TEDC2

Summary

TEDC2 (tubulin epsilon and delta complex 2, HGNC:25849) is a protein-coding gene on chromosome 16p13.3, encoding Tubulin epsilon and delta complex protein 2 (Q7L2K0). Acts as a positive regulator of ciliary hedgehog signaling. It is a selective cancer dependency (DepMap: 32.1% of cell lines).

Predicted to be involved in positive regulation of smoothened signaling pathway. Predicted to be located in centriole and cilium.

Source: NCBI Gene 80178 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 19 total
• Cancer dependency (DepMap): dependent in 32.1% of screened cell lines
• MANE Select transcript: NM_025108

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25849
Approved symbol	TEDC2
Name	tubulin epsilon and delta complex 2
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13909
Ensembl gene	ENSG00000162062
Ensembl biotype	protein_coding
Entrez	80178

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 6 retained_intron, 1 nonsense_mediated_decay

ENST00000361837, ENST00000483320, ENST00000562253, ENST00000563531, ENST00000565537, ENST00000565716, ENST00000566580, ENST00000567489, ENST00000568753, ENST00000569496, ENST00000569664, ENST00000569665, ENST00000569994, ENST00000929534

RefSeq mRNA: 1 — MANE Select: NM_025108 NM_025108

CCDS: CCDS10468

Canonical transcript exons

ENST00000361837 — 10 exons

Exon	Start	End
ENSE00001291787	2464039	2464229
ENSE00001861908	2464522	2464963
ENSE00002590995	2460109	2460170
ENSE00003477716	2460283	2460381
ENSE00003528125	2460816	2461224
ENSE00003536760	2460623	2460693
ENSE00003575307	2462415	2462526
ENSE00003596218	2462631	2462732
ENSE00003608967	2462149	2462239
ENSE00003662649	2461747	2461800

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 88.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.8476 / max 83.3943, expressed in 1368 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152225	8.8476	1368

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.53	gold quality
mucosa of transverse colon	UBERON:0004991	80.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.33	gold quality
ventricular zone	UBERON:0003053	79.27	gold quality
ganglionic eminence	UBERON:0004023	78.97	gold quality
right testis	UBERON:0004534	74.10	gold quality
cortical plate	UBERON:0005343	73.92	gold quality
testis	UBERON:0000473	73.17	gold quality
left testis	UBERON:0004533	73.17	gold quality
apex of heart	UBERON:0002098	72.83	gold quality
stromal cell of endometrium	CL:0002255	72.70	gold quality
prefrontal cortex	UBERON:0000451	71.76	gold quality
frontal cortex	UBERON:0001870	71.39	gold quality
right frontal lobe	UBERON:0002810	71.09	gold quality
superior frontal gyrus	UBERON:0002661	70.64	gold quality
vermiform appendix	UBERON:0001154	69.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	69.83	gold quality
esophagus mucosa	UBERON:0002469	69.71	gold quality
placenta	UBERON:0001987	69.63	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	69.47	gold quality
cerebral cortex	UBERON:0000956	69.40	gold quality
lymph node	UBERON:0000029	68.73	gold quality
bone marrow	UBERON:0002371	68.67	gold quality
primary visual cortex	UBERON:0002436	68.53	gold quality
nucleus accumbens	UBERON:0001882	67.95	gold quality
putamen	UBERON:0001874	67.77	gold quality
anterior cingulate cortex	UBERON:0009835	67.53	gold quality
lower esophagus mucosa	UBERON:0035834	66.99	gold quality
metanephros cortex	UBERON:0010533	66.68	gold quality
brain	UBERON:0000955	66.61	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting TEDC2, 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-9-5P	100.00	72.28	2361
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-4796-3P	99.08	68.38	1681
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-6741-3P	89.67	61.63	69

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 32.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• TEDC2 correlated with prognosis and immune microenvironment in lung adenocarcinoma. (PMID:36973475)
• TEDC2 plays an oncogenic role and serves as a therapeutic target of hepatocellular carcinoma. (PMID:37867019)
• A pan-cancer analysis of the prognostic implication and oncogenic role of tubulin epsilon and delta complex 2 (TEDC2) in human tumors. (PMID:38239349)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tedc2	ENSMUSG00000024118
rattus_norvegicus	Tedc2	ENSRNOG00000007436

Protein

Protein identifiers

Tubulin epsilon and delta complex protein 2 — Q7L2K0 (reviewed: Q7L2K0)

All UniProt accessions (5): Q7L2K0, H3BND0, H3BPH1, H3BTF6, H3BU38

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a positive regulator of ciliary hedgehog signaling. Required for centriole stability.

Subunit / interactions. Interacts with TEDC1. Found in a complex with TEDC1, TEDC2, TUBE1 and TUBD1.

Subcellular location. Cell projection. Cilium. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7L2K0-1	1	yes
Q7L2K0-2	2
Q7L2K0-3	3

RefSeq proteins (1): NP_079384* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031518	DUF4693	Family

Pfam: PF15764

UniProt features (11 total): region of interest 3, splice variant 3, compositionally biased region 2, chain 1, sequence variant 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L2K0-F1	68.13	0.14

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): 159

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 88 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, KESHELAVA_MULTIPLE_DRUG_RESISTANCE, SMID_BREAST_CANCER_LUMINAL_B_UP, GOCC_CENTROSOME, GOBP_REGULATION_OF_SMOOTHENED_SIGNALING_PATHWAY, GOBP_SMOOTHENED_SIGNALING_PATHWAY, FISCHER_DREAM_TARGETS, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, GOBP_POSITIVE_REGULATION_OF_SMOOTHENED_SIGNALING_PATHWAY, GOCC_CENTRIOLE, NUYTTEN_EZH2_TARGETS_DN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_CILIUM, BOCHKIS_FOXA2_TARGETS, CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN

GO Biological Process (1): positive regulation of smoothened signaling pathway (GO:0045880)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): centriole (GO:0005814), cilium (GO:0005929), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	2
cellular anatomical structure	2
smoothened signaling pathway	1
regulation of smoothened signaling pathway	1
positive regulation of signal transduction	1
binding	1
microtubule organizing center	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

644 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TEDC2	TUBD1	Q9UJT1	638
TEDC2	TEDC1	Q86SX3	610
TEDC2	PHAF1	Q9BSU1	541
TEDC2	ZNF311	Q5JNZ3	505
TEDC2	SLC2A4RG	Q9NR83	469
TEDC2	CEP44	Q9C0F1	453
TEDC2	C19orf25	Q9UFG5	446
TEDC2	BRICD5	Q6PL45	418
TEDC2	CCDC107	Q8WV48	418
TEDC2	SPINDOC	Q9BUA3	417
TEDC2	ARHGAP36	Q6ZRI8	400
TEDC2	TUBE1	Q9UJT0	377
TEDC2	IPO13	O94829	376
TEDC2	RNF151	Q2KHN1	373
TEDC2	RTTN	Q86VV8	371

IntAct

33 interactions, top by confidence:

A	B	Type	Score
	TEDC2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	TEDC2	psi-mi:“MI:0915”(physical association)	0.560
TEDC2	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLA	TEDC2	psi-mi:“MI:0915”(physical association)	0.560
TEDC2	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	TEDC2	psi-mi:“MI:0915”(physical association)	0.560
TEDC2	NOTCH2NLA	psi-mi:“MI:0915”(physical association)	0.560
TEDC2		psi-mi:“MI:0915”(physical association)	0.560
TEDC2	MDFI	psi-mi:“MI:0915”(physical association)	0.560
TEDC2	KRT27	psi-mi:“MI:0915”(physical association)	0.560
TEDC2	MIS18A	psi-mi:“MI:0915”(physical association)	0.560
TUBE1	TEDC2	psi-mi:“MI:0914”(association)	0.530
TEDC2	TEDC1	psi-mi:“MI:0915”(physical association)	0.500
TEDC2	TEDC1	psi-mi:“MI:0914”(association)	0.500
TEDC2	TEDC1	psi-mi:“MI:0915”(physical association)	0.400
KDM1A	TEDC2	psi-mi:“MI:0915”(physical association)	0.370
FGL1	DNM1L	psi-mi:“MI:0914”(association)	0.350
LURAP1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
KNSTRN	TRIM24	psi-mi:“MI:0914”(association)	0.350
FEM1A	RNF113A	psi-mi:“MI:0914”(association)	0.350
TEDC2	KRT27	psi-mi:“MI:0915”(physical association)	0.000
TEDC2	MDFI	psi-mi:“MI:0915”(physical association)	0.000
TEDC2	MIS18A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (44): KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), C16orf59 (Affinity Capture-MS), C16orf59 (Affinity Capture-MS), C16orf59 (Affinity Capture-MS), C16orf59 (Affinity Capture-MS), C14orf80 (Affinity Capture-MS), C16orf59 (Affinity Capture-RNA), C16orf59 (Two-hybrid), C16orf59 (Two-hybrid), KRT27 (Two-hybrid), C16orf59 (Negative Genetic), C16orf59 (Reconstituted Complex)

ESM2 similar proteins: A0A096LP49, A0A1B0GVZ6, A2VE02, A5D7I0, A6NDZ8, A6NE82, A6NGG8, A6NJ08, A6NJI1, A6QP24, A7YY35, A8MYA2, O94850, P50617, Q0P5M0, Q2KIL8, Q2KIS6, Q3SY00, Q3ZBU3, Q497N6, Q4R736, Q5BMD4, Q5JTZ5, Q5M844, Q5VZ46, Q5XIK6, Q66MI6, Q6AXP4, Q6PAC4, Q6ZRC1, Q7L2K0, Q7Z591, Q80TS7, Q80VW7, Q8BFY7, Q8BHW6, Q8IXW0, Q8IYS4, Q8IYX3, Q8N4L8

Diamond homologs: Q3ZBU3, Q6GQV0, Q7L2K0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1724 predictions. Top by Δscore:

Variant	Effect	Δscore
16:2461799:AGGT:A	donor_loss	1.0000
16:2461801:GT:G	donor_loss	1.0000
16:2461802:T:G	donor_loss	1.0000
16:2462626:T:TA	acceptor_gain	1.0000
16:2462628:CA:C	acceptor_loss	1.0000
16:2462629:A:AG	acceptor_gain	1.0000
16:2462630:G:GA	acceptor_gain	1.0000
16:2462630:GC:G	acceptor_gain	1.0000
16:2462630:GCC:G	acceptor_gain	1.0000
16:2462630:GCCC:G	acceptor_gain	1.0000
16:2462630:GCCCC:G	acceptor_gain	1.0000
16:2462731:AG:A	donor_loss	1.0000
16:2462732:GG:G	donor_loss	1.0000
16:2462733:G:GA	donor_loss	1.0000
16:2464245:G:GT	donor_gain	1.0000
16:2461222:GGG:G	donor_gain	0.9900
16:2461223:GGG:G	donor_gain	0.9900
16:2461741:CGACA:C	acceptor_loss	0.9900
16:2461742:GACAG:G	acceptor_loss	0.9900
16:2461743:ACAGG:A	acceptor_loss	0.9900
16:2461744:CA:C	acceptor_loss	0.9900
16:2461745:A:AG	acceptor_gain	0.9900
16:2461745:A:G	acceptor_loss	0.9900
16:2461746:G:GG	acceptor_gain	0.9900
16:2461798:GAG:G	donor_gain	0.9900
16:2462733:G:GG	donor_gain	0.9900
16:2464035:ACAGC:A	acceptor_gain	0.9900
16:2464037:A:AG	acceptor_gain	0.9900
16:2464037:AGC:A	acceptor_gain	0.9900
16:2464038:G:GA	acceptor_gain	0.9900

AlphaMissense

2721 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:2462216:T:C	F243L	0.972
16:2462218:C:A	F243L	0.972
16:2462218:C:G	F243L	0.972
16:2461205:T:C	F196L	0.958
16:2461207:C:A	F196L	0.958
16:2461207:C:G	F196L	0.958
16:2464146:T:G	Y358D	0.941
16:2460878:G:C	A87P	0.940
16:2462217:T:C	F243S	0.926
16:2460866:G:C	A83P	0.919
16:2464606:A:C	S414R	0.918
16:2464608:C:A	S414R	0.918
16:2464608:C:G	S414R	0.918
16:2464146:T:A	Y358N	0.917
16:2461795:C:A	N218K	0.907
16:2461795:C:G	N218K	0.907
16:2464165:T:C	L364P	0.903
16:2462155:G:C	W222C	0.897
16:2462155:G:T	W222C	0.897
16:2460870:T:C	L84P	0.895
16:2464146:T:C	Y358H	0.892
16:2462217:T:G	F243C	0.886
16:2464538:T:C	L391P	0.883
16:2460879:C:A	A87D	0.877
16:2462682:T:C	L305P	0.873
16:2460623:G:C	W42C	0.863
16:2460623:G:T	W42C	0.863
16:2460858:T:C	L80P	0.863
16:2460891:G:C	R91P	0.860
16:2460877:G:C	K86N	0.858

dbSNP variants (sampled 300 via entrez): RS1000288682 (16:2465120 C>G,T), RS1000319816 (16:2460643 C>G,T), RS1000430269 (16:2464931 G>A), RS1000681638 (16:2460115 G>A,C,T), RS1001729051 (16:2461507 G>A,T), RS1003594721 (16:2458415 A>G,T), RS1003948955 (16:2458566 C>T), RS1004037238 (16:2458162 G>A,T), RS1004220943 (16:2460195 G>A,T), RS1004313609 (16:2461931 T>TA), RS1004594255 (16:2464863 G>A), RS1004908342 (16:2463042 C>G,T), RS1005498493 (16:2462739 C>A), RS1005711874 (16:2465270 C>G,T), RS1006071159 (16:2460545 G>A,C,T)

Disease associations

OMIM: gene `` | 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):

Study	Trait	p-value
GCST008163_488	Height	1.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	4
methacrylaldehyde	affects cotreatment, increases oxidation, decreases expression, increases abundance	2
Acrolein	affects cotreatment, increases oxidation, decreases expression, increases abundance	2
Cisplatin	affects cotreatment, increases expression	2
Ozone	increases oxidation, decreases expression, increases abundance, affects cotreatment	2
GSK-J4	decreases expression	1
afuresertib	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
beta-lapachone	decreases expression, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
chromium hexavalent ion	decreases expression, increases abundance	1
K 7174	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Copper	decreases expression, affects binding	1
Lead	affects expression	1
Oxygen	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1

Clinical trials (associated diseases)

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