DYNLT2

Summary

DYNLT2 (dynein light chain Tctex-type 2, HGNC:11695) is a protein-coding gene on chromosome 6q27, encoding Dynein light chain Tctex-type protein 2 (Q8IZS6). Component of dynein, a family of motor proteins essential for movement along microtubules.

Predicted to enable dynein intermediate chain binding activity. Predicted to be involved in microtubule-based movement. Predicted to be located in cytosol and sperm flagellum. Predicted to be part of cytoplasmic dynein complex. Predicted to be active in cytoplasm.

Source: NCBI Gene 6991 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_174910

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11695
Approved symbol	DYNLT2
Name	dynein light chain Tctex-type 2
Location	6q27
Locus type	gene with protein product
Status	Approved
Aliases	TCTEX1D3, TCTEX2, Tctex4, oda12
Ensembl gene	ENSG00000184786
Ensembl biotype	protein_coding
OMIM	186977
Entrez	6991

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000366774, ENST00000628156, ENST00000940845

RefSeq mRNA: 1 — MANE Select: NM_174910 NM_174910

CCDS: CCDS5310

Canonical transcript exons

ENST00000366774 — 4 exons

Exon	Start	End
ENSE00001307780	169744068	169744274
ENSE00001321513	169743080	169743238
ENSE00001442585	169740109	169740295
ENSE00001442589	169751339	169751572

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 86.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0705 / max 146.8102, expressed in 1358 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
76800	4.0705	1358

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.72	gold quality
left testis	UBERON:0004533	85.86	gold quality
testis	UBERON:0000473	85.63	gold quality
right testis	UBERON:0004534	84.65	gold quality
left ovary	UBERON:0002119	77.31	gold quality
ovary	UBERON:0000992	76.21	gold quality
right uterine tube	UBERON:0001302	76.16	gold quality
right ovary	UBERON:0002118	75.23	gold quality
pituitary gland	UBERON:0000007	74.98	gold quality
endometrium	UBERON:0001295	74.77	gold quality
mucosa of transverse colon	UBERON:0004991	74.72	gold quality
adenohypophysis	UBERON:0002196	74.69	gold quality
spleen	UBERON:0002106	74.43	gold quality
metanephros cortex	UBERON:0010533	74.34	gold quality
lymph node	UBERON:0000029	74.27	gold quality
body of uterus	UBERON:0009853	73.92	gold quality
popliteal artery	UBERON:0002250	73.82	gold quality
tibial artery	UBERON:0007610	73.81	gold quality
cortical plate	UBERON:0005343	73.72	gold quality
calcaneal tendon	UBERON:0003701	73.43	gold quality
ganglionic eminence	UBERON:0004023	73.24	gold quality
lower esophagus mucosa	UBERON:0035834	73.17	gold quality
right hemisphere of cerebellum	UBERON:0014890	73.12	gold quality
left lobe of thyroid gland	UBERON:0001120	73.04	gold quality
thyroid gland	UBERON:0002046	72.99	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.99	gold quality
lower esophagus	UBERON:0013473	72.97	gold quality
cortex of kidney	UBERON:0001225	72.92	gold quality
prostate gland	UBERON:0002367	72.89	gold quality
cerebellar hemisphere	UBERON:0002245	72.79	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-CURD-10	no	92.61
E-ANND-3	no	0.16

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Because TCTE3 encodes a putative light chain of the outer dynein arm of cilia and human diseases caused by ciliary dysfunction show various phenotypes including skeletal defect, TCTE3 may be a genetic candidate influencing CDH. (PMID:21085971)
• TCTE3 is a useful marker of pancreatobiliary differentiation and may aid in the diagnosis of pancreatobiliary adenocarcinomas. (PMID:29079176)
• Study of Linc00574 Regulatory Effect on the TCTE3 Expression in Sperm Motility. (PMID:32749594)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Dynlt2a1	ENSMUSG00000079707
mus_musculus	Dynlt2a2	ENSMUSG00000079710
mus_musculus	Dynlt2a3	ENSMUSG00000116780
rattus_norvegicus	Dynlt2	ENSRNOG00000015293

Paralogs (5): DYNLT1 (ENSG00000146425), DYNLT5 (ENSG00000152760), DYNLT3 (ENSG00000165169), DYNLT4 (ENSG00000188396), DYNLT2B (ENSG00000213123)

Protein

Protein identifiers

Dynein light chain Tctex-type protein 2 — Q8IZS6 (reviewed: Q8IZS6)

Alternative names: T-complex testis-specific protein 3, T-complex-associated testis-expressed protein 3, Tctex1 domain-containing protein 3

All UniProt accessions (1): Q8IZS6

UniProt curated annotations — full annotation on UniProt →

Function. Component of dynein, a family of motor proteins essential for movement along microtubules. Required for structural and functional integrity of cilia. Candidate for involvement in male sterility.

Subunit / interactions. Part of the ciliary outer dynein arms (ODAs), at least consisting of dynein axonemal heavy chains, light chains and intermediate chains. The ODAs interacts with DNAAF9; this interaction inactivates the dyneins. Interacts with CCDC159. Interacts with CSNK2B.

Subcellular location. Cytoplasm. Cytoskeleton. Cytoplasmic granule. Membrane.

Tissue specificity. Expressed predominantly in testis. Also expressed in brain, lung and trachea.

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

RefSeq proteins (1): NP_777570* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005334	Tctex-1-like	Family
IPR038586	Tctex-1-like_sf	Homologous_superfamily

Pfam: PF03645

UniProt features (6 total): sequence variant 3, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZS6-F1	77.20	0.45

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5620924	Intraflagellar transport

MSigDB gene sets: 56 (showing top): LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, GERY_CEBP_TARGETS, chr6q27, JACKSON_DNMT1_TARGETS_UP, BOYLAN_MULTIPLE_MYELOMA_C_D_UP, MARSON_BOUND_BY_FOXP3_STIMULATED, GOCC_CYTOPLASMIC_DYNEIN_COMPLEX, GOCC_DYNEIN_COMPLEX, SCGGAAGY_ELK1_02, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, PHESSE_TARGETS_OF_APC_AND_MBD2_UP, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOMF_DYNEIN_INTERMEDIATE_CHAIN_BINDING, REACTOME_ORGANELLE_BIOGENESIS_AND_MAINTENANCE

GO Biological Process (1): microtubule-based movement (GO:0007018)

GO Molecular Function (2): dynein intermediate chain binding (GO:0045505), protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), cytoplasmic dynein complex (GO:0005868), microtubule (GO:0005874), membrane (GO:0016020), cytoskeleton (GO:0005856), dynein complex (GO:0030286)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
microtubule-based process	1
protein binding	1
binding	1
intracellular anatomical structure	1
dynein complex	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
intracellular membraneless organelle	1
microtubule associated complex	1
catalytic complex	1

Protein interactions and networks

STRING

762 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DYNLT2	Q12799	Q12799	893
DYNLT2	DRC5	Q5JU00	830
DYNLT2	WDR27	A2RRH5	759
DYNLT2	TCP1	P17987	744
DYNLT2	DYNLT1	P63172	671
DYNLT2	DYNC1I2	Q13409	671
DYNLT2	THBS2	P35442	657
DYNLT2	PHF10	Q8WUB8	642
DYNLT2	CHM	P24386	618
DYNLT2	DYNLL1	P63167	596
DYNLT2	FRMD1	Q8N878	574
DYNLT2	C6orf120	Q7Z4R8	571
DYNLT2	KIF25	Q9UIL4	558
DYNLT2	DACT2	Q5SW24	543
DYNLT2	SMOC2	Q9H3U7	499

IntAct

4 interactions, top by confidence:

A	B	Type	Score
DYNLT2	DCDC2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (3): TCTE3 (Synthetic Lethality), TCTE3 (Affinity Capture-RNA), TCTE3 (Affinity Capture-MS)

ESM2 similar proteins: A7T1N0, B2RR83, F1QMY1, F1S5L4, O13648, O42857, O75343, P08487, P10686, P11985, P19174, P22717, P56523, P97311, P97564, Q04861, Q09315, Q14566, Q14BI7, Q21557, Q28BS0, Q28CM3, Q29JI9, Q2KIZ8, Q32P71, Q39579, Q3MHU3, Q4V339, Q5FWY4, Q5JTY5, Q5R746, Q5RIA9, Q5ZI74, Q61586, Q62077, Q6DNF3, Q8IUF1, Q8IZS6, Q8NDG6, Q8VEH6

Diamond homologs: F1QMY1, P11985, P51807, Q32P71, Q66IC8, Q8CDY7, Q8IZS6, Q8WW35, Q94524, Q9CQ66

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

924 predictions. Top by Δscore:

Variant	Effect	Δscore
6:169744066:A:AC	donor_gain	1.0000
6:169744067:C:CC	donor_gain	1.0000
6:169751337:A:AC	donor_gain	1.0000
6:169751338:C:CC	donor_gain	1.0000
6:169751338:CTG:C	donor_gain	1.0000
6:169751365:T:TA	donor_gain	1.0000
6:169751374:T:A	donor_gain	1.0000
6:169744275:C:CC	acceptor_gain	0.9900
6:169751036:T:A	donor_gain	0.9900
6:169751141:TTAGC:T	donor_gain	0.9900
6:169751234:T:TA	donor_gain	0.9900
6:169751289:TAA:T	donor_gain	0.9900
6:169751290:A:AC	donor_gain	0.9900
6:169751290:AAA:A	donor_gain	0.9900
6:169751337:ACTG:A	donor_gain	0.9900
6:169751338:CTGC:C	donor_gain	0.9900
6:169751343:T:TA	donor_gain	0.9900
6:169751434:T:TA	donor_gain	0.9900
6:169740292:CAAT:C	acceptor_gain	0.9800
6:169740295:TCTG:T	acceptor_loss	0.9800
6:169740296:C:CC	acceptor_gain	0.9800
6:169740296:C:T	acceptor_loss	0.9800
6:169740297:T:G	acceptor_loss	0.9800
6:169743078:A:AC	donor_gain	0.9800
6:169743079:C:CC	donor_gain	0.9800
6:169751028:G:C	donor_gain	0.9800
6:169751150:A:AC	donor_gain	0.9800
6:169751291:A:C	donor_gain	0.9800
6:169751340:G:GA	donor_gain	0.9800
6:169751370:T:A	donor_gain	0.9800

AlphaMissense

1298 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:169740262:C:G	D174H	0.993
6:169740287:G:C	S165R	0.992
6:169740287:G:T	S165R	0.992
6:169740289:T:G	S165R	0.992
6:169740261:T:G	D174A	0.991
6:169740261:T:A	D174V	0.990
6:169740201:G:T	A194D	0.987
6:169743135:C:G	R144P	0.986
6:169744072:A:G	L108P	0.985
6:169740260:G:C	D174E	0.984
6:169740260:G:T	D174E	0.984
6:169743168:A:T	I133K	0.983
6:169743128:C:A	K146N	0.982
6:169743128:C:G	K146N	0.982
6:169743136:G:T	R144S	0.981
6:169740207:A:T	V192E	0.978
6:169743156:A:T	V137D	0.978
6:169740277:A:G	W169R	0.977
6:169740277:A:T	W169R	0.977
6:169744111:A:G	F95S	0.977
6:169743168:A:C	I133R	0.976
6:169743231:A:G	L112P	0.976
6:169751351:G:C	F36L	0.975
6:169751351:G:T	F36L	0.975
6:169751353:A:G	F36L	0.975
6:169744096:A:T	V100E	0.974
6:169744110:G:C	F95L	0.972
6:169744110:G:T	F95L	0.972
6:169744112:A:G	F95L	0.972
6:169740219:G:T	A188E	0.971

dbSNP variants (sampled 300 via entrez): RS1000078260 (6:169737011 C>T), RS1000126669 (6:169744535 T>C), RS1000135718 (6:169751822 C>G,T), RS1000232405 (6:169726788 TA>T,TAA), RS1000310022 (6:169726293 T>G), RS1000420338 (6:169750660 G>A), RS1000541844 (6:169724943 A>T), RS1000681942 (6:169726038 G>T), RS1000733918 (6:169733875 G>A), RS1000892020 (6:169744793 T>C,G), RS1000976469 (6:169738088 C>T), RS1001072112 (6:169730692 A>G), RS1001103117 (6:169730965 A>G), RS1001615513 (6:169731858 G>A), RS1001836608 (6:169730202 C>T)

Disease associations

OMIM: gene MIM:186977 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001255_3	Type 1 diabetes	8.000000e-09
GCST009391_743	Metabolite levels	9.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, decreases methylation	5
methylmercuric chloride	decreases expression	1
ferrous chloride	increases expression	1
pentanal	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	increases expression	1
Ethyl Methanesulfonate	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Vincristine	decreases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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