ACTR1B

gene
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Also known as Arp1B

Summary

ACTR1B (actin related protein 1B, HGNC:168) is a protein-coding gene on chromosome 2q11.2, encoding Beta-centractin (P42025). Component of a multi-subunit complex involved in microtubule based vesicle motility.

This gene encodes a 42.3 kD subunit of dynactin, a macromolecular complex consisting of 10 subunits ranging in size from 22 to 150 kD. Dynactin binds to both microtubules and cytoplasmic dynein and is involved in a diverse array of cellular functions, including ER-to-Golgi transport, the centripetal movement of lysosomes and endosomes, spindle formation, chromosome movement, nuclear positioning, and axonogenesis. This subunit, like ACTR1A, is an actin-related protein. These two proteins, which are of equal length and share 90% amino acid identity, are present in a constant ratio of approximately 1:15 in the dynactin complex.

Source: NCBI Gene 10120 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 85 total — 3 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_005735

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:168
Approved symbolACTR1B
Nameactin related protein 1B
Location2q11.2
Locus typegene with protein product
StatusApproved
AliasesArp1B
Ensembl geneENSG00000115073
Ensembl biotypeprotein_coding
OMIM605144
Entrez10120

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 2 retained_intron

ENST00000289228, ENST00000451664, ENST00000460427, ENST00000855773, ENST00000855774, ENST00000855775, ENST00000855776, ENST00000855777, ENST00000855778, ENST00000936775, ENST00000936776, ENST00000936777, ENST00000936778

RefSeq mRNA: 1 — MANE Select: NM_005735 NM_005735

CCDS: CCDS2033

Canonical transcript exons

ENST00000289228 — 11 exons

ExonStartEnd
ENSE000007713009765842797658643
ENSE000007713029765794397658117
ENSE000007713049765715297657192
ENSE000008041459765593997656960
ENSE000013466529766384397664044
ENSE000024492889765744897657509
ENSE000024636419765887997659003
ENSE000035085679765935297659477
ENSE000035751619766188297661946
ENSE000036352349766057197660646
ENSE000036566949765822497658316

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 97.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1656 / max 88.9980, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
2982015.16561803

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right frontal lobeUBERON:000281097.39gold quality
right hemisphere of cerebellumUBERON:001489097.38gold quality
prefrontal cortexUBERON:000045196.94gold quality
cerebellar hemisphereUBERON:000224596.94gold quality
cerebellar cortexUBERON:000212996.90gold quality
body of pancreasUBERON:000115096.61gold quality
apex of heartUBERON:000209896.28gold quality
Brodmann (1909) area 9UBERON:001354096.28gold quality
right uterine tubeUBERON:000130296.24gold quality
left adrenal gland cortexUBERON:003582596.21gold quality
right adrenal glandUBERON:000123396.20gold quality
left adrenal glandUBERON:000123496.15gold quality
cerebellumUBERON:000203796.11gold quality
body of uterusUBERON:000985396.09gold quality
metanephros cortexUBERON:001053396.06gold quality
right adrenal gland cortexUBERON:003582796.05gold quality
body of stomachUBERON:000116195.89gold quality
right lobe of thyroid glandUBERON:000111995.81gold quality
adrenal cortexUBERON:000123595.79gold quality
left ovaryUBERON:000211995.79gold quality
muscle layer of sigmoid colonUBERON:003580595.73gold quality
esophagogastric junction muscularis propriaUBERON:003584195.65gold quality
lower esophagus muscularis layerUBERON:003583395.64gold quality
lower esophagusUBERON:001347395.63gold quality
right ovaryUBERON:000211895.62gold quality
ascending aortaUBERON:000149695.61gold quality
thoracic aortaUBERON:000151595.61gold quality
left uterine tubeUBERON:000130395.59gold quality
frontal cortexUBERON:000187095.57gold quality
frontal lobeUBERON:001652595.57gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting ACTR1B, 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-6867-5P100.0082.213464
HSA-MIR-4692100.0067.322066
HSA-MIR-4673100.0066.641490
HSA-MIR-451499.9967.101870
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-493-5P99.9672.472382
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-95-5P99.8972.173973
HSA-MIR-94499.8270.853042
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-613299.6065.831554
HSA-MIR-6836-5P99.6065.621538
HSA-MIR-426999.5569.891373
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-580-5P99.2870.941776
HSA-MIR-146A-3P99.1368.991881
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-4742-5P98.8968.411542
HSA-MIR-76098.8166.651392
HSA-MIR-6761-5P98.7168.031504
HSA-MIR-1301-3P98.6468.271071
HSA-MIR-504798.6468.621035
HSA-MIR-6873-5P98.4566.141417
HSA-MIR-6826-3P98.1966.321153
HSA-MIR-466097.7967.441328
HSA-MIR-3620-3P97.7864.88772
HSA-MIR-7154-3P97.6565.02985

Literature-anchored findings (GeneRIF, showing 2)

  • Down-regulation of beta-centractin is associated with hepatocellular carcinoma immune escape (PMID:17619203)
  • Data show that 4-oxo-4-HPR inhibited tubulin polymerization and modulated gene expression of spindle aberration associated genes Kif 1C, Kif 2A, Eg5, Tara, tankyrase-1, centractin, and TOGp. (PMID:19996280)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusActr1bENSMUSG00000037351
rattus_norvegicusActr1bENSRNOG00000016789

Paralogs (26): ACTR6 (ENSG00000075089), ACTB (ENSG00000075624), ACTL6B (ENSG00000077080), ACTR5 (ENSG00000101442), ACTR3C (ENSG00000106526), ACTA2 (ENSG00000107796), ACTR8 (ENSG00000113812), 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

Beta-centractinP42025 (reviewed: P42025)

Alternative names: Actin-related protein 1B

All UniProt accessions (1): P42025

UniProt curated annotations — full annotation on UniProt →

Function. Component of a multi-subunit complex involved in microtubule based vesicle motility. It is associated with the centrosome.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Similarity. Belongs to the actin family. ARP1 subfamily.

RefSeq proteins (1): NP_005726* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004000ActinFamily
IPR004001Actin_CSConserved_site
IPR020902Actin/actin-like_CSConserved_site
IPR043129ATPase_NBDHomologous_superfamily

Pfam: PF00022

UniProt features (5 total): modified residue 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P42025-F193.340.86

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): 1, 4

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-2132295MHC class II antigen presentation
R-HSA-6798695Neutrophil degranulation
R-HSA-1280218Adaptive Immune System
R-HSA-168249Innate Immune System
R-HSA-168256Immune System

MSigDB gene sets: 144 (showing top): TAATAAT_MIR126, REACTOME_INNATE_IMMUNE_SYSTEM, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOCC_SECRETORY_GRANULE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, BROWNE_HCMV_INFECTION_48HR_DN, GOCC_CENTROSOME, MODULE_98, LEE_AGING_MUSCLE_UP, GOCC_SECRETORY_VESICLE, GOCC_VESICLE_LUMEN, MODULE_438, BLALOCK_ALZHEIMERS_DISEASE_DN

GO Biological Process (0):

GO Molecular Function (3): ATP binding (GO:0005524), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (11): extracellular region (GO:0005576), cytoplasm (GO:0005737), centrosome (GO:0005813), cytosol (GO:0005829), dynactin complex (GO:0005869), membrane (GO:0016020), secretory granule lumen (GO:0034774), extracellular exosome (GO:0070062), ficolin-1-rich granule lumen (GO:1904813), microtubule organizing center (GO:0005815), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Immune System2
Adaptive Immune System1
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
intracellular anatomical structure1
centriole1
microtubule organizing center1
cytoplasm1
microtubule associated complex1
actin cytoskeleton1
secretory granule1
cytoplasmic vesicle lumen1
extracellular vesicle1
intracellular organelle lumen1
ficolin-1-rich granule1
microtubule cytoskeleton1
intracellular membraneless organelle1

Protein interactions and networks

STRING

3261 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ACTR1BDCTN2Q13561726
ACTR1BMYO1AQ9UBC5715
ACTR1BOTPQ5XKR4665
ACTR1BDCTN4Q9UJW0649
ACTR1BDCTN1Q14203634
ACTR1BCAPZA2P47755559
ACTR1BCAPZA1P52907548
ACTR1BCAPZBP47756538
ACTR1BPITX1P78337507
ACTR1BRNF181Q9P0P0506
ACTR1BDCTN3O75935502
ACTR1BOTX1P32242490
ACTR1BARHGDIAP52565452
ACTR1BPITX2Q99697451
ACTR1BDCTN6O00399441

IntAct

110 interactions, top by confidence:

ABTypeScore
DCTN1DCTN6psi-mi:“MI:0914”(association)0.780
DCTN2DCTN6psi-mi:“MI:0914”(association)0.730
DCTN2DCTN3psi-mi:“MI:0914”(association)0.730
DCTN1DCTN3psi-mi:“MI:0914”(association)0.710
DYNC1I2DYNC1LI2psi-mi:“MI:0914”(association)0.680
ACTR1BDCTN1psi-mi:“MI:0915”(physical association)0.650
MIS18ADCTN6psi-mi:“MI:0914”(association)0.640
CCT2PPP6Cpsi-mi:“MI:0914”(association)0.640
CAPZBCNOT1psi-mi:“MI:0914”(association)0.640
CAPZA2CNOT1psi-mi:“MI:0914”(association)0.640
DCTN5DCTN6psi-mi:“MI:0914”(association)0.640
PDCL3PEX7psi-mi:“MI:0914”(association)0.640
Dctn2DCTN6psi-mi:“MI:0914”(association)0.560
ACTR1BHTTpsi-mi:“MI:0915”(physical association)0.560
UQCRHDCTN6psi-mi:“MI:0914”(association)0.530
GPS2DCTN6psi-mi:“MI:0914”(association)0.530
RPS19BP1DCTN6psi-mi:“MI:0914”(association)0.530
BMERB1DCTN6psi-mi:“MI:0914”(association)0.530
DEFB127DCTN6psi-mi:“MI:0914”(association)0.530
DCTN6ZBTB43psi-mi:“MI:0914”(association)0.530

BioGRID (210): ACTR1B (Two-hybrid), ACTR1B (Affinity Capture-MS), ACTR1B (Affinity Capture-MS), ACTR1B (Affinity Capture-MS), ACTR1B (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), CCT4 (Affinity Capture-MS), DCTN4 (Affinity Capture-MS), ACTR1A (Affinity Capture-MS), ACTR10 (Affinity Capture-MS), DCTN5 (Affinity Capture-MS), CCT3 (Affinity Capture-MS), DCTN6 (Affinity Capture-MS), SCCPDH (Affinity Capture-MS), CCT7 (Affinity Capture-MS)

ESM2 similar proteins: A2WNB0, A2XMK6, A2YUL5, A3ANB5, A4FUX8, A4IFE3, F2Z5G5, O94241, O94630, O94805, O96019, O96621, P02583, P32381, P38673, P42025, P45888, P45889, P45890, P45891, P47117, P51775, P53489, P85515, P86173, Q09443, Q09849, Q0IEG8, Q2TA43, Q4R333, Q4R6J9, Q54I79, Q5BL41, Q5NBI2, Q61JZ2, Q6AY16, Q6C982, Q6Z256, Q74ZV8, Q7ZTP2

Diamond homologs: A2BDB0, A2XLF2, A2XNS1, A3C6D7, A4IFE3, F2Z5G5, O17320, O18840, O65314, O81221, P02578, P04829, P0C539, P0CJ46, P0CJ47, P0DM41, P0DM42, P10981, P10984, P10986, P10990, P17304, P30162, P30163, P30167, P30171, P38673, P42023, P42025, P45885, P45886, P45889, P48465, P48975, P53455, P53456, P53457, P53458, P53470, P53471

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 89 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
COPI-independent Golgi-to-ER retrograde traffic1136.2×2e-12
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand1133.8×3e-12
Sensory processing of sound524.5×9e-05
COPI-mediated anterograde transport1119.2×8e-10
MHC class II antigen presentation1217.0×5e-10
Sensory processing of sound by inner hair cells of the cochlea615.5×1e-04
Loss of Nlp from mitotic centrosomes615.1×1e-04
Loss of proteins required for interphase microtubule organization from the centrosome615.1×1e-04

GO biological processes:

GO termPartnersFoldFDR
axonogenesis510.6×8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic1
Uncertain significance56
Likely benign6
Benign2

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
394206GRCh37/hg19 2q11.1-11.2(chr2:95691600-100587394)Pathogenic
395690GRCh37/hg19 2q11.1-12.3(chr2:95529039-108518266)Pathogenic
59145GRCh38/hg38 2p11.2-q11.2(chr2:91443218-102334856)x3Pathogenic
2685857GRCh37/hg19 2q11.1-11.2(chr2:95773428-102550061)x3Likely pathogenic

SpliceAI

2097 predictions. Top by Δscore:

VariantEffectΔscore
2:97656958:CCG:Cacceptor_gain1.0000
2:97656959:CG:Cacceptor_gain1.0000
2:97656959:CGC:Cacceptor_gain1.0000
2:97656961:C:CCacceptor_gain1.0000
2:97657442:CCTCA:Cdonor_loss1.0000
2:97657443:CTCAC:Cdonor_loss1.0000
2:97657444:TCA:Tdonor_loss1.0000
2:97657445:CAC:Cdonor_loss1.0000
2:97657446:A:ACdonor_gain1.0000
2:97657447:C:CCdonor_gain1.0000
2:97657508:GCC:Gacceptor_loss1.0000
2:97657509:CCTG:Cacceptor_loss1.0000
2:97657510:C:CCacceptor_gain1.0000
2:97657510:CTGTG:Cacceptor_loss1.0000
2:97657939:GTA:Gdonor_loss1.0000
2:97657940:TA:Tdonor_loss1.0000
2:97658098:C:CTacceptor_gain1.0000
2:97658217:CACTT:Cdonor_loss1.0000
2:97658218:ACTT:Adonor_loss1.0000
2:97658219:CTT:Cdonor_loss1.0000
2:97658220:TTA:Tdonor_loss1.0000
2:97658221:TACAT:Tdonor_loss1.0000
2:97658222:A:ACdonor_gain1.0000
2:97658222:ACA:Adonor_loss1.0000
2:97658223:C:CTdonor_gain1.0000
2:97658223:CA:Cdonor_gain1.0000
2:97658223:CAT:Cdonor_gain1.0000
2:97658223:CATCA:Cdonor_gain1.0000
2:97658312:GCTCG:Gacceptor_gain1.0000
2:97658313:CTCG:Cacceptor_gain1.0000

AlphaMissense

2443 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:97656958:C:TG344D1.000
2:97657152:C:TG343D1.000
2:97656930:A:CF353L0.999
2:97656930:A:TF353L0.999
2:97656932:A:GF353L0.999
2:97656940:A:GL350P0.999
2:97656946:G:TA348D0.999
2:97656949:A:GL347P0.999
2:97656959:C:GG344R0.999
2:97657153:C:AG343C0.999
2:97657153:C:GG343R0.999
2:97657159:A:GW341R0.999
2:97657159:A:TW341R0.999
2:97657497:C:GR313P0.999
2:97658430:T:AK218N0.999
2:97658430:T:GK218N0.999
2:97658562:A:CF174L0.999
2:97658562:A:TF174L0.999
2:97658564:A:GF174L0.999
2:97658620:C:TG155E0.999
2:97658639:C:GA149P0.999
2:97658881:A:CS146R0.999
2:97658881:A:TS146R0.999
2:97658883:T:GS146R0.999
2:97658993:A:GL109P0.999
2:97659399:A:GW90R0.999
2:97659399:A:TW90R0.999
2:97659420:A:GW83R0.999
2:97659420:A:TW83R0.999
2:97661929:T:AK22N0.999

dbSNP variants (sampled 300 via entrez): RS1000420174 (2:97656499 C>G), RS1000524736 (2:97656004 GTTT>G,GTT), RS1000797664 (2:97661564 C>T), RS1000849924 (2:97661282 T>C), RS1001400126 (2:97660905 A>G), RS1001444121 (2:97660712 C>T), RS1001692163 (2:97655610 C>T), RS1002265733 (2:97662953 C>A,T), RS1002564841 (2:97664269 G>A,C), RS1002580055 (2:97658167 C>G,T), RS1002641219 (2:97662643 G>A,T), RS1002791733 (2:97664372 G>A), RS1003007775 (2:97664565 A>G), RS1003220741 (2:97665496 G>A), RS1003579374 (2:97665882 ATCC>A)

Disease associations

OMIM: gene MIM:605144 | disease phenotypes: MIM:126800

GenCC curated gene-disease

Mondo (1): Duane retraction syndrome (MONDO:0007473)

Orphanet (1): Duane retraction syndrome (Orphanet:233)

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST007328_33Alcohol consumption (drinks per week)2.000000e-10
GCST008103_128Bipolar disorder2.000000e-06
GCST008522_43Bitter alcoholic beverage consumption4.000000e-09
GCST010697_1Cortical surface area (min-P)6.000000e-12
GCST010698_17Subcortical volume (min-P)9.000000e-09
GCST010699_105Brain morphology (min-P)2.000000e-11
GCST010700_9Cortical thickness (MOSTest)9.000000e-14
GCST010701_54Cortical surface area (MOSTest)2.000000e-16
GCST010702_79Subcortical volume (MOSTest)5.000000e-09
GCST010703_322Brain morphology (MOSTest)1.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0010092bitter alcoholic beverage consumption measurement
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness

MeSH disease descriptors (1)

DescriptorNameTree numbers
D004370Duane Retraction SyndromeC10.292.562.700.375.500; C11.270.235; C11.590.436.400.500; C16.320.290.235

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression4
Arsenicdecreases expression, increases abundance, affects cotreatment2
ginger extractdecreases expression, increases abundance1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
zinc chromateincreases abundance, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
CC-8490decreases expression1
bisphenol Saffects cotreatment, increases methylation1
Temozolomidedecreases expression1
Arsenic Trioxidedecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Atrazineincreases expression1
Diethylhexyl Phthalatedecreases expression1
Dimethyl Sulfoxideincreases expression1
Ivermectindecreases expression1
Oils, Volatiledecreases expression, increases abundance1
Phthalic Acidsdecreases methylation1
Quercetinincreases expression1
Seleniumincreases expression1
Smokedecreases expression1
Tamoxifendecreases expression1
Valproic Aciddecreases expression1
Vitamin Eincreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Acrylamidedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03059420Not specifiedRECRUITINGGenetic Studies of Strabismus, Congenital Cranial Dysinnervation Disorders (CCDDs), and Their Associated Anomalies
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Duane retraction syndrome