TMED9

Summary

TMED9 (transmembrane p24 trafficking protein 9, HGNC:24878) is a protein-coding gene on chromosome 5q35.3, encoding Transmembrane emp24 domain-containing protein 9 (Q9BVK6). Appears to be involved in vesicular protein trafficking, mainly in the early secretory pathway.

This gene is a member of a family of genes encoding transport proteins located in the endoplasmic reticulum and the Golgi. A similar gene in mouse is the target of microRNA miR-296, which is part of an imprinted cluster.

Source: NCBI Gene 54732 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 25 total
• Druggable target: yes
• MANE Select transcript: NM_017510

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24878
Approved symbol	TMED9
Name	transmembrane p24 trafficking protein 9
Location	5q35.3
Locus type	gene with protein product
Status	Approved
Aliases	HSGP25L2G, p24alpha2, p24a2
Ensembl gene	ENSG00000184840
Ensembl biotype	protein_coding
OMIM	620436
Entrez	54732

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000332598, ENST00000505521, ENST00000507578, ENST00000507723, ENST00000510499, ENST00000513799, ENST00000884817, ENST00000937296, ENST00000937297, ENST00000937298, ENST00000937299

RefSeq mRNA: 1 — MANE Select: NM_017510 NM_017510

CCDS: CCDS4428

Canonical transcript exons

ENST00000332598 — 5 exons

Exon	Start	End
ENSE00001322571	177592203	177592398
ENSE00001324321	177595267	177597242
ENSE00003556056	177594139	177594285
ENSE00003623827	177593650	177593775
ENSE00003681144	177592575	177592675

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 117.2455 / max 546.6957, expressed in 1828 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60501	114.2502	1828
60500	1.8626	1203
60502	0.8514	478
60503	0.2814	125

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	99.55	gold quality
cervix squamous epithelium	UBERON:0006922	99.48	gold quality
tibia	UBERON:0000979	99.33	gold quality
stromal cell of endometrium	CL:0002255	99.20	gold quality
pylorus	UBERON:0001166	99.13	gold quality
pericardium	UBERON:0002407	99.06	gold quality
choroid plexus epithelium	UBERON:0003911	99.05	gold quality
germinal epithelium of ovary	UBERON:0001304	98.97	gold quality
body of pancreas	UBERON:0001150	98.92	gold quality
parotid gland	UBERON:0001831	98.91	gold quality
visceral pleura	UBERON:0002401	98.90	gold quality
gingival epithelium	UBERON:0001949	98.89	gold quality
squamous epithelium	UBERON:0006914	98.88	gold quality
trachea	UBERON:0003126	98.79	gold quality
esophagus squamous epithelium	UBERON:0006920	98.68	gold quality
amniotic fluid	UBERON:0000173	98.60	gold quality
epithelium of esophagus	UBERON:0001976	98.59	gold quality
superior surface of tongue	UBERON:0007371	98.59	gold quality
cardia of stomach	UBERON:0001162	98.57	gold quality
gingiva	UBERON:0001828	98.54	gold quality
tongue squamous epithelium	UBERON:0006919	98.53	gold quality
pleura	UBERON:0000977	98.50	gold quality
epithelium of nasopharynx	UBERON:0001951	98.48	gold quality
endothelial cell	CL:0000115	98.42	gold quality
parietal pleura	UBERON:0002400	98.40	gold quality
hair follicle	UBERON:0002073	98.35	gold quality
renal glomerulus	UBERON:0000074	98.34	gold quality
type B pancreatic cell	CL:0000169	98.33	gold quality
corpus epididymis	UBERON:0004359	98.31	gold quality
saliva-secreting gland	UBERON:0001044	98.26	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-CURD-88	yes	93.20
E-MTAB-9467	yes	55.29
E-HCAD-4	yes	52.70
E-CURD-122	yes	42.24
E-HCAD-1	yes	39.06
E-HCAD-5	yes	38.30
E-CURD-46	yes	34.52
E-HCAD-9	yes	18.49
E-MTAB-10553	yes	9.85
E-CURD-112	yes	8.58
E-MTAB-7052	no	395.71
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting TMED9, 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-5193	100.00	67.26	1744
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-194-5P	99.01	69.65	1465
HSA-MIR-3619-5P	99.00	68.87	2308

Literature-anchored findings (GeneRIF, showing 3)

• TMED9/TMED3 antagonism impacts WNT-TCF and GLI signaling, where TMED9 primacy over TMED3 leads to the establishment of a positive feedback loop together with CNIH4, TGFalpha, and GLI1 that enhances metastases (PMID:31253868)
• High expression of transmembrane P24 trafficking protein 9 predicts poor prognosis in breast carcinoma. (PMID:34635011)
• Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway. (PMID:39303030)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmed9	ENSDARG00000004261
mus_musculus	Tmed9	ENSMUSG00000058569
rattus_norvegicus	Tmed9	ENSRNOG00000021882
drosophila_melanogaster	p24-1	FBGN0030341
caenorhabditis_elegans		WBGENE00013360

Paralogs (8): TMED2 (ENSG00000086598), TMED1 (ENSG00000099203), TMED5 (ENSG00000117500), TMED7 (ENSG00000134970), TMED6 (ENSG00000157315), TMED4 (ENSG00000158604), TMED3 (ENSG00000166557), TMED10 (ENSG00000170348)

Protein

Protein identifiers

Transmembrane emp24 domain-containing protein 9 — Q9BVK6 (reviewed: Q9BVK6)

Alternative names: GMP25, Glycoprotein 25L2, p24 family protein alpha-2, p25

All UniProt accessions (1): Q9BVK6

UniProt curated annotations — full annotation on UniProt →

Function. Appears to be involved in vesicular protein trafficking, mainly in the early secretory pathway. In COPI vesicle-mediated retrograde transport involved in the coatomer recruitment to membranes of the early secretory pathway. Increases coatomer-dependent activity of ARFGAP2. Thought to play a crucial role in the specific retention of p24 complexes in cis-Golgi membranes; specifically contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network. May be involved in organization of intracellular membranes, such as of the ER-Golgi intermediate compartment and the Golgi apparatus. Involved in ER localization of PTPN2 isoform PTPB.

Subunit / interactions. Monomer and homodimer in endoplasmic reticulum. Predominantly monomeric and to lesser extent homodimeric in endoplasmic reticulum-Golgi intermediate compartment and cis-Golgi network. Probably oligomerizes with other members of the EMP24/GP25L family such as TMED2, TMED7 and TMED10. Interacts with TMED5. Interacts (via C-terminus) with COPG1; the interaction involves dimeric TMED9. Interacts with PTPN2 and SPAST. Interacts with STX17; the interaction is direct.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus. cis-Golgi network membrane. Endoplasmic reticulum-Golgi intermediate compartment membrane. trans-Golgi network membrane.

Post-translational modifications. N-linked glycosylated containing high mannose.

Similarity. Belongs to the EMP24/GP25L family.

RefSeq proteins (1): NP_059980* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009038	GOLD_dom	Domain
IPR015720	Emp24-like	Family

Pfam: PF01105

UniProt features (19 total): sequence conflict 5, topological domain 2, short sequence motif 2, signal peptide 1, chain 1, modified residue 1, glycosylation site 1, sequence variant 1, mutagenesis site 1, transmembrane region 1, domain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
9CJK	ELECTRON MICROSCOPY	3.7
9CJL	ELECTRON MICROSCOPY	5.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BVK6-F1	84.57	0.48

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): 160

Glycosylation sites (1): 125

Mutagenesis-validated functional residues (1):

Position	Phenotype
232–233	localization to plasma membrane and endocytosis.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6807878	COPI-mediated anterograde transport
R-HSA-6811434	COPI-dependent Golgi-to-ER retrograde traffic

MSigDB gene sets: 182 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GGTGTGT_MIR329, GOBP_VESICLE_LOCALIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, MORF_HDAC1, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, GHO_ATF5_TARGETS_DN, RIZKI_TUMOR_INVASIVENESS_3D_DN, REACTOME_MEMBRANE_TRAFFICKING, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, AGTCTTA_MIR499, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, MARTINEZ_RB1_TARGETS_DN

GO Biological Process (6): intracellular protein transport (GO:0006886), endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), Golgi organization (GO:0007030), positive regulation of organelle organization (GO:0010638), COPI coating of Golgi vesicle (GO:0048205), protein transport (GO:0015031)

GO Molecular Function (2): syntaxin binding (GO:0019905), protein binding (GO:0005515)

GO Cellular Component (12): Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), Golgi apparatus (GO:0005794), synaptic vesicle (GO:0008021), transport vesicle (GO:0030133), COPII-coated ER to Golgi transport vesicle (GO:0030134), trans-Golgi network transport vesicle (GO:0030140), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Golgi-to-ER retrograde transport	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
endomembrane system	3
intracellular membrane-bounded organelle	3
intracellular protein localization	2
intracellular transport	2
organelle organization	2
bounding membrane of organelle	2
protein transport	1
intercellular transport	1
Golgi vesicle transport	1
endomembrane system organization	1
regulation of organelle organization	1
positive regulation of cellular component organization	1
COPI-coated vesicle budding	1
Golgi transport vesicle coating	1
transport	1
establishment of protein localization	1
SNARE binding	1
binding	1
Golgi apparatus	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
exocytic vesicle	1
presynapse	1
cytoplasmic vesicle	1
coated vesicle	1
Golgi-associated vesicle	1
transport vesicle	1
clathrin-coated vesicle	1
endoplasmic reticulum-Golgi intermediate compartment	1
extracellular vesicle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1134 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMED9	TMED5	Q9Y3A6	944
TMED9	TMED10	P49755	795
TMED9	TMED1	Q13445	678
TMED9	TMED2	Q15363	668
TMED9	PREB	Q9HCU5	553
TMED9	TMED6	Q8WW62	542
TMED9	CNIH4	Q9P003	492
TMED9	SURF4	O15260	449
TMED9	FAM193B	Q96PV7	446
TMED9	ACBD3	Q9H3P7	422
TMED9	PRR7	Q8TB68	410
TMED9	B4GALT7	Q9UBV7	402
TMED9	SEC22B	O75396	395
TMED9	CASR	P41180	386
TMED9	SMIM13	P0DJ93	365

IntAct

136 interactions, top by confidence:

A	B	Type	Score
TMED2	TMED10	psi-mi:“MI:0914”(association)	0.910
TMED10	TMED2	psi-mi:“MI:0914”(association)	0.910
TMED7	TMED10	psi-mi:“MI:0914”(association)	0.730
TMED9	TMED10	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SURF4	TMED10	psi-mi:“MI:0915”(physical association)	0.660
CHST8	CANX	psi-mi:“MI:0914”(association)	0.640
ITM2A	TMED9	psi-mi:“MI:0915”(physical association)	0.560
TMED9	TMEM60	psi-mi:“MI:0915”(physical association)	0.560
AQP9	TMED9	psi-mi:“MI:0915”(physical association)	0.560
PLPPR2	TMED9	psi-mi:“MI:0915”(physical association)	0.560
SEC22A	TMED9	psi-mi:“MI:0915”(physical association)	0.560
TMED9	PTPN2	psi-mi:“MI:0915”(physical association)	0.540
PTPN2	TMED9	psi-mi:“MI:0915”(physical association)	0.540
TMED9	PTPN2	psi-mi:“MI:0403”(colocalization)	0.540
FGF3	GTPBP10	psi-mi:“MI:0914”(association)	0.530
LIPG	NRP1	psi-mi:“MI:0914”(association)	0.530
SPPL2B	UQCRQ	psi-mi:“MI:0914”(association)	0.530
TMED9	COPB2	psi-mi:“MI:0914”(association)	0.530
rev	TMED10	psi-mi:“MI:0914”(association)	0.460
TMED9	TMED9	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
CKMT2	TMED9	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (216): TMED9 (Affinity Capture-RNA), TMED9 (Affinity Capture-RNA), TMED9 (Affinity Capture-MS), TMED9 (Affinity Capture-MS), TMED9 (Affinity Capture-MS), TMED9 (Affinity Capture-MS), TMED9 (Co-fractionation), TMED9 (Co-fractionation), TMED9 (Co-fractionation), TMED9 (Co-fractionation), TMED9 (Proximity Label-MS), TMED9 (Proximity Label-MS), TMED9 (Affinity Capture-MS), TMED9 (Affinity Capture-MS), TMED9 (Affinity Capture-MS)

ESM2 similar proteins: A0AQ71, B3LVB0, B3P6T8, B4GE47, B4HJV5, B4JYU5, B4K4G5, B4KB41, B4LYB8, B4MGF8, B4NIY1, B4NKL0, B4PUZ3, B4PVC6, B4QWH9, F4J4Y0, O13770, O13946, O14324, O35587, O81045, P27869, P32803, P38819, P49755, P53198, Q05359, Q12403, Q12450, Q28735, Q3T133, Q4P958, Q54BN0, Q5E971, Q5I0E7, Q5RE32, Q63584, Q6C503, Q759T8, Q8GYG1

Diamond homologs: B3MTS8, B3NZM5, B4GMC3, B4HJV5, B4JG34, B4KB41, B4LYB8, B4NKL0, B4PVC6, B4QWH9, O14324, O35587, P0CN72, P0CN73, P27869, P49755, P53198, Q28735, Q295B2, Q3T133, Q4WQL0, Q5B5L5, Q5E971, Q5I0E7, Q5RE32, Q63584, Q6BTC2, Q6CWW7, Q759T8, Q769F9, Q7Z7H5, Q8R1V4, Q90515, Q99KF1, Q9BVK6, Q9D1D4, Q9D2R4, Q9I7K5, Q9P7I9, P38819

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 135 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.

GO biological processes:

GO term	Partners	Fold	FDR
endoplasmic reticulum to Golgi vesicle-mediated transport	10	11.6×	2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

408 predictions. Top by Δscore:

Variant	Effect	Δscore
5:177592355:G:GT	donor_gain	1.0000
5:177592380:G:GT	donor_gain	1.0000
5:177592572:AAG:A	acceptor_gain	1.0000
5:177592573:A:G	acceptor_gain	1.0000
5:177592673:AAGGT:A	donor_loss	1.0000
5:177592675:GGTG:G	donor_loss	1.0000
5:177592676:G:A	donor_loss	1.0000
5:177592677:T:A	donor_loss	1.0000
5:177593647:CA:C	acceptor_loss	1.0000
5:177593648:A:AC	acceptor_loss	1.0000
5:177593648:A:AG	acceptor_gain	1.0000
5:177593649:G:GA	acceptor_gain	1.0000
5:177593649:GGTC:G	acceptor_gain	1.0000
5:177593776:G:A	donor_loss	1.0000
5:177593777:T:TC	donor_loss	1.0000
5:177594126:T:TA	acceptor_gain	1.0000
5:177594130:T:TA	acceptor_gain	1.0000
5:177594134:CTCA:C	acceptor_loss	1.0000
5:177594136:CA:C	acceptor_loss	1.0000
5:177594137:A:AC	acceptor_loss	1.0000
5:177594137:A:AG	acceptor_gain	1.0000
5:177594138:G:GG	acceptor_gain	1.0000
5:177594138:GA:G	acceptor_gain	1.0000
5:177594138:GAGA:G	acceptor_gain	1.0000
5:177594281:AGCGG:A	donor_gain	1.0000
5:177594282:GCGG:G	donor_gain	1.0000
5:177594282:GCGGG:G	donor_gain	1.0000
5:177594283:CGG:C	donor_gain	1.0000
5:177594284:GG:G	donor_gain	1.0000
5:177594284:GGG:G	donor_gain	1.0000

AlphaMissense

1522 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:177593699:C:T	S112F	1.000
5:177594239:T:C	L171P	1.000
5:177595286:G:C	R193P	1.000
5:177592359:T:A	C49S	0.999
5:177592359:T:C	C49R	0.999
5:177592360:G:C	C49S	0.999
5:177592363:T:C	F50S	0.999
5:177592363:T:G	F50C	0.999
5:177592575:G:A	G62E	0.999
5:177593680:G:C	G106R	0.999
5:177593687:T:C	F108S	0.999
5:177593692:T:C	F110L	0.999
5:177593693:T:C	F110S	0.999
5:177593693:T:G	F110C	0.999
5:177593694:C:A	F110L	0.999
5:177593694:C:G	F110L	0.999
5:177593699:C:A	S112Y	0.999
5:177593710:G:T	G116C	0.999
5:177593711:G:T	G116V	0.999
5:177593716:C:G	H118D	0.999
5:177593723:T:A	I120N	0.999
5:177593723:T:C	I120T	0.999
5:177593723:T:G	I120S	0.999
5:177593725:T:A	C121S	0.999
5:177593725:T:C	C121R	0.999
5:177593726:G:A	C121Y	0.999
5:177593726:G:C	C121S	0.999
5:177593729:T:C	L122P	0.999
5:177594149:T:C	L141P	0.999
5:177594163:G:T	G146C	0.999

dbSNP variants (sampled 300 via entrez): RS1000707620 (5:177597590 T>G), RS1000845826 (5:177594775 T>C), RS1001240543 (5:177597650 A>G,T), RS1001447061 (5:177593284 T>C), RS1001804361 (5:177590561 C>G,T), RS1002008906 (5:177592514 G>A,T), RS1002068386 (5:177591049 A>T), RS1002395408 (5:177592157 G>A), RS1003258373 (5:177596796 G>C), RS1003491696 (5:177595992 C>A), RS1003585291 (5:177595611 T>C), RS1004499054 (5:177594409 G>A,C,T), RS1005137484 (5:177591502 A>C), RS1005271770 (5:177591183 T>C), RS1006326278 (5:177592557 C>A,T)

Disease associations

OMIM: gene MIM:620436 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001762_65	Obesity-related traits	8.000000e-06
GCST005956_15	Waist-to-hip ratio adjusted for BMI	1.000000e-07
GCST005957_13	Waist-to-hip ratio adjusted for BMI (age <50)	3.000000e-07
GCST005962_42	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066330 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.40	Kd	3.956	nM	CHEMBL5653589
8.40	ED50	3.956	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149604: Binding affinity to human TMED9 incubated for 45 mins by Kinobead based pull down assay	kd	0.0040	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases expression, affects cotreatment	3
Tobacco Smoke Pollution	affects expression, increases expression	2
Tunicamycin	increases expression	2
Cyclosporine	increases expression	2
Cadmium Chloride	increases abundance, increases expression	2
Thapsigargin	increases expression	2
bisphenol F	increases expression	1
lead acetate	increases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
chloropicrin	decreases expression	1
ICG 001	increases expression	1
bisphenol B	increases expression	1
jinfukang	increases expression	1
bisphenol AF	increases 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
Air Pollutants	decreases expression, increases abundance	1
Aspirin	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases expression, increases abundance	1
Cytarabine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Dihydrotestosterone	increases expression	1
Sulindac	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652646	Binding	Binding affinity to human TMED9 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3JF	Abcam HEK293T TMED9 KO	Transformed cell line	Female
CVCL_TS74	HAP1 TMED9 (-) 1	Cancer cell line	Male
CVCL_XU35	HAP1 TMED9 (-) 2	Cancer cell line	Male
CVCL_XU36	HAP1 TMED9 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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