DCTN3

gene
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Also known as DCTN-22

Summary

DCTN3 (dynactin subunit 3, HGNC:2713) is a protein-coding gene on chromosome 9p13.3, encoding Dynactin subunit 3 (O75935). Part of the dynactin complex that activates the molecular motor dynein for ultra-processive transport along microtubules. It is a selective cancer dependency (DepMap: 87.3% of cell lines).

This gene encodes the smallest 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. It is involved in a diverse array of cellular functions, including ER-to-Golgi transport, the centripetal movement of lysosomes and endosomes, spindle formation, cytokinesis, chromosome movement, nuclear positioning, and axonogenesis. This subunit, like most other dynactin subunits, exists only as a part of the dynactin complex. It is primarily an alpha-helical protein with very little coiled coil, and binds directly to the largest subunit (p150) of dynactin. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 11258 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 39 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 87.3% of screened cell lines
  • MANE Select transcript: NM_007234

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2713
Approved symbolDCTN3
Namedynactin subunit 3
Location9p13.3
Locus typegene with protein product
StatusApproved
AliasesDCTN-22
Ensembl geneENSG00000137100
Ensembl biotypeprotein_coding
OMIM607387
Entrez11258

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 12 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000259632, ENST00000341694, ENST00000378911, ENST00000378913, ENST00000378916, ENST00000421919, ENST00000472074, ENST00000472418, ENST00000477738, ENST00000479399, ENST00000481438, ENST00000888986, ENST00000888987, ENST00000940739, ENST00000962454, ENST00000962455

RefSeq mRNA: 5 — MANE Select: NM_007234 NM_001281425, NM_001281426, NM_001281427, NM_007234, NM_024348

CCDS: CCDS65028, CCDS65029, CCDS6560, CCDS6561

Canonical transcript exons

ENST00000259632 — 7 exons

ExonStartEnd
ENSE000008329273461603034616113
ENSE000008329283461788534617971
ENSE000008329293461867634618760
ENSE000011900263462036934620495
ENSE000035213703461471034614768
ENSE000035667973461404234614101
ENSE000038503733461354634613871

Expression profiles

Bgee: expression breadth ubiquitous, 298 present calls, max score 98.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 64.2891 / max 245.6869, expressed in 1823 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
10052764.28911823

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534398.41gold quality
ganglionic eminenceUBERON:000402398.16gold quality
prefrontal cortexUBERON:000045198.06gold quality
ventricular zoneUBERON:000305398.00gold quality
right frontal lobeUBERON:000281097.94gold quality
adenohypophysisUBERON:000219697.80gold quality
right hemisphere of cerebellumUBERON:001489097.78gold quality
pituitary glandUBERON:000000797.71gold quality
cerebellar hemisphereUBERON:000224597.59gold quality
Brodmann (1909) area 9UBERON:001354097.59gold quality
cerebellar cortexUBERON:000212997.58gold quality
nucleus accumbensUBERON:000188297.52gold quality
hindlimb stylopod muscleUBERON:000425297.44gold quality
skin of legUBERON:000151197.43gold quality
dorsolateral prefrontal cortexUBERON:000983497.42gold quality
skin of abdomenUBERON:000141697.36gold quality
cingulate cortexUBERON:000302797.34gold quality
anterior cingulate cortexUBERON:000983597.27gold quality
caudate nucleusUBERON:000187397.17gold quality
amygdalaUBERON:000187697.14gold quality
parotid glandUBERON:000183197.10gold quality
cerebellumUBERON:000203797.10gold quality
frontal cortexUBERON:000187097.05gold quality
frontal lobeUBERON:001652597.05gold quality
neocortexUBERON:000195097.03gold quality
heart left ventricleUBERON:000208497.02gold quality
monocyteCL:000057696.99gold quality
ponsUBERON:000098896.98gold quality
right atrium auricular regionUBERON:000663196.96gold quality
zone of skinUBERON:000001496.95gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-ANND-3yes11.23
E-MTAB-10553yes7.06
E-MTAB-6379no427.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting DCTN3, 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-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-4786-3P99.3668.351390
HSA-MIR-431299.3467.30511
HSA-MIR-7109-5P99.1866.131057
HSA-MIR-570198.9769.541502
HSA-MIR-6780A-3P98.4267.491518
HSA-MIR-7843-3P98.3167.94803
HSA-MIR-4684-3P98.2469.911075
HSA-MIR-6728-5P97.7966.33891
HSA-MIR-668-3P96.1865.80673

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 87.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Study found that in peripheral blood mononuclear cells the median expression of KIFC3, KIF1B, and KIF5C was much lower than the expression of dynactin subunits DCTN1 and DCTN3, in both sporadic amyotrophic lateral sclerosis and healthy cases (PMID:26954557)
  • Study on the Prognostic Values of Dynactin Genes in Low-Grade Glioma. (PMID:33896271)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriodctn3ENSDARG00000041363
mus_musculusDctn3ENSMUSG00000028447
rattus_norvegicusDctn3l1ENSRNOG00000081039

Protein

Protein identifiers

Dynactin subunit 3O75935 (reviewed: O75935)

Alternative names: Dynactin complex subunit 22 kDa subunit

All UniProt accessions (5): A0A0A0MRV8, O75935, X6RA56, X6RCK5, X6RLR1

UniProt curated annotations — full annotation on UniProt →

Function. Part of the dynactin complex that activates the molecular motor dynein for ultra-processive transport along microtubules. Together with dynein may be involved in spindle assembly and cytokinesis.

Subunit / interactions. Subunit of dynactin, a multiprotein complex part of a tripartite complex with dynein and a adapter, such as BICDL1, BICD2 or HOOK3. The dynactin complex is built around ACTR1A/ACTB filament and consists of an actin-related filament composed of a shoulder domain, a pointed end and a barbed end. Its length is defined by its flexible shoulder domain. The soulder is composed of 2 DCTN1 subunits, 4 DCTN2 and 2 DCTN3. The 4 DCNT2 (via N-terminus) bind the ACTR1A filament and act as molecular rulers to determine the length. The pointed end is important for binding dynein-dynactin cargo adapters. Consists of 4 subunits: ACTR10, DCNT4, DCTN5 and DCTN6. The barbed end is composed of a CAPZA1:CAPZB heterodimers, which binds ACTR1A/ACTB filament and dynactin and stabilizes dynactin.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Chromosome. Centromere. Kinetochore. Spindle. Cleavage furrow. Midbody.

Tissue specificity. Ubiquitously expressed. Highly expressed in muscle and pancreas and detected at lower levels in brain.

Similarity. Belongs to the dynactin subunit 3 family.

Isoforms (3)

UniProt IDNamesCanonical?
O75935-11yes
O75935-22
O75935-33

RefSeq proteins (5): NP_001268354, NP_001268355, NP_001268356, NP_009165, NP_077324 (=MANE)

Domains & families (InterPro)

IDNameType
IPR009991DCTN3Family

Pfam: PF07426

UniProt features (6 total): splice variant 2, initiator methionine 1, chain 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9B7JELECTRON MICROSCOPY3.49

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75935-F188.580.53

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 (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

IDPathway
R-HSA-2132295MHC class II antigen presentation
R-HSA-2565942Regulation of PLK1 Activity at G2/M Transition
R-HSA-3371497HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand
R-HSA-380259Loss of Nlp from mitotic centrosomes
R-HSA-380270Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-380320Recruitment of NuMA to mitotic centrosomes
R-HSA-5620912Anchoring of the basal body to the plasma membrane
R-HSA-6807878COPI-mediated anterograde transport
R-HSA-6811436COPI-independent Golgi-to-ER retrograde traffic
R-HSA-8854518AURKA Activation by TPX2

MSigDB gene sets: 184 (showing top): RNGTGGGC_UNKNOWN, FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, MODULE_255, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MODULE_317, MODULE_128, REACTOME_MEMBRANE_TRAFFICKING, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_CYTOKINESIS, TGCTGAY_UNKNOWN, OCT1_03, chr9p13, GOCC_CENTROSOME

GO Biological Process (4): mitotic cell cycle (GO:0000278), microtubule-based process (GO:0007017), cytoskeleton-dependent cytokinesis (GO:0061640), cell division (GO:0051301)

GO Molecular Function (2): structural molecule activity (GO:0005198), protein binding (GO:0005515)

GO Cellular Component (18): kinetochore (GO:0000776), nucleolus (GO:0005730), centrosome (GO:0005813), spindle (GO:0005819), cytosol (GO:0005829), dynactin complex (GO:0005869), midbody (GO:0030496), cleavage furrow (GO:0032154), perinuclear theca (GO:0033011), perinuclear region of cytoplasm (GO:0048471), sperm midpiece (GO:0097225), sperm principal piece (GO:0097228), sperm glycocalyx (GO:0120238), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), microtubule associated complex (GO:0005875)

Reactome top-level categories

Rollup of top-9 pathways:

CategoryPathways
G2/M Transition2
Centrosome maturation2
Adaptive Immune System1
Cellular responses to stress1
Loss of proteins required for interphase microtubule organization from the centrosome1
Mitotic Prometaphase1
Assembly of the 9+0 primary cilium1
ER to Golgi Anterograde Transport1
Golgi-to-ER retrograde transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
intracellular membraneless organelle5
cellular process2
microtubule cytoskeleton2
cytoplasm2
sperm flagellum2
cell cycle1
mitotic nuclear division1
cytokinesis1
molecular_function1
binding1
condensed chromosome, centromeric region1
supramolecular complex1
nuclear lumen1
centriole1
microtubule organizing center1
microtubule associated complex1
actin cytoskeleton1
cell division site1
plasma membrane region1
cytoskeleton1
perinuclear region of cytoplasm1
glycocalyx1
chromosomal region1
intracellular anatomical structure1
protein-containing complex1

Protein interactions and networks

STRING

1230 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DCTN3DCTN1Q14203938
DCTN3DCTN6O00399859
DCTN3DCTN2Q13561832
DCTN3DCTN5Q9BTE1773
DCTN3ACTR1AP42024695
DCTN3ACTR10Q9NZ32689
DCTN3DCTN4Q9UJW0669
DCTN3RPP25LQ8N5L8609
DCTN3FAM219AQ8IW50584
DCTN3ACTR1BP42025502
DCTN3ENHOQ6UWT2470
DCTN3ACTBP02570444
DCTN3CAPZA2P47755421
DCTN3RBM18Q96H35418
DCTN3CAPZA1P52907417

IntAct

98 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:2364”(proximity)0.900
GPS2HDAC3psi-mi:“MI:0914”(association)0.900
DCTN1DCTN6psi-mi:“MI:0914”(association)0.780
DCTN2DCTN6psi-mi:“MI:0914”(association)0.730
DCTN2DCTN3psi-mi:“MI:0914”(association)0.730
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
DCTN1DCTN3psi-mi:“MI:0914”(association)0.710
DYNC1I2DYNC1LI2psi-mi:“MI:0914”(association)0.680
CAPZBCNOT1psi-mi:“MI:0914”(association)0.640
CAPZA2CNOT1psi-mi:“MI:0914”(association)0.640
DCTN5DCTN6psi-mi:“MI:0914”(association)0.640
MIS18ADCTN6psi-mi:“MI:0914”(association)0.640
DYNC1LI1DYNC1LI2psi-mi:“MI:0914”(association)0.530
ACTBL2POTEFpsi-mi:“MI:0914”(association)0.530
CAPZA1CNOT1psi-mi:“MI:0914”(association)0.530
DEFB127DCTN6psi-mi:“MI:0914”(association)0.530
RPS19BP1DCTN6psi-mi:“MI:0914”(association)0.530
PDGFDDCTN6psi-mi:“MI:0914”(association)0.530
DCTN6ZBTB43psi-mi:“MI:0914”(association)0.530
ACTR1ADCTN3psi-mi:“MI:0914”(association)0.530
DCTN6DCTN3psi-mi:“MI:0914”(association)0.530

BioGRID (186): DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Proximity Label-MS), DCTN3 (Proximity Label-MS), DCTN3 (Proximity Label-MS), DCTN3 (Affinity Capture-MS), DCTN3 (Affinity Capture-MS)

ESM2 similar proteins: A3LPQ8, C5DMF2, F1SEC0, F4IK01, O75935, O94376, P45966, P47149, P47822, P87310, P97372, Q06213, Q09248, Q09858, Q0P5A1, Q0VIA1, Q16G71, Q1HQF2, Q23679, Q28Y46, Q3ZCF2, Q4R6W4, Q5E9G3, Q5R6P5, Q61BU1, Q63798, Q68RJ5, Q6C5U8, Q6CVN3, Q6DJ25, Q6IP67, Q755V6, Q758M1, Q7K2D2, Q7PZ25, Q8I1C8, Q8I1H7, Q8LDS5, Q949S9, Q95SK3

Diamond homologs: F1SEC0, O75935, Q0P5A1, Q9Z0Y1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 99 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 traffic1236.1×1e-13
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand1233.7×1e-13
COPI-mediated anterograde transport1219.1×8e-11
MHC class II antigen presentation1418.1×3e-12
Aggrephagy518.0×1e-04
Loss of Nlp from mitotic centrosomes716.1×7e-06
Loss of proteins required for interphase microtubule organization from the centrosome716.1×7e-06
AURKA Activation by TPX2715.4×8e-06

GO biological processes:

GO termPartnersFoldFDR
mitotic spindle organization515.6×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1150 predictions. Top by Δscore:

VariantEffectΔscore
9:34617879:CATTA:Cdonor_loss1.0000
9:34617880:ATTAC:Adonor_loss1.0000
9:34617881:TTA:Tdonor_loss1.0000
9:34617882:TACCT:Tdonor_loss1.0000
9:34617883:A:Cdonor_loss1.0000
9:34617884:C:CGdonor_loss1.0000
9:34617884:CCTG:Cdonor_gain1.0000
9:34617967:TTCAA:Tacceptor_gain1.0000
9:34617968:TCAA:Tacceptor_gain1.0000
9:34617969:CAA:Cacceptor_gain1.0000
9:34617969:CAAC:Cacceptor_gain1.0000
9:34617970:AA:Aacceptor_gain1.0000
9:34617970:AAC:Aacceptor_loss1.0000
9:34617971:ACTA:Aacceptor_loss1.0000
9:34617972:C:CCacceptor_gain1.0000
9:34617980:G:Cacceptor_gain1.0000
9:34617980:G:GCacceptor_gain1.0000
9:34617985:A:Tacceptor_gain1.0000
9:34618672:TTA:Tdonor_loss1.0000
9:34618673:TA:Tdonor_loss1.0000
9:34618674:A:ACdonor_gain1.0000
9:34618674:ACT:Adonor_gain1.0000
9:34618675:C:CTdonor_gain1.0000
9:34618675:CT:Cdonor_gain1.0000
9:34618675:CTC:Cdonor_gain1.0000
9:34618675:CTCT:Cdonor_gain1.0000
9:34618675:CTCTT:Cdonor_gain1.0000
9:34618756:GCCAC:Gacceptor_gain1.0000
9:34618757:CCAC:Cacceptor_gain1.0000
9:34618757:CCACC:Cacceptor_gain1.0000

AlphaMissense

1204 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:34613841:A:GW168R0.994
9:34613841:A:TW168R0.994
9:34613849:A:GF165S0.983
9:34613859:A:GS162P0.982
9:34617950:A:GL68P0.982
9:34617962:A:GL64P0.981
9:34614053:A:CY154D0.978
9:34618704:C:AR51S0.977
9:34618704:C:GR51S0.977
9:34614053:A:GY154H0.976
9:34613839:C:AW168C0.974
9:34613839:C:GW168C0.974
9:34614744:A:GL126P0.972
9:34613861:A:GL161P0.969
9:34613848:G:CF165L0.968
9:34613848:G:TF165L0.968
9:34613850:A:GF165L0.968
9:34614052:T:GY154S0.968
9:34618698:C:AR53S0.967
9:34618698:C:GR53S0.967
9:34617893:A:TI87N0.965
9:34614714:T:GQ136P0.964
9:34618696:A:TV54E0.964
9:34614061:A:GL151P0.961
9:34613828:A:GL172P0.959
9:34613861:A:TL161H0.954
9:34616080:A:GL101P0.954
9:34617904:C:AK83N0.954
9:34617904:C:GK83N0.954
9:34618681:T:AK59I0.954

dbSNP variants (sampled 300 via entrez): RS1001062661 (9:34618484 T>C), RS1001760727 (9:34616366 T>C), RS1002036972 (9:34615607 G>A), RS1002330887 (9:34616733 G>A), RS1002741828 (9:34620236 G>A), RS1003030642 (9:34614845 G>A), RS1003074463 (9:34615017 T>G), RS1003193049 (9:34620154 G>A), RS1003801732 (9:34613216 G>T), RS1004324586 (9:34613608 G>A), RS1004918399 (9:34617191 T>C), RS1005169515 (9:34618918 C>G), RS1005274554 (9:34616971 G>A,T), RS1005508062 (9:34617138 G>A), RS1005576968 (9:34614149 T>A)

Disease associations

OMIM: gene MIM:607387 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST90000025_469Appendicular lean mass1.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067000 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, affects expression, increases expression4
bisphenol Adecreases expression2
aristolochic acid Iincreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
potassium perchloratedecreases expression1
arseniteaffects binding, increases reaction1
sodium arseniteincreases expression1
ICG 001decreases expression1
bisphenol Bincreases expression1
bisphenol Sincreases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Cisplatinincreases expression1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Vitamin Eincreases expression1
Copper Sulfatedecreases expression1
Particulate Matterincreases abundance, decreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651246BindingBinding affinity to human DCTN3 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.