CTAGE1

Summary

CTAGE1 (cutaneous T cell lymphoma-associated antigen 1, HGNC:24346) is a protein-coding gene on chromosome 18q11.2, encoding cTAGE family member 2 (Q96RT6).

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein secretion; and vesicle cargo loading. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum exit site and endoplasmic reticulum membrane.

Source: NCBI Gene 64693 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 152 total
• MANE Select transcript: NM_172241

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24346
Approved symbol	CTAGE1
Name	cutaneous T cell lymphoma-associated antigen 1
Location	18q11.2
Locus type	gene with protein product
Status	Approved
Aliases	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2
Ensembl gene	ENSG00000212710
Ensembl biotype	protein_coding
OMIM	608856
Entrez	64693

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000391403, ENST00000525417

RefSeq mRNA: 1 — MANE Select: NM_172241 NM_172241

CCDS: CCDS45837

Canonical transcript exons

ENST00000391403 — 1 exons

Exon	Start	End
ENSE00001732514	22413599	22417915

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 76.30.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0053 / max 3.3286, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
208514	0.0053	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	76.30	gold quality
left testis	UBERON:0004533	75.12	gold quality
testis	UBERON:0000473	74.59	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.08	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.94	gold quality
duodenum	UBERON:0002114	41.10	gold quality
cortical plate	UBERON:0005343	39.80	gold quality
skeletal muscle tissue	UBERON:0001134	38.98	gold quality
stromal cell of endometrium	CL:0002255	38.77	gold quality
placenta	UBERON:0001987	38.70	silver quality
muscle tissue	UBERON:0002385	38.37	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
right atrium auricular region	UBERON:0006631	36.47	silver quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	35.83	gold quality
gall bladder	UBERON:0002110	35.75	gold quality
liver	UBERON:0002107	35.58	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
endometrium	UBERON:0001295	35.44	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.35	gold quality
thoracic aorta	UBERON:0001515	35.21	silver quality
ascending aorta	UBERON:0001496	34.99	silver quality
granulocyte	CL:0000094	34.89	gold quality
left coronary artery	UBERON:0001626	34.81	gold quality
vermiform appendix	UBERON:0001154	34.78	gold quality
right coronary artery	UBERON:0001625	34.34	gold quality
right lobe of liver	UBERON:0001114	34.15	gold quality
monocyte	CL:0000576	33.77	gold quality
leukocyte	CL:0000738	33.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.33
E-GEOD-75367	no	0.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

109 targeting CTAGE1, 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-3163	100.00	77.23	8605
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-6739-5P	99.80	67.87	2806

Literature-anchored findings (GeneRIF, showing 3)

• cTAGE-1 and cTAGE-5 are new cancer germline antigens and that tumor-specific splicing of cTAGE genes may lead to further candidate proteins for specific immunotherapy of cutaneous T cell lymphoma and other malignancies. (PMID:12839582)
• Loss of TSC2 in the brain correlates with survival and abnormal behavior. (PMID:22752306)
• SYCP1, cTAGE1, and GTSF1 are expressed in cutaneous T-cell lymphoma, but not in normal skin or benign inflammatory dermatoses. (PMID:24850846)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mia2	ENSMUSG00000021000
rattus_norvegicus	Mia2	ENSRNOG00000005101
drosophila_melanogaster	Tango1	FBGN0286898

Paralogs (10): OTOR (ENSG00000125879), MIA2 (ENSG00000150527), MIA3 (ENSG00000154305), SPZ1 (ENSG00000164299), CTAGE9 (ENSG00000236761), MIA (ENSG00000261857), CTAGE15 (ENSG00000271079), CTAGE6 (ENSG00000271321), CTAGE4 (ENSG00000288784), CTAGE8 (ENSG00000289604)

Protein

Protein identifiers

cTAGE family member 2 — Q96RT6 (reviewed: Q96RT6, Q9HC47)

Alternative names: Cancer/testis antigen 21.2

All UniProt accessions (2): Q96RT6, Q9HC47

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Testis. Not found in tumor.

Similarity. Belongs to the cTAGE family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96RT6-1	2, cTAGE-2	yes
Q9HC47-1	1, cTAGE-1

RefSeq proteins (1): NP_758441* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051500	cTAGE_MIA/OTOR	Family

UniProt features (17 total): sequence conflict 4, transmembrane region 3, chain 2, region of interest 2, coiled-coil region 2, compositionally biased region 2, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96RT6-F1	70.45	0.47
AF-Q9HC47-F1	61.57	0.00

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): 267

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): XU_GH1_AUTOCRINE_TARGETS_UP, MODULE_511, GOBP_VESICLE_MEDIATED_TRANSPORT, COUP_01, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, BLALOCK_ALZHEIMERS_DISEASE_UP, HEN1_01, GOBP_SECRETION, HNF4_01, XU_GH1_EXOGENOUS_TARGETS_UP, chr18q11, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, XU_AKT1_TARGETS_48HR, GOBP_GOLGI_VESICLE_TRANSPORT

GO Biological Process (4): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein secretion (GO:0009306), vesicle cargo loading (GO:0035459), biological_process (GO:0008150)

GO Molecular Function (0):

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum exit site (GO:0070971), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cytoplasm	1
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
protein transport	1
secretion by cell	1
establishment of protein localization to extracellular region	1
protein localization to extracellular region	1
transport	1
vesicle-mediated transport	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
endoplasmic reticulum	1

Protein interactions and networks

STRING

875 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTAGE1	CCDC68	Q9H2F9	955
CTAGE1	A0A1B0GVM2	A0A1B0GVM2	545
CTAGE1	SPANXA1	Q9NS26	479
CTAGE1	GAGE4	P0DSO3	479
CTAGE1	MAGEA12	P43365	474
CTAGE1	DDX43	Q9NXZ2	435
CTAGE1	PREB	Q9HCU5	400
CTAGE1	FTHL17	Q9BXU8	398
CTAGE1	CABLES1	Q8TDN4	395
CTAGE1	CTAG2	O75638	394
CTAGE1	PRAME	P78395	382
CTAGE1	CTAG1A	P78358	380
CTAGE1	MIA	Q16674	380
CTAGE1	CSAG1	Q6PB30	373
CTAGE1	CT47A11	Q5JQC4	371

IntAct

8 interactions, top by confidence:

A	B	Type	Score
MIA2	RGPD3	psi-mi:“MI:0914”(association)	0.530
CTAGE1	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440
CTAGE1	CCT6A	psi-mi:“MI:0915”(physical association)	0.400
GRIPAP1	CTAGE1	psi-mi:“MI:0915”(physical association)	0.400
MIA3	CTAGE1	psi-mi:“MI:0915”(physical association)	0.400
MSH3	CTAGE1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (14): CTAGE1 (Affinity Capture-MS), CTAGE1 (Proximity Label-MS), CTAGE1 (Proximity Label-MS), CTAGE1 (Proximity Label-MS), CTAGE1 (Proximity Label-MS), CTAGE1 (Affinity Capture-MS), CTAGE1 (Cross-Linking-MS (XL-MS)), CTAGE1 (Cross-Linking-MS (XL-MS)), CTAGE1 (Cross-Linking-MS (XL-MS)), CTAGE1 (Cross-Linking-MS (XL-MS)), CTAGE1 (Cross-Linking-MS (XL-MS)), CTAGE1 (Cross-Linking-MS (XL-MS)), CTAGE1 (Affinity Capture-MS), CTAGE1 (Affinity Capture-MS)

ESM2 similar proteins: A0JMQ7, A2BGP7, A4D2H0, A4FU28, B4F7A7, O75665, P0C219, P0CG41, Q05D60, Q15025, Q28BZ7, Q28C41, Q2T9X8, Q32LC2, Q499E4, Q4PJT6, Q4R7I4, Q5FWP9, Q5U3Z6, Q5U465, Q5XIA0, Q5XJA2, Q5ZJA3, Q6AXZ4, Q6NRH3, Q6P926, Q6PCG6, Q7M6Y5, Q80Z25, Q865V0, Q86UF2, Q86W54, Q86XR8, Q86YF9, Q86Z20, Q8BMD2, Q8CEE0, Q8IX94, Q8IYJ2, Q8IYX8

Diamond homologs: A4D2H0, A4FU28, P0CG41, Q86UF2, Q8IX94, Q8IX95, Q91ZV0, Q96PC5, Q96RT6, Q9I8P5, Q9I8P6, Q9JIE3, Q9NRC9, Q16674, Q61865, Q62946

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	136
Likely benign	10
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

14 predictions. Top by Δscore:

Variant	Effect	Δscore
18:22417723:C:CT	acceptor_gain	0.4700
18:22417808:TCA:T	donor_gain	0.3100
18:22417810:A:T	donor_gain	0.2700
18:22415462:A:C	donor_gain	0.2400
18:22417808:TCATA:T	donor_loss	0.2400
18:22417809:CATAC:C	donor_loss	0.2400
18:22417810:ATAC:A	donor_loss	0.2400
18:22417811:TACCT:T	donor_loss	0.2400
18:22417812:ACCT:A	donor_loss	0.2400
18:22417813:CCTTC:C	donor_loss	0.2400
18:22416247:C:T	acceptor_gain	0.2300
18:22417814:C:T	donor_loss	0.2200
18:22416243:TCCCC:T	acceptor_gain	0.2100
18:22417807:CTCAT:C	donor_loss	0.2000

AlphaMissense

4905 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:22416832:A:G	L327P	0.902
18:22416769:A:G	L348P	0.899
18:22417334:C:G	A160P	0.891
18:22416757:A:G	L352P	0.889
18:22416607:C:G	R402P	0.888
18:22416944:C:G	A290P	0.875
18:22417716:A:C	S32R	0.862
18:22417716:A:T	S32R	0.862
18:22417718:T:G	S32R	0.862
18:22417249:A:G	L188P	0.859
18:22417748:C:G	G22R	0.856
18:22417748:C:T	G22R	0.856
18:22416853:A:G	L320P	0.840
18:22417364:A:G	S150P	0.832
18:22416903:T:A	R303S	0.819
18:22416903:T:G	R303S	0.819
18:22416589:A:G	L408P	0.809
18:22416955:A:G	L286P	0.794
18:22416947:C:G	A289P	0.793
18:22417738:G:T	A25D	0.789
18:22416599:C:G	A405P	0.785
18:22417354:A:G	L153P	0.780
18:22417747:C:T	G22E	0.779
18:22416932:C:G	A294P	0.772
18:22417186:A:G	L209P	0.771
18:22417271:C:G	A181P	0.763
18:22417311:A:C	F167L	0.760
18:22417311:A:T	F167L	0.760
18:22417313:A:G	F167L	0.760
18:22417713:A:C	F33L	0.759

dbSNP variants (sampled 300 via entrez): RS1001626340 (18:22419616 T>A,C), RS1001824798 (18:22415947 C>T), RS1002629093 (18:22414752 A>G), RS1002673509 (18:22414536 C>T), RS1003677600 (18:22413540 A>G), RS1003884620 (18:22417896 C>G,T), RS1003956914 (18:22418055 C>A,G,T), RS1004838003 (18:22414135 T>C), RS1004947536 (18:22419341 C>A,T), RS1005763280 (18:22415093 TTTTTTTAAA>T), RS1006249572 (18:22415351 A>T), RS1007232735 (18:22415383 C>G), RS1008231171 (18:22416247 C>T), RS1008529796 (18:22413794 T>C), RS1009752323 (18:22417580 C>T)

Disease associations

OMIM: gene MIM:608856 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST000764_14	Tuberculosis	7.000000e-09
GCST002829_28	Urate levels in overweight individuals	2.000000e-06
GCST003818_10	Resting heart rate	1.000000e-07
GCST005194_240	Coronary artery disease	4.000000e-07
GCST005575_2	Moyamoya disease	2.000000e-11
GCST006481_23	Lung function (FEV1)	5.000000e-08
GCST006481_34	Lung function (FEV1)	4.000000e-07
GCST006630_80	Diastolic blood pressure	2.000000e-11
GCST007507_21	Benign prostatic hyperplasia and lower urinary tract symptoms	5.000000e-06
GCST010244_313	Triglyceride levels	9.000000e-12
GCST010796_1354	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-09
GCST010796_1355	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-09
GCST010866_158	Coronary artery disease	8.000000e-13
GCST010867_19	Coronary artery disease	5.000000e-09
GCST011365_156	Myocardial infarction	5.000000e-06
GCST011496_9	Abdominal aortic aneurysm	4.000000e-14

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004531	urate measurement
EFO:0004314	forced expiratory volume
EFO:0006336	diastolic blood pressure
EFO:0008008	lower urinary tract symptom
EFO:0004530	triglyceride measurement
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Folic Acid	decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	decreases expression	1

Clinical trials (associated diseases)

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