DYNLT5

Summary

DYNLT5 (dynein light chain Tctex-type family member 5, HGNC:26882) is a protein-coding gene on chromosome 1p31.3, encoding Dynein light chain Tctex-type 5 (Q8N7M0).

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

Source: NCBI Gene 200132 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_152665

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26882
Approved symbol	DYNLT5
Name	dynein light chain Tctex-type family member 5
Location	1p31.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40873
Ensembl gene	ENSG00000152760
Ensembl biotype	protein_coding
OMIM	619994
Entrez	200132

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000282670, ENST00000448074, ENST00000489510, ENST00000491611, ENST00000525663, ENST00000528352, ENST00000909939, ENST00000909940

RefSeq mRNA: 1 — MANE Select: NM_152665 NM_152665

CCDS: CCDS633

Canonical transcript exons

ENST00000282670 — 5 exons

Exon	Start	End
ENSE00001258266	66770387	66770478
ENSE00001258281	66777251	66779047
ENSE00002148392	66752459	66752584
ENSE00003546914	66754656	66754777
ENSE00003601934	66776279	66776403

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 99.31.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1942 / max 302.5122, expressed in 452 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
3383	0.6141	253
3377	0.5176	63
3384	0.4411	179
3380	0.1721	35
3381	0.1642	45
3379	0.1501	30
3378	0.0889	29
3382	0.0462	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.31	gold quality
oviduct epithelium	UBERON:0004804	92.53	gold quality
bronchial epithelial cell	CL:0002328	92.52	gold quality
bronchus	UBERON:0002185	90.81	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.83	gold quality
fallopian tube	UBERON:0003889	85.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.53	gold quality
hypothalamus	UBERON:0001898	84.26	gold quality
right lung	UBERON:0002167	82.43	gold quality
mucosa of paranasal sinus	UBERON:0005030	82.20	gold quality
apex of heart	UBERON:0002098	82.15	gold quality
endothelial cell	CL:0000115	80.65	silver quality
epithelium of nasopharynx	UBERON:0001951	78.59	gold quality
caudate nucleus	UBERON:0001873	78.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	78.35	gold quality
right frontal lobe	UBERON:0002810	78.22	gold quality
heart left ventricle	UBERON:0002084	77.07	gold quality
upper lobe of left lung	UBERON:0008952	76.70	gold quality
endocervix	UBERON:0000458	76.47	gold quality
cardiac ventricle	UBERON:0002082	76.29	gold quality
right lobe of liver	UBERON:0001114	75.35	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	75.30	gold quality
upper lobe of lung	UBERON:0008948	75.23	gold quality
anterior cingulate cortex	UBERON:0009835	75.20	gold quality
buccal mucosa cell	CL:0002336	74.76	silver quality
amygdala	UBERON:0001876	74.21	gold quality
lower esophagus	UBERON:0013473	73.91	gold quality
lower esophagus muscularis layer	UBERON:0035833	73.91	gold quality
heart	UBERON:0000948	73.85	gold quality
tibial nerve	UBERON:0001323	73.80	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.02
E-MTAB-9388	yes	7.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

75 targeting DYNLT5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4639-5P	99.81	67.37	1028
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-4530	99.69	66.47	1509

Literature-anchored findings (GeneRIF, showing 1)

• TCTEX1D1 is a genetic modifier of disease progression in Duchenne muscular dystrophy. (PMID:31896777)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	dynlt5	ENSDARG00000103545
mus_musculus	Dynlt5	ENSMUSG00000028523
rattus_norvegicus	Dynlt5	ENSRNOG00000023100

Paralogs (5): DYNLT1 (ENSG00000146425), DYNLT3 (ENSG00000165169), DYNLT2 (ENSG00000184786), DYNLT4 (ENSG00000188396), DYNLT2B (ENSG00000213123)

Protein

Protein identifiers

Dynein light chain Tctex-type 5 — Q8N7M0 (reviewed: Q8N7M0)

Alternative names: Tctex1 domain-containing protein 1

All UniProt accessions (2): Q8N7M0, E9PI84

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with ZMYND10.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N7M0-1	1	yes
Q8N7M0-2	2

RefSeq proteins (1): NP_689878* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF03645

UniProt features (3 total): sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7M0-F1	77.94	0.58

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5620924	Intraflagellar transport

MSigDB gene sets: 108 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, GTTAAAG_MIR302B, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, TGGAAA_NFAT_Q4_01, ZHENG_BOUND_BY_FOXP3, GOCC_CYTOPLASMIC_DYNEIN_COMPLEX, GOCC_DYNEIN_COMPLEX, GCACTTT_MIR175P_MIR20A_MIR106A_MIR106B_MIR20B_MIR519D, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GCTCTTG_MIR335, NOUSHMEHR_GBM_SILENCED_BY_METHYLATION, GOMF_DYNEIN_INTERMEDIATE_CHAIN_BINDING, REACTOME_ORGANELLE_BIOGENESIS_AND_MAINTENANCE, REACTOME_CILIUM_ASSEMBLY

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 (2): cytoplasm (GO:0005737), cytoplasmic dynein complex (GO:0005868)

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
microtubule-based process	1
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
dynein complex	1

Protein interactions and networks

STRING

593 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DYNLT5	DNAI4	Q5VTH9	611
DYNLT5	DNAI2	Q9GZS0	598
DYNLT5	SSUH2	Q9Y2M2	527
DYNLT5	DYNLT1	P63172	517
DYNLT5	TMEM89	A2RUT3	507
DYNLT5	ANKUB1	A6NFN9	495
DYNLT5	DYNLRB2	Q8TF09	485
DYNLT5	DYNC1LI2	O43237	483
DYNLT5	GTF2A1	P52655	478
DYNLT5	DNAL4	O96015	468
DYNLT5	DYNC1I1	O14576	457
DYNLT5	LRRC71	Q8N4P6	455
DYNLT5	DYNC1LI1	Q9Y6G9	452
DYNLT5	DYNLT3	P51808	444
DYNLT5	LTBP4	Q8N2S1	434
DYNLT5	SGIP1	Q9BQI5	434

IntAct

6 interactions, top by confidence:

A	B	Type	Score
MEOX2	DYNLT5	psi-mi:“MI:0915”(physical association)	0.560
DYNLT5	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
DYNLT5	GAPDHS	psi-mi:“MI:0915”(physical association)	0.400
DYNLT5	SVIL	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): TCTEX1D1 (Two-hybrid), RBMXL1 (Affinity Capture-MS), SVIL (Affinity Capture-MS), PPP1R9A (Affinity Capture-MS), LIMA1 (Affinity Capture-MS), ITPR3 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), NME2 (Cross-Linking-MS (XL-MS)), NME1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2A2Y4, A2VDD2, A7MBL8, B2RQE8, B9EJ86, D4A1F2, E9Q4Z2, E9Q5G3, F1MF74, F1ND48, F1QDI9, G9CGD6, O00763, O08874, O94851, O95630, P0C928, P78563, Q0P4Q4, Q0VGY8, Q16513, Q2TBH6, Q3B8D7, Q498D5, Q4U2V3, Q5R803, Q62698, Q66IC8, Q6F6B3, Q6P9H4, Q6ZMV9, Q76N33, Q7ZU92, Q7ZYZ7, Q8BHD4, Q8BML1, Q8BPM2, Q8IVH8, Q8IZC4, Q8K394

Diamond homologs: A2VDD2, Q32P71, Q3B8D7, Q4VYA0, Q54PG1, Q5JR98, Q66IC8, Q8CDY7, Q8N7M0, Q8WW35, Q9CQ66, Q9D5I4, F1QMY1, P11985, Q94524, Q9Z336, P63171, P63172

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

952 predictions. Top by Δscore:

Variant	Effect	Δscore
1:66752582:CAGGT:C	donor_loss	1.0000
1:66752583:AGG:A	donor_loss	1.0000
1:66752584:GG:G	donor_loss	1.0000
1:66752585:GTA:G	donor_loss	1.0000
1:66754714:G:GT	donor_gain	1.0000
1:66754776:GA:G	donor_gain	1.0000
1:66754778:G:GG	donor_gain	1.0000
1:66770385:A:AG	acceptor_gain	1.0000
1:66770386:G:GA	acceptor_gain	1.0000
1:66770386:GTTCT:G	acceptor_gain	1.0000
1:66770474:GTTGG:G	donor_gain	1.0000
1:66770475:T:G	donor_gain	1.0000
1:66776273:TTTCA:T	acceptor_loss	1.0000
1:66776274:TTCA:T	acceptor_loss	1.0000
1:66776275:TCA:T	acceptor_loss	1.0000
1:66776276:CA:C	acceptor_loss	1.0000
1:66776277:A:AG	acceptor_gain	1.0000
1:66776277:AGGTC:A	acceptor_loss	1.0000
1:66776278:G:GA	acceptor_gain	1.0000
1:66776278:G:GT	acceptor_loss	1.0000
1:66776278:GGT:G	acceptor_gain	1.0000
1:66776400:TGAGG:T	donor_loss	1.0000
1:66776401:GAG:G	donor_gain	1.0000
1:66776404:G:C	donor_loss	1.0000
1:66776405:T:A	donor_loss	1.0000
1:66752586:T:A	donor_loss	0.9900
1:66754775:AGA:A	donor_gain	0.9900
1:66754776:GAG:G	donor_gain	0.9900
1:66770386:GTT:G	acceptor_gain	0.9900
1:66776278:GGTC:G	acceptor_gain	0.9900

AlphaMissense

1192 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:66777350:A:C	S146R	0.977
1:66777352:C:A	S146R	0.977
1:66777352:C:G	S146R	0.977
1:66777420:C:A	A169D	0.976
1:66777432:T:A	V173D	0.973
1:66777295:A:C	K127N	0.970
1:66777295:A:T	K127N	0.970
1:66777362:T:A	W150R	0.963
1:66777362:T:C	W150R	0.963
1:66777416:T:C	F168L	0.961
1:66777418:C:A	F168L	0.961
1:66777418:C:G	F168L	0.961
1:66777267:T:A	V118D	0.959
1:66776309:T:A	V81D	0.958
1:66777438:C:A	A175E	0.955
1:66777426:C:A	A171E	0.950
1:66777294:A:T	K127I	0.949
1:66777377:G:C	D155H	0.947
1:66777378:A:T	D155V	0.946
1:66777318:G:A	G135E	0.944
1:66777414:T:C	L167P	0.942
1:66777288:G:C	R125P	0.941
1:66776321:T:G	L85W	0.939
1:66777379:T:A	D155E	0.939
1:66777379:T:G	D155E	0.939
1:66777419:G:C	A169P	0.938
1:66777378:A:C	D155A	0.936
1:66777398:T:C	F162L	0.935
1:66777400:C:A	F162L	0.935
1:66777400:C:G	F162L	0.935

dbSNP variants (sampled 300 via entrez): RS1000030072 (1:66757361 T>A), RS1000152934 (1:66751192 C>A,T), RS1000210427 (1:66763310 G>A), RS1000342801 (1:66759760 A>G,T), RS1000398110 (1:66769849 C>T), RS1000429065 (1:66770161 T>C), RS1000664209 (1:66775320 T>G), RS1000678698 (1:66763489 T>A), RS1000679336 (1:66771569 C>A,T), RS1000730811 (1:66776773 A>G), RS1000765689 (1:66768708 G>A), RS1000772534 (1:66759424 A>G), RS1000894345 (1:66778708 G>C,T), RS1001200813 (1:66772002 A>G), RS1001247280 (1:66770765 G>A)

Disease associations

OMIM: gene MIM:619994 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004131_16	Inflammatory bowel disease	5.000000e-111
GCST004132_7	Crohn’s disease	6.000000e-93
GCST004133_2	Ulcerative colitis	4.000000e-41

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
pirinixic acid	affects binding, decreases expression, increases activity	1
CGP 52608	affects binding, increases reaction	1
belinostat	increases expression	1
Decitabine	affects expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cisplatin	affects expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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