TANGO6

Summary

TANGO6 (transport and golgi organization 6 homolog, HGNC:25749) is a protein-coding gene on chromosome 16q22.1, encoding Transport and Golgi organization protein 6 homolog (Q9C0B7). It is a common-essential gene (DepMap: required in 99.7% of cancer cell lines).

Predicted to be involved in protein secretion. Predicted to be located in membrane.

Source: NCBI Gene 79613 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 176 total
• Cancer dependency (DepMap): dependent in 99.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_024562

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25749
Approved symbol	TANGO6
Name	transport and golgi organization 6 homolog
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12688, KIAA1746
Ensembl gene	ENSG00000103047
Ensembl biotype	protein_coding
OMIM	620188
Entrez	79613

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 10 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000261778, ENST00000561566, ENST00000561856, ENST00000561931, ENST00000562000, ENST00000562491, ENST00000564180, ENST00000565037, ENST00000565852, ENST00000568361, ENST00000883663, ENST00000883664, ENST00000883665, ENST00000883666, ENST00000915345, ENST00000915346, ENST00000953308, ENST00000953309, ENST00000953310

RefSeq mRNA: 1 — MANE Select: NM_024562 NM_024562

CCDS: CCDS45516

Canonical transcript exons

ENST00000261778 — 18 exons

Exon	Start	End
ENSE00000691111	68927568	68928083
ENSE00000691140	68909211	68909402
ENSE00000844411	68907443	68907575
ENSE00000946469	68930238	68930295
ENSE00001111640	68875154	68875290
ENSE00001111643	68867079	68867220
ENSE00001111645	69083485	69085182
ENSE00001111651	68878118	68878280
ENSE00001111652	68843531	68843711
ENSE00003459545	69022828	69022979
ENSE00003479359	68902328	68902504
ENSE00003546296	68859884	68860524
ENSE00003571455	68974028	68974168
ENSE00003615832	69040308	69040421
ENSE00003641791	68880548	68880630
ENSE00003655292	68862945	68863061
ENSE00003657328	68919085	68919219
ENSE00003662500	68900434	68900546

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 86.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.5236 / max 107.9616, expressed in 1798 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154791	8.6660	1777
154792	4.8385	1586
154793	0.0191	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	86.76	silver quality
bone marrow cell	CL:0002092	85.36	gold quality
tibialis anterior	UBERON:0001385	85.30	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.66	gold quality
cortical plate	UBERON:0005343	83.35	gold quality
calcaneal tendon	UBERON:0003701	82.96	gold quality
right lobe of liver	UBERON:0001114	82.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.43	gold quality
ganglionic eminence	UBERON:0004023	82.16	gold quality
ventricular zone	UBERON:0003053	82.15	gold quality
colonic epithelium	UBERON:0000397	82.09	gold quality
gastrocnemius	UBERON:0001388	81.01	gold quality
muscle of leg	UBERON:0001383	80.90	gold quality
sural nerve	UBERON:0015488	80.51	gold quality
ileal mucosa	UBERON:0000331	80.50	silver quality
left testis	UBERON:0004533	80.40	gold quality
liver	UBERON:0002107	80.26	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.14	gold quality
right testis	UBERON:0004534	80.00	gold quality
stromal cell of endometrium	CL:0002255	79.53	gold quality
leukocyte	CL:0000738	79.52	gold quality
monocyte	CL:0000576	79.50	gold quality
testis	UBERON:0000473	79.11	gold quality
prefrontal cortex	UBERON:0000451	78.08	gold quality
islet of Langerhans	UBERON:0000006	77.91	gold quality
skeletal muscle organ	UBERON:0014892	77.52	gold quality
popliteal artery	UBERON:0002250	77.43	gold quality
tibial artery	UBERON:0007610	77.42	gold quality
smooth muscle tissue	UBERON:0001135	76.72	gold quality
granulocyte	CL:0000094	76.66	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.47
E-ENAD-17	no	104.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting TANGO6, 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-340-5P	100.00	72.50	4437
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-4721	99.26	66.05	818
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-6744-3P	99.22	64.41	972

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.7% of screened cell lines, common-essential.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tango6	ENSDARG00000034001
mus_musculus	Tango6	ENSMUSG00000041949
drosophila_melanogaster	Tango6	FBGN0032728
caenorhabditis_elegans		WBGENE00011806

Protein

Protein identifiers

Transport and Golgi organization protein 6 homolog — Q9C0B7 (reviewed: Q9C0B7)

Alternative names: Transmembrane and coiled-coil domain-containing protein 7

All UniProt accessions (3): Q9C0B7, J3KT80, J3QL82

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the Tango6 family.

RefSeq proteins (1): NP_078838* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR019414	Rtp1_C2	Domain
IPR019451	Rtp1_C1	Domain
IPR039600	TANGO6/Rtp1	Family
IPR057347	TANGO6_N	Domain
IPR057407	HEAT_TANGO6	Domain

Pfam: PF10304, PF10363, PF23565, PF25267

UniProt features (9 total): compositionally biased region 3, repeat 2, chain 1, transmembrane region 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C0B7-F1	79.25	0.30

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): 556

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, chr16q22, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_SECRETION, MODULE_207, XU_GH1_EXOGENOUS_TARGETS_DN, GSE14415_ACT_VS_CTRL_NATURAL_TREG_DN, CIITA_TARGET_GENES, MAFG_TARGET_GENES, SFMBT1_TARGET_GENES, ZNF592_TARGET_GENES, MIR518C_5P, MIR12131, MIR330_5P

GO Biological Process (1): protein secretion (GO:0009306)

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein transport	1
secretion by cell	1
establishment of protein localization to extracellular region	1
protein localization to extracellular region	1
cellular anatomical structure	1

Protein interactions and networks

STRING

728 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TANGO6	MACF1	Q9UPN3	697
TANGO6	MSL1	Q68DK7	528
TANGO6	PRAMEF20	Q5VT98	488
TANGO6	GPN2	Q9H9Y4	460
TANGO6	CEP295NL	Q96MC4	447
TANGO6	SLC7A6OS	Q96CW6	442
TANGO6	SAAL1	Q96ER3	438
TANGO6	TMCO2	Q7Z6W1	429
TANGO6	HEATR4	Q86WZ0	417
TANGO6	PLEKHM3	Q6ZWE6	402
TANGO6	MROH7	Q68CQ1	397
TANGO6	OR51A2	Q8NGJ7	397
TANGO6	ISOC1	Q96CN7	386
TANGO6	FASTKD1	Q53R41	385
TANGO6	RPAP2	Q8IXW5	365

IntAct

63 interactions, top by confidence:

A	B	Type	Score
TSSK6	HSP90AA1	psi-mi:“MI:0914”(association)	0.740
POLR2J	POLR2D	psi-mi:“MI:0914”(association)	0.730
DNAJC7	PLD2	psi-mi:“MI:0914”(association)	0.640
POLR2L	RCCD1	psi-mi:“MI:0914”(association)	0.640
MAGEA4	MAGEB16	psi-mi:“MI:0914”(association)	0.530
GPN2	POLR2C	psi-mi:“MI:0914”(association)	0.530
DNAJB8	DNAJB6	psi-mi:“MI:0914”(association)	0.530
SLC31A1	PRORP	psi-mi:“MI:0914”(association)	0.530
TANGO6	MACF1	psi-mi:“MI:0915”(physical association)	0.370
CAPZA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
UBE3A	IGLC7	psi-mi:“MI:0914”(association)	0.350
UBE3A	TXNL1	psi-mi:“MI:0914”(association)	0.350
UBE3A	POTEF	psi-mi:“MI:0914”(association)	0.350
P4HA2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
DNAJC7	HSPA8	psi-mi:“MI:0914”(association)	0.350
POLR2B	PALM3	psi-mi:“MI:0914”(association)	0.350
POLR2K	BDP1	psi-mi:“MI:0914”(association)	0.350
RAB18	ASDURF	psi-mi:“MI:0914”(association)	0.350
RUVBL2	ASDURF	psi-mi:“MI:0914”(association)	0.350
RUVBL1	ASDURF	psi-mi:“MI:0914”(association)	0.350
B4GALT2	LENG9	psi-mi:“MI:0914”(association)	0.350
AMZ1	IFT56	psi-mi:“MI:0914”(association)	0.350
ATG7	IFT56	psi-mi:“MI:0914”(association)	0.350
FAM167A	IFT56	psi-mi:“MI:0914”(association)	0.350
TRMU	IFT56	psi-mi:“MI:0914”(association)	0.350
INF2	PIPSL	psi-mi:“MI:0914”(association)	0.350
HSPA8	SBNO1	psi-mi:“MI:0914”(association)	0.350
AFG2B	RCCD1	psi-mi:“MI:0914”(association)	0.350
PLEKHG7	MROH6	psi-mi:“MI:0914”(association)	0.350
UBXN6	ZSWIM8	psi-mi:“MI:0914”(association)	0.350

BioGRID (79): TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Two-hybrid), TANGO6 (Proximity Label-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-MS), TANGO6 (Affinity Capture-RNA), TANGO6 (Proximity Label-MS), TANGO6 (Synthetic Lethality), TANGO6 (Affinity Capture-MS)

ESM2 similar proteins: A0JML8, A0JP70, A2BID5, A2CEI4, A6NNW6, A9JTS5, E7FAW3, F1QNV4, O75153, O75800, O95248, P0CI65, P56192, P97874, Q08CY4, Q0VC30, Q14689, Q17QN2, Q1LWH4, Q1LXZ7, Q29S07, Q2T9L8, Q32PH0, Q3B7U4, Q3U308, Q3UAW9, Q3UH60, Q3UY23, Q4R4F1, Q641Y9, Q68FL6, Q6DG91, Q6GPP1, Q6PJN8, Q6TEN6, Q6ZNJ1, Q6ZPE2, Q6ZQA0, Q7T006, Q8BWT5

Diamond homologs: Q8C3S2, Q9C0B7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 105 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:

Pathway	Partners	Fold	FDR
FGFR2 mutant receptor activation	6	71.4×	2e-08
Signaling by FGFR2 IIIa TM	6	56.4×	4e-08
Abortive elongation of HIV-1 transcript in the absence of Tat	6	46.5×	1e-07
Telomere Maintenance	8	46.0×	2e-09
PIWI-interacting RNA (piRNA) biogenesis	7	43.1×	2e-08
MicroRNA (miRNA) biogenesis	6	42.8×	2e-07
Activation of HOX genes during differentiation	6	41.2×	2e-07
Signaling by FGFR in disease	6	39.6×	3e-07

GO biological processes:

GO term	Partners	Fold	FDR
protein folding	9	10.1×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	142
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3847 predictions. Top by Δscore:

Variant	Effect	Δscore
16:68843709:G:GT	donor_gain	1.0000
16:68843709:G:T	donor_gain	1.0000
16:68843710:AGGT:A	donor_loss	1.0000
16:68843711:GGTGA:G	donor_loss	1.0000
16:68843712:GTGAG:G	donor_loss	1.0000
16:68843713:T:G	donor_loss	1.0000
16:68843719:G:GT	donor_gain	1.0000
16:68862939:TTTTA:T	acceptor_loss	1.0000
16:68862940:TTTA:T	acceptor_loss	1.0000
16:68862941:TTAG:T	acceptor_loss	1.0000
16:68862942:TA:T	acceptor_loss	1.0000
16:68863047:G:GT	donor_gain	1.0000
16:68863048:G:T	donor_gain	1.0000
16:68863057:CCCAG:C	donor_loss	1.0000
16:68863058:CCAGG:C	donor_loss	1.0000
16:68863059:CAGG:C	donor_loss	1.0000
16:68863060:AGG:A	donor_loss	1.0000
16:68863061:GGTAC:G	donor_loss	1.0000
16:68863063:T:A	donor_loss	1.0000
16:68875148:T:TA	acceptor_gain	1.0000
16:68875152:A:AG	acceptor_gain	1.0000
16:68875152:AGC:A	acceptor_gain	1.0000
16:68875152:AGCG:A	acceptor_gain	1.0000
16:68875153:G:GC	acceptor_gain	1.0000
16:68875153:GC:G	acceptor_gain	1.0000
16:68875153:GCG:G	acceptor_gain	1.0000
16:68875153:GCGG:G	acceptor_gain	1.0000
16:68875289:AGGTA:A	donor_loss	1.0000
16:68875290:GGTAA:G	donor_loss	1.0000
16:68875291:GT:G	donor_loss	1.0000

AlphaMissense

7097 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:68927671:T:C	L744P	0.993
16:69022914:A:C	S977R	0.993
16:69022916:C:A	S977R	0.993
16:69022916:C:G	S977R	0.993
16:68867124:T:A	W300R	0.992
16:68867124:T:C	W300R	0.992
16:69022911:A:C	S976R	0.991
16:69022913:C:A	S976R	0.991
16:69022913:C:G	S976R	0.991
16:68863033:T:C	L275P	0.989
16:69083570:C:A	A1065D	0.989
16:69083579:C:A	A1068D	0.987
16:68867194:T:A	V323D	0.986
16:68878176:C:A	A397D	0.986
16:69083569:G:C	A1065P	0.986
16:69083591:T:C	L1072P	0.986
16:68863024:T:A	V272D	0.984
16:68867182:T:A	V319D	0.983
16:68919193:G:C	A701P	0.983
16:69022927:T:C	L981P	0.983
16:69083522:T:C	L1049P	0.983
16:68878173:T:A	V396D	0.982
16:68919194:C:A	A701D	0.981
16:68927661:G:C	A741P	0.981
16:68927662:C:A	A741D	0.981
16:68867126:G:C	W300C	0.979
16:68867126:G:T	W300C	0.979
16:68878175:G:C	A397P	0.978
16:68930295:G:A	G901R	0.978
16:68930295:G:C	G901R	0.978

dbSNP variants (sampled 300 via entrez): RS1000005278 (16:68971956 T>C), RS1000007416 (16:68991196 A>T), RS1000010981 (16:68968572 T>C,G), RS1000040963 (16:68852932 T>C), RS1000051683 (16:68893304 C>G), RS1000061930 (16:68942222 T>C), RS1000077664 (16:68946277 C>T), RS1000078995 (16:68883175 C>T), RS1000086434 (16:69029553 A>G), RS1000098307 (16:68859849 T>C), RS1000107734 (16:68879356 G>A,C), RS1000113534 (16:69010649 A>C), RS1000122686 (16:68946799 A>T), RS1000134843 (16:69061516 G>A), RS1000156709 (16:69058529 C>T)

Disease associations

OMIM: gene MIM:620188 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): myoepithelial tumor (MONDO:0002380)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004030_23	Primary sclerosing cholangitis	7.000000e-07
GCST005951_13	Body mass index	5.000000e-11
GCST010241_68	Apolipoprotein A1 levels	5.000000e-14
GCST010242_316	HDL cholesterol levels	5.000000e-14
GCST010703_183	Brain morphology (MOSTest)	5.000000e-11

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004346	neuroimaging measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D009208	Myoepithelioma	C04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
gossypol acetic acid	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
cylindrospermopsin	increases expression	1
NSC 689534	affects binding, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Cadmium	increases abundance, increases expression	1
Copper	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E1E6	Ubigene U-251 MG TANGO6 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03600649	PHASE1	UNKNOWN	Clinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196	PHASE1/PHASE2	UNKNOWN	A Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272	PHASE1/PHASE2	RECRUITING	NRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190	PHASE1/PHASE2	RECRUITING	Alpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420	Not specified	COMPLETED	Malignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis