DYNLT3

gene
On this page

Also known as TCTEX1L

Summary

DYNLT3 (dynein light chain Tctex-type 3, HGNC:11694) is a protein-coding gene on chromosome Xp11.4, encoding Dynein light chain Tctex-type 3 (P51808). Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function.

This gene encodes a member of a subclass of dynein light chains. The encoded protein homodimerizes and forms the light chain component of the cytoplasmic dynein motor protein complex. This protein may be important for binding dynein to specific cargos including the spindle checkpoint protein BUB3. This protein may also function independently of dynein as a transcriptional modulator. Pseudogenes of this gene are found on chromosomes 2 and 20.

Source: NCBI Gene 6990 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 40 total — 1 pathogenic
  • MANE Select transcript: NM_006520

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11694
Approved symbolDYNLT3
Namedynein light chain Tctex-type 3
LocationXp11.4
Locus typegene with protein product
StatusApproved
AliasesTCTEX1L
Ensembl geneENSG00000165169
Ensembl biotypeprotein_coding
OMIM300302
Entrez6990

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000378578, ENST00000378581, ENST00000432389, ENST00000859528, ENST00000859529

RefSeq mRNA: 1 — MANE Select: NM_006520 NM_006520

CCDS: CCDS14243

Canonical transcript exons

ENST00000378578 — 5 exons

ExonStartEnd
ENSE000010909213784102837841105
ENSE000010909233784631737846358
ENSE000013122933783883637840651
ENSE000013240863784178237841905
ENSE000014780053784748137847571

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.4054 / max 588.4982, expressed in 1758 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
19888517.23401731
19888610.67301701
1988870.3777183
1988880.120637

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gingivaUBERON:000182899.14gold quality
gingival epitheliumUBERON:000194999.14gold quality
esophagus squamous epitheliumUBERON:000692099.10gold quality
tongue squamous epitheliumUBERON:000691999.05gold quality
ponsUBERON:000098898.97gold quality
squamous epitheliumUBERON:000691498.60gold quality
dorsal motor nucleus of vagus nerveUBERON:000287098.59gold quality
substantia nigra pars compactaUBERON:000196598.53gold quality
Brodmann (1909) area 23UBERON:001355498.51gold quality
lateral nuclear group of thalamusUBERON:000273698.38gold quality
cranial nerve IIUBERON:000094198.32gold quality
oral cavityUBERON:000016798.29gold quality
renal glomerulusUBERON:000007498.27gold quality
dorsal root ganglionUBERON:000004498.22gold quality
metanephric glomerulusUBERON:000473698.20gold quality
epithelium of esophagusUBERON:000197698.13gold quality
superior vestibular nucleusUBERON:000722797.91gold quality
nephron tubuleUBERON:000123197.88gold quality
postcentral gyrusUBERON:000258197.86gold quality
substantia nigra pars reticulataUBERON:000196697.85gold quality
cartilage tissueUBERON:000241897.84gold quality
hair follicleUBERON:000207397.78gold quality
superior frontal gyrusUBERON:000266197.64gold quality
trigeminal ganglionUBERON:000167597.59gold quality
parietal lobeUBERON:000187297.59gold quality
kidney epitheliumUBERON:000481997.48gold quality
entorhinal cortexUBERON:000272897.39gold quality
pharyngeal mucosaUBERON:000035597.26gold quality
middle temporal gyrusUBERON:000277197.19gold quality
medulla oblongataUBERON:000189697.09gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-10287yes37.68
E-MTAB-6701yes18.39
E-MTAB-9388yes10.22
E-MTAB-6142no164.05
E-HCAD-13no3.51
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

159 targeting DYNLT3, 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-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
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-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-477599.9875.006394
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-56899.9869.862084
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-1213699.9872.815713
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-590-3P99.9674.346478
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-302E99.9670.742669
HSA-MIR-548AB99.9571.313488

Literature-anchored findings (GeneRIF, showing 4)

  • The N-terminal half of pUL35, in particular residues 30-43, was identified as a common region for the binding of DYNLT1 and DYNLT3. (PMID:20668116)
  • These data show that both DYNLT1 and DYNLT3 interact with L2 of human papillomavirus 16 during virus infection. (PMID:21166973)
  • Age-associated genes in human mammary gland drive human breast cancer progression. (PMID:32539762)
  • The role of DYNLT3 in breast cancer proliferation, migration, and invasion via epithelial-to-mesenchymal transition. (PMID:37260179)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriodynlt3ENSDARG00000046132
mus_musculusDynlt3ENSMUSG00000031176
rattus_norvegicusDynlt3ENSRNOG00000003611

Paralogs (5): DYNLT1 (ENSG00000146425), DYNLT5 (ENSG00000152760), DYNLT2 (ENSG00000184786), DYNLT4 (ENSG00000188396), DYNLT2B (ENSG00000213123)

Protein

Protein identifiers

Dynein light chain Tctex-type 3P51808 (reviewed: P51808)

Alternative names: Protein 91/23, T-complex-associated testis-expressed 1-like

All UniProt accessions (3): A6NGJ0, P51808, F2Z328

UniProt curated annotations — full annotation on UniProt →

Function. Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Probably binds BUB3 as part of transport cargo. Required for the efficient progression through mitosis.

Subunit / interactions. Homodimer. The cytoplasmic dynein 1 complex consists of two catalytic heavy chains (HCs) and a number of non-catalytic subunits presented by intermediate chains (ICs), light intermediate chains (LICs) and light chains (LCs); the composition seems to vary in respect to the IC, LIC and LC composition. The heavy chain homodimer serves as a scaffold for the probable homodimeric assembly of the respective non-catalytic subunits. The ICs and LICs bind directly to the HC dimer and the LCs assemble on the IC dimer. DYNLT1 and DYNLT3 compete for association with dynein IC (DYNC1I1 or DYNC1I2). Self-associates. Interacts with DYNC1I1 and DYNC1I2. Interacts with BUB3. Interacts with SATB1 in nucleus to form complex with matrix attachment regions (MARs) of DNA.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Chromosome. Centromere. Kinetochore.

Similarity. Belongs to the dynein light chain Tctex-type family.

RefSeq proteins (1): NP_006511* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005334Tctex-1-likeFamily
IPR038586Tctex-1-like_sfHomologous_superfamily

Pfam: PF03645

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P51808-F190.460.84

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): 4

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 286 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_CELL_CYCLE_CHECKPOINT, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, ZHAN_LATE_DIFFERENTIATION_GENES_UP, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOZGIT_ESR1_TARGETS_DN, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_CELL_CYCLE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_CHROMOSOME_SEPARATION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1

GO Biological Process (4): microtubule-based movement (GO:0007018), regulation of mitotic cell cycle (GO:0007346), positive regulation of mitotic cell cycle (GO:0045931), cell division (GO:0051301)

GO Molecular Function (3): identical protein binding (GO:0042802), dynein intermediate chain binding (GO:0045505), protein binding (GO:0005515)

GO Cellular Component (10): kinetochore (GO:0000776), nucleus (GO:0005634), cytoplasm (GO:0005737), cytoplasmic dynein complex (GO:0005868), mitotic spindle astral microtubule (GO:0061673), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoskeleton (GO:0005856), microtubule (GO:0005874), dynein complex (GO:0030286)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle3
mitotic cell cycle2
protein binding2
microtubule-based process1
regulation of cell cycle1
regulation of mitotic cell cycle1
positive regulation of cell cycle1
cellular process1
binding1
condensed chromosome, centromeric region1
supramolecular complex1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
dynein complex1
astral microtubule1
mitotic spindle1
chromosomal region1
microtubule cytoskeleton1
polymeric cytoskeletal fiber1
microtubule associated complex1
catalytic complex1

Protein interactions and networks

STRING

1200 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DYNLT3BUB3O43684880
DYNLT3DYNLL2Q96FJ2825
DYNLT3DYNLL1P63167791
DYNLT3DYNLRB2Q8TF09786
DYNLT3DYNLRB1Q9NP97743
DYNLT3DYNLT2BQ8WW35709
DYNLT3DYNC1LI2O43237683
DYNLT3DYNC2LI1Q8TCX1667
DYNLT3DYNC2I2Q96EX3636
DYNLT3DYNC2I1Q8WVS4635
DYNLT3DYNC1H1Q14204633
DYNLT3DYNC1LI1Q9Y6G9626
DYNLT3DYNC1I1O14576590
DYNLT3DRC5Q5JU00543
DYNLT3DYNC1I2Q13409518

IntAct

56 interactions, top by confidence:

ABTypeScore
DYNC1I2DYNLT3psi-mi:“MI:0915”(physical association)0.750
DYNLT3DYNLT3psi-mi:“MI:0915”(physical association)0.740
DYNLT3DYNLT1psi-mi:“MI:0915”(physical association)0.730
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
DYNC1I2DYNC1LI2psi-mi:“MI:0914”(association)0.680
DYNLT1DYNC1LI2psi-mi:“MI:0914”(association)0.640
DYNLT3NIF3L1psi-mi:“MI:0915”(physical association)0.560
NIF3L1DYNLT3psi-mi:“MI:0915”(physical association)0.560
DYNLT3DYNC1I2psi-mi:“MI:0915”(physical association)0.560
DYNLT3PMS1psi-mi:“MI:0915”(physical association)0.560
DYNLT3CCL28psi-mi:“MI:0915”(physical association)0.560
DYNLT3C2orf15psi-mi:“MI:0915”(physical association)0.560
DYNLT3ZC3H14psi-mi:“MI:0915”(physical association)0.560
DYNC1LI1DYNC1LI2psi-mi:“MI:0914”(association)0.530
PAFAH1B1DYNLT3psi-mi:“MI:0914”(association)0.510
DYNLT2BTIPRLpsi-mi:“MI:0914”(association)0.510
BMP2KDYNLT3psi-mi:“MI:0915”(physical association)0.490
BUB3DYNLT3psi-mi:“MI:0407”(direct interaction)0.440
HTRA1DYNLT3psi-mi:“MI:0915”(physical association)0.370
DYNLT3TESCpsi-mi:“MI:0915”(physical association)0.370
Dynlrb1DYNC1LI2psi-mi:“MI:0914”(association)0.350
DYNC1H1psi-mi:“MI:0914”(association)0.350
MAPRE1SCAMP1psi-mi:“MI:0914”(association)0.350

BioGRID (57): DYNLT3 (Two-hybrid), NIF3L1 (Two-hybrid), DYNLT3 (Affinity Capture-MS), DYNLT3 (Two-hybrid), TESC (Two-hybrid), DYNLT3 (Two-hybrid), DYNLT3 (Affinity Capture-MS), DYNLT3 (Affinity Capture-MS), PAFAH1B1 (Affinity Capture-MS), DYNLT3 (Affinity Capture-MS), TCTEX1D2 (Affinity Capture-MS), DYNLT3 (Affinity Capture-MS), DYNLT3 (Proximity Label-MS), DYNLT3 (Proximity Label-MS), DYNLT3 (Proximity Label-MS)

ESM2 similar proteins: A6SM77, A7F3L0, B4MYA1, F1QMY1, O02173, O04420, O61820, O74366, O95433, P11645, P32502, P34605, P34686, P36149, P38886, P51808, P56387, P87123, Q08CN0, Q13257, Q1HPS4, Q23400, Q28IG8, Q2F5R8, Q32P71, Q54EY2, Q54LT2, Q54PG1, Q5NVF5, Q5ZKP4, Q66IC8, Q6DG85, Q6XXL8, Q7QGK4, Q84WI4, Q86K94, Q8BK64, Q8H0S3, Q8N9S3, Q8SPS9

Diamond homologs: F1QMY1, P51807, P51808, P56387, P63171, P63172, Q54PG1, Q5NVF5, Q6XXL8, Q8SPS9, Q94524, Q9Z336, Q8WW35, Q9CQ66, A2VDD2, P11985, Q3B8D7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 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
Aggrephagy699.3×1e-10
COPI-independent Golgi-to-ER retrograde traffic796.9×3e-12
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand677.4×5e-10
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal969.9×6e-14
EML4 and NUDC in mitotic spindle formation955.7×2e-13
Loss of Nlp from mitotic centrosomes552.9×1e-07
Loss of proteins required for interphase microtubule organization from the centrosome552.9×1e-07
Resolution of Sister Chromatid Cohesion951.9×3e-13

GO biological processes:

GO termPartnersFoldFDR
microtubule-based movement567.2×8e-07
cell division510.5×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance10
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2685701GRCh37/hg19 Xp22.11-11.3(chrX:24633854-44236178)x1Pathogenic

SpliceAI

580 predictions. Top by Δscore:

VariantEffectΔscore
X:37840648:GTTCC:Gacceptor_loss1.0000
X:37840650:TC:Tacceptor_gain1.0000
X:37840651:CC:Cacceptor_gain1.0000
X:37840652:C:CCacceptor_gain1.0000
X:37840652:C:Gacceptor_loss1.0000
X:37841022:TCTTA:Tdonor_loss1.0000
X:37841023:CTTA:Cdonor_loss1.0000
X:37841024:TTAC:Tdonor_loss1.0000
X:37841025:TA:Tdonor_loss1.0000
X:37841026:A:AGdonor_loss1.0000
X:37841027:C:Adonor_loss1.0000
X:37841104:CA:Cacceptor_gain1.0000
X:37841106:C:CCacceptor_gain1.0000
X:37841135:T:Cacceptor_gain1.0000
X:37841776:ACTT:Adonor_loss1.0000
X:37841778:TTA:Tdonor_loss1.0000
X:37841779:TAC:Tdonor_loss1.0000
X:37841780:A:ACdonor_gain1.0000
X:37841780:AC:Adonor_gain1.0000
X:37841781:C:CAdonor_gain1.0000
X:37841781:CC:Cdonor_gain1.0000
X:37841781:CCA:Cdonor_gain1.0000
X:37841781:CCAA:Cdonor_gain1.0000
X:37841781:CCAAT:Cdonor_gain1.0000
X:37841901:ACACA:Aacceptor_gain1.0000
X:37841902:CACA:Cacceptor_gain1.0000
X:37841902:CACAC:Cacceptor_gain1.0000
X:37841904:CA:Cacceptor_gain1.0000
X:37841906:C:CCacceptor_gain1.0000
X:37846313:TCACC:Tdonor_loss1.0000

AlphaMissense

774 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:37841046:A:GW86R0.999
X:37841046:A:TW86R0.999
X:37841789:T:AK63N0.999
X:37841789:T:GK63N0.999
X:37840596:A:CF110L0.998
X:37840596:A:TF110L0.998
X:37840598:A:GF110L0.998
X:37841031:C:GD91H0.998
X:37841044:C:AW86C0.998
X:37841044:C:GW86C0.998
X:37841814:A:GL55P0.998
X:37840600:A:TV109D0.997
X:37840611:A:CC105W0.997
X:37841030:T:AD91V0.997
X:37841060:G:TA81D0.997
X:37841098:A:CC68W0.997
X:37841100:A:GC68R0.997
X:37841790:T:AK63I0.997
X:37841791:T:CK63E0.997
X:37841838:A:TI47K0.997
X:37840594:G:TA111D0.996
X:37840606:A:TV107D0.996
X:37841029:A:CD91E0.996
X:37841029:A:TD91E0.996
X:37841045:C:GW86S0.996
X:37841061:C:GA81P0.996
X:37846324:A:TV22D0.996
X:37841030:T:GD91A0.995
X:37841031:C:AD91Y0.995
X:37841099:C:TC68Y0.995

dbSNP variants (sampled 300 via entrez): RS1000210049 (X:37842677 C>A,T), RS1000220055 (X:37845070 T>A,C), RS1000655595 (X:37845433 T>G), RS1002294228 (X:37847223 C>G,T), RS1002528651 (X:37845625 T>C), RS1002674938 (X:37842336 C>A,T), RS1002705960 (X:37842792 A>G), RS1002768931 (X:37845292 C>T), RS1003530498 (X:37847566 C>T), RS1003563687 (X:37849515 T>C), RS1003682089 (X:37840437 A>C), RS1003773040 (X:37847278 C>A), RS1004002896 (X:37838363 G>A), RS1004213960 (X:37846688 C>T), RS1004243644 (X:37848965 A>G)

Disease associations

OMIM: gene MIM:300302 | 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

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression2
Resveratroldecreases expression, affects cotreatment, increases expression2
Estradiolincreases expression, increases reaction2
Phenylmercuric Acetateincreases expression, affects cotreatment2
dicrotophosdecreases expression1
alpha phellandreneincreases expression1
triphenyl phosphateaffects expression1
kojic aciddecreases expression1
trichostatin Aaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydeincreases expression1
potassium chromate(VI)decreases expression1
4-hydroxy-2-nonenalaffects binding1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, increases expression1
Air Pollutantsdecreases expression, increases abundance1
Antimycin Adecreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation, increases methylation1
Carbamazepineaffects expression1
Cisplatinincreases expression1
Coumestrolaffects cotreatment, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diethylhexyl Phthalateincreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Quercetinincreases expression1
Rotenoneincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B1QIAbcam HeLa DYNLT3 KOCancer cell lineFemale

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.