transcription, and this function may be independent of H2A.Z.

Subunit / interactions. Component of the chromatin-remodeling SRCAP complex composed of at least SRCAP, DMAP1, RUVBL1, RUVBL2, ACTL6A, YEATS4, ACTR6 and ZNHIT1. Interacts with CBX1, CBX3 and CBX5.

Subcellular location. Cytoplasm. Cytoskeleton. Nucleus. Nucleolus.

Similarity. Belongs to the actin family. ARP6 subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q9GZN1-11yes
Q9GZN1-22

RefSeq proteins (1): NP_071941* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004000ActinFamily
IPR043129ATPase_NBDHomologous_superfamily

Pfam: PF00022

UniProt features (9 total): sequence conflict 3, modified residue 2, splice variant 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

9 structures.

PDBMethodResolution (Å)
8X15ELECTRON MICROSCOPY3.2
8X19ELECTRON MICROSCOPY3.2
8X1CELECTRON MICROSCOPY3.2
9CA7ELECTRON MICROSCOPY3.35
9CA9ELECTRON MICROSCOPY3.56
9CA8ELECTRON MICROSCOPY3.92
9CABELECTRON MICROSCOPY3.94
6IGMELECTRON MICROSCOPY4
9CAAELECTRON MICROSCOPY4.04

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9GZN1-F194.370.87

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 2, 260

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): MODULE_255, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, MODULE_317, PATIL_LIVER_CANCER, MODULE_331, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_NUCLEUS_ORGANIZATION, ZHANG_BREAST_CANCER_PROGENITORS_UP, ACEVEDO_LIVER_CANCER_UP, GOBP_CHROMATIN_REMODELING, MODULE_207, OSMAN_BLADDER_CANCER_DN, GOCC_INO80_TYPE_COMPLEX, GOMF_CHROMATIN_BINDING, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN

GO Biological Process (5): chromatin remodeling (GO:0006338), regulation of DNA-templated transcription (GO:0006355), nucleolus organization (GO:0007000), negative regulation of transcription by RNA polymerase I (GO:0016479), positive regulation of transcription by RNA polymerase I (GO:0045943)

GO Molecular Function (2): nucleosome binding (GO:0031491), protein binding (GO:0005515)

GO Cellular Component (6): nucleosome (GO:0000786), Swr1 complex (GO:0000812), nucleus (GO:0005634), nucleolus (GO:0005730), cytoskeleton (GO:0005856), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase I2
transcription by RNA polymerase I2
intracellular membraneless organelle2
chromatin organization1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
nucleus organization1
negative regulation of DNA-templated transcription1
positive regulation of DNA-templated transcription1
chromatin binding1
protein-containing complex binding1
binding1
chromatin1
protein-DNA complex1
histone deacetylase complex1
nuclear chromosome1
INO80-type complex1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1660 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ACTR6H2AZ1P0C0S5620
ACTR6DMAP1Q9NPF5524
ACTR6KLHL38Q2WGJ6494
ACTR6NEURL1BA8MQ27486
ACTR6ZNHIT1O43257463
ACTR6CAPZA3Q96KX2461
ACTR6DEPDC4Q8N2C3458
ACTR6HIPK4Q8NE63455
ACTR6HIP1RO75146426
ACTR6TRIP12Q14669414
ACTR6MYO10Q9HD67409
ACTR6TADA2AO75478405
ACTR6ANAPC5Q9UJX4398
ACTR6HCLS1P14317391
ACTR6RUVBL2Q9Y230389

IntAct

81 interactions, top by confidence:

ABTypeScore
UBXN2BVCPpsi-mi:“MI:0914”(association)0.910
RUVBL1ZNHIT1psi-mi:“MI:0914”(association)0.860
ACTR6ZNHIT1psi-mi:“MI:0914”(association)0.820
ACTR6ZNHIT1psi-mi:“MI:0915”(physical association)0.820
RUVBL2ZNHIT1psi-mi:“MI:0914”(association)0.810
YEATS4ZNHIT1psi-mi:“MI:0914”(association)0.790
ZNHIT1YEATS4psi-mi:“MI:0914”(association)0.790
H2AZ1ZNHIT1psi-mi:“MI:0914”(association)0.770
ZNHIT1H2AZ1psi-mi:“MI:0914”(association)0.770
ACTL6AZNHIT1psi-mi:“MI:0914”(association)0.720
VPS72ZNHIT1psi-mi:“MI:0914”(association)0.690
ACTR6H2AZ1psi-mi:“MI:0915”(physical association)0.670
H2BC1PPM1Gpsi-mi:“MI:0914”(association)0.640
P4HA3FAM171A2psi-mi:“MI:0914”(association)0.640
QPRTPIK3C2Apsi-mi:“MI:0914”(association)0.640
RUVBL1POLR3Apsi-mi:“MI:0914”(association)0.640

BioGRID (89): ACTR6 (Affinity Capture-MS), ACTR6 (Affinity Capture-MS), ACTR6 (Affinity Capture-MS), DMAP1 (Affinity Capture-MS), SRCAP (Affinity Capture-MS), ZNHIT1 (Affinity Capture-MS), ACTR6 (Affinity Capture-MS), ACTR6 (Affinity Capture-MS), ACTR6 (Co-fractionation), CHMP5 (Co-fractionation), PUS7 (Co-fractionation), RUVBL1 (Co-fractionation), RUVBL2 (Co-fractionation), YWHAE (Co-fractionation), ACTR6 (Proximity Label-MS)

ESM2 similar proteins: A2X6S3, A2XLF2, A2XNS1, A2YR10, O16808, O81221, P0DM41, P0DM42, P10990, P30162, P30163, P30168, P32390, P42528, P45886, P47117, P53460, P53461, P53463, P53464, P53490, P69004, P69005, P78712, P81228, P81229, P92179, P93374, P93375, P93376, P93584, P93586, P93587, Q10AZ4, Q10DV7, Q26065, Q61WW9, Q6K908, Q6NVA9, Q6ZJW9

Diamond homologs: A2BDB0, A2WNB0, O18840, O74258, O94241, P02578, P04751, P07829, P0CM04, P0CM05, P10984, P10986, P10990, P10995, P12716, P14235, P17128, P17304, P20399, P27131, P29751, P30162, P30163, P45890, P48975, P49055, P53455, P53458, P53459, P53472, P53479, P53486, P53505, P60009, P60010, P60011, P60706, P60708, P60709, P60710

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
HATs acetylate histones1117.4×1e-08
FXIIa activates plasma kallikrein-kinin system517.3×8e-04
Deposition of new CENPA-containing nucleosomes at the centromere515.9×1e-03
UCH proteinases614.9×4e-04
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks514.6×1e-03
RUNX1 regulates transcription of genes involved in differentiation of HSCs713.3×2e-04
Amyloid fiber formation612.3×8e-04
Formation of the beta-catenin:TCF transactivating complex512.0×2e-03

GO biological processes:

GO termPartnersFoldFDR
regulation of double-strand break repair652.8×3e-07
positive regulation of double-strand break repair via homologous recombination634.8×2e-06
regulation of embryonic development630.0×4e-06
positive regulation of DNA repair527.2×5e-05
regulation of DNA repair520.9×1e-04
chromatin remodeling1112.2×3e-07
regulation of apoptotic process911.4×6e-06
regulation of cell cycle1011.3×2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic2
Uncertain significance36
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
59817GRCh38/hg38 12q23.1(chr12:100078579-100273980)x3Pathogenic
148826GRCh38/hg38 12q23.1-23.2(chr12:97394550-101410225)x3Likely pathogenic
563984GRCh37/hg19 12q23.1(chr12:96719383-101537641)x3Likely pathogenic

SpliceAI

1585 predictions. Top by Δscore:

VariantEffectΔscore
12:100204931:T:TAacceptor_gain1.0000
12:100204937:TA:Tacceptor_loss1.0000
12:100204938:A:AGacceptor_gain1.0000
12:100204938:AG:Aacceptor_gain1.0000
12:100204938:AGG:Aacceptor_gain1.0000
12:100204938:AGGGT:Aacceptor_loss1.0000
12:100204939:G:GTacceptor_gain1.0000
12:100204939:GG:Gacceptor_gain1.0000
12:100204939:GGG:Gacceptor_gain1.0000
12:100204939:GGGT:Gacceptor_gain1.0000
12:100204939:GGGTT:Gacceptor_gain1.0000
12:100205053:AAAAG:Adonor_loss1.0000
12:100205055:AAGGT:Adonor_loss1.0000
12:100205056:AGG:Adonor_loss1.0000
12:100205058:GTA:Gdonor_loss1.0000
12:100205059:T:Adonor_loss1.0000
12:100207658:TATA:Tacceptor_loss1.0000
12:100207661:A:ACacceptor_loss1.0000
12:100207661:AGGTT:Aacceptor_gain1.0000
12:100207662:G:Aacceptor_loss1.0000
12:100207662:GGTT:Gacceptor_gain1.0000
12:100207662:GGTTG:Gacceptor_gain1.0000
12:100207719:A:AGacceptor_gain1.0000
12:100207784:ATGGT:Adonor_loss1.0000
12:100207785:TGGT:Tdonor_loss1.0000
12:100207786:GGTGA:Gdonor_loss1.0000
12:100207787:G:GGdonor_gain1.0000
12:100207787:GTG:Gdonor_loss1.0000
12:100207788:TGA:Tdonor_loss1.0000
12:100207789:GAG:Gdonor_loss1.0000

AlphaMissense

2645 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:100205676:G:CG63R1.000
12:100205712:T:AW75R1.000
12:100205712:T:CW75R1.000
12:100210306:G:AG176E1.000
12:100210330:T:CL184P1.000
12:100210344:T:CS189P1.000
12:100210351:G:CR191T1.000
12:100210351:G:TR191M1.000
12:100212301:A:CK206N1.000
12:100212301:A:TK206N1.000
12:100212491:T:CL238S1.000
12:100212494:C:AP239H1.000
12:100220080:G:CR332P1.000
12:100200877:G:AG9E0.999
12:100204963:G:CR31P0.999
12:100205047:C:AP59H0.999
12:100205047:C:GP59R0.999
12:100205677:G:AG63D0.999
12:100205691:T:AW68R0.999
12:100205691:T:CW68R0.999
12:100207710:C:AN101K0.999
12:100207710:C:GN101K0.999
12:100207751:A:TE115V0.999
12:100210136:T:AV148D0.999
12:100210157:C:AT155K0.999
12:100210305:G:AG176R0.999
12:100210305:G:CG176R0.999
12:100210306:G:TG176V0.999
12:100210321:C:TT181I0.999
12:100210325:T:AN182K0.999

dbSNP variants (sampled 300 via entrez): RS1000093090 (12:100215528 T>C), RS1000113729 (12:100200047 C>T), RS1000148765 (12:100213485 A>G), RS1000193578 (12:100205465 A>G), RS1000377215 (12:100212689 A>G), RS1000464910 (12:100199557 A>G,T), RS1000546841 (12:100220021 T>A), RS1000639079 (12:100219713 C>A,T), RS1000754106 (12:100211891 G>A), RS1001290926 (12:100212368 C>T), RS1001517107 (12:100198908 G>A,T), RS1001645776 (12:100218028 C>T), RS1001879493 (12:100210516 C>T), RS1001900277 (12:100198881 CTCAGGTGGGAGGA>C,CTCAGGTGGGAGGATCAGGTGGGAGGA), RS1001934597 (12:100202994 A>G)

Disease associations

OMIM: gene MIM:619729 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression, affects cotreatment, increases abundance4
Arsenicincreases abundance, increases expression, affects cotreatment2
Valproic Acidincreases expression2
Cadmium Chlorideincreases expression, increases abundance2
bisphenol Faffects cotreatment, increases expression1
dicrotophosdecreases expression1
bisphenol Adecreases methylation1
arseniteaffects binding, increases reaction1
cobaltous chlorideincreases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
ICG 001decreases expression1
bisphenol Sincreases methylation1
jinfukangdecreases expression1
Resveratrolincreases expression, affects cotreatment1
Temozolomideincreases expression1
Cadmiumincreases abundance, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Hydrogen Peroxideaffects expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Plant Extractsincreases expression, affects cotreatment1
Quercetindecreases expression1
Tretinoindecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Aflatoxin B1increases methylation1
Aflatoxin M1decreases expression1

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.