CTAG1A

Summary

CTAG1A (cancer/testis antigen 1A, HGNC:24198) is a protein-coding gene on chromosome Xq28, encoding Cancer/testis antigen 1 (P78358).

The protein encoded by this gene is a tumor cell antigen found in various types of cancers, which makes it a good candidate for a cancer vaccine. This gene is also highly expressed in normal ovary and testis tissues. An identical copy of this gene is found on the same chromosome.

Source: NCBI Gene 246100 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total — 1 pathogenic
• Druggable target: yes
• MANE Select transcript: NM_139250

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24198
Approved symbol	CTAG1A
Name	cancer/testis antigen 1A
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	LAGE2A, ESO1
Ensembl gene	ENSG00000268651
Ensembl biotype	protein_coding
OMIM	300657
Entrez	246100

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000593606, ENST00000599837

RefSeq mRNA: 1 — MANE Select: NM_139250 NM_139250

CCDS: CCDS44025

Canonical transcript exons

ENST00000599837 — 3 exons

Exon	Start	End
ENSE00003017728	154586526	154586816
ENSE00003078218	154585133	154585475
ENSE00003099719	154586152	154586286

Expression profiles

Bgee: expression breadth broad, 26 present calls, max score 87.56.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6534 / max 44.8461, expressed in 133 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198198	0.6534	133

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.56	gold quality
right testis	UBERON:0004534	77.35	gold quality
left testis	UBERON:0004533	76.05	gold quality
testis	UBERON:0000473	75.62	gold quality
mucosa of stomach	UBERON:0001199	47.45	gold quality
colonic epithelium	UBERON:0000397	43.06	silver quality
bone marrow cell	CL:0002092	42.87	gold quality
apex of heart	UBERON:0002098	42.75	silver quality
skeletal muscle tissue	UBERON:0001134	38.65	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow	UBERON:0002371	36.21	gold quality
muscle tissue	UBERON:0002385	34.93	gold quality
blood	UBERON:0000178	34.83	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
urinary bladder	UBERON:0001255	31.83	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	31.83	gold quality
tibial artery	UBERON:0007610	31.67	silver quality
popliteal artery	UBERON:0002250	31.55	silver quality
prefrontal cortex	UBERON:0000451	31.18	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
lymph node	UBERON:0000029	28.94	gold quality
placenta	UBERON:0001987	28.84	silver quality
monocyte	CL:0000576	28.65	gold quality
multicellular organism	UBERON:0000468	28.58	gold quality
leukocyte	CL:0000738	28.56	gold quality
cortex of kidney	UBERON:0001225	28.35	silver quality
thoracic mammary gland	UBERON:0005200	28.34	gold quality
right uterine tube	UBERON:0001302	28.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-9435	yes	611.10
E-ANND-3	no	0.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting CTAG1A, 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-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-193A-3P	98.59	66.36	769
HSA-MIR-193B-3P	98.59	66.62	748
HSA-MIR-6854-5P	96.77	65.96	848
HSA-MIR-1273C	95.96	65.86	66

Literature-anchored findings (GeneRIF, showing 3)

• Expression may represent potential targets for cancer immunotherapy in patients with non small cell lung carcinoma. (PMID:16596224)
• Involvement of NY-ESO-1 and MAGE-A4 in the pathogenesis of desmoid tumors. (PMID:37266606)
• Expression and Prognostic Significance of PD-L1 and NY-ESO1 in Gallbladder Carcinoma. (PMID:37369470)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000116344
mus_musculus	Ctag2	ENSMUSG00000031181
mus_musculus	Ctag2l2	ENSMUSG00000079532
mus_musculus	Ctag2l1	ENSMUSG00000079536
rattus_norvegicus	Ctag2	ENSRNOG00000012560
rattus_norvegicus	Ctag2l1	ENSRNOG00000060839
rattus_norvegicus	Ctag2l2	ENSRNOG00000061511
rattus_norvegicus	Ctag2l2	ENSRNOG00000066963
drosophila_melanogaster	Tcs6	FBGN0260224

Paralogs (3): CTAG2 (ENSG00000126890), CTAG1B (ENSG00000184033), LAGE3 (ENSG00000196976)

Protein

Protein identifiers

Cancer/testis antigen 1 — P78358 (reviewed: P78358)

Alternative names: Autoimmunogenic cancer/testis antigen NY-ESO-1, Cancer/testis antigen 6.1, L antigen family member 2

All UniProt accessions (2): P78358, A0A0A0MTT5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in testis and ovary and in a wide variety of cancers. Detected in uterine myometrium. Expressed from 18 weeks until birth in human fetal testis. In the adult testis, is strongly expressed in spermatogonia and in primary spermatocytes, but not in post-meiotic cells or in testicular somatic cells (at protein level).

Similarity. Belongs to the CTAG/PCC1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
P78358-1	1	yes
P78358-2	2

RefSeq proteins (1): NP_640343* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR015419	CTAG/Pcc1	Family

Pfam: PF09341

UniProt features (7 total): compositionally biased region 2, chain 1, region of interest 1, splice variant 1, helix 1, turn 1

Structure

Experimental structures (PDB)

23 structures.

PDB	Method	Resolution (Å)
6AT5	X-RAY DIFFRACTION	1.5
3KLA	X-RAY DIFFRACTION	1.65
2BNQ	X-RAY DIFFRACTION	1.7
2P5E	X-RAY DIFFRACTION	1.89
2BNR	X-RAY DIFFRACTION	1.9
3GJF	X-RAY DIFFRACTION	1.9
6AVF	X-RAY DIFFRACTION	2.03
9MIN	X-RAY DIFFRACTION	2.05
2F53	X-RAY DIFFRACTION	2.1
1S9W	X-RAY DIFFRACTION	2.2
2P5W	X-RAY DIFFRACTION	2.2
2PYE	X-RAY DIFFRACTION	2.3
9DL1	X-RAY DIFFRACTION	2.3
6RPB	X-RAY DIFFRACTION	2.5
6RPA	X-RAY DIFFRACTION	2.56
6AVG	X-RAY DIFFRACTION	2.6
2F54	X-RAY DIFFRACTION	2.7
3HAE	X-RAY DIFFRACTION	2.9
9FE1	ELECTRON MICROSCOPY	3.1
6RP9	X-RAY DIFFRACTION	3.12
9HKQ	ELECTRON MICROSCOPY	3.3
9C3E	ELECTRON MICROSCOPY	3.5
9NNF	ELECTRON MICROSCOPY	3.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P78358-F1	67.38	0.15

Antibody-complex structures (SAbDab): 3 — 3GJF, 3HAE, 9HKQ

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): GOBP_TRNA_METABOLIC_PROCESS, GOBP_TRNA_THREONYLCARBAMOYLADENOSINE_METABOLIC_PROCESS, chrXq28, FORTSCHEGGER_PHF8_TARGETS_UP, CTIP_DN.V1_UP, BMI1_DN.V1_DN, MIR4328

GO Biological Process (1): tRNA threonylcarbamoyladenosine metabolic process (GO:0070525)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tRNA metabolic process	1
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1006 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTAG1A	MAGEA3	P43357	960
CTAG1A	MAGEA4	P43358	925
CTAG1A	MAGEA1	P43355	872
CTAG1A	TYR	P14679	861
CTAG1A	HLA-A	P01891	857
CTAG1A	PMEL	P40967	857
CTAG1A	LY75	O60449	853
CTAG1A	CAGE1	Q8TC20	840
CTAG1A	CCDC73	Q6ZRK6	829
CTAG1A	MAGEA2B	P43356	812
CTAG1A	CD4	P01730	787
CTAG1A	MAGEA6	P43360	786
CTAG1A	MAGEC1	O60732	767
CTAG1A	TPTE	P56180	732
CTAG1A	CD8A	P01732	728
CTAG1A	PRAME	P78395	728

IntAct

273 interactions, top by confidence:

A	B	Type	Score
CTAG1A	UBQLN1	psi-mi:“MI:0915”(physical association)	0.720
UBQLN1	CTAG1A	psi-mi:“MI:0915”(physical association)	0.720
CTAG1A	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
UBQLN1	CTAG1A	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	HMG20A	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	DDIT4L	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	BORCS8	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	CDKN2AIPNL	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	LONRF3	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	SIKE1	psi-mi:“MI:0915”(physical association)	0.560
FCHSD2	CTAG1A	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	NAB2	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	GNG13	psi-mi:“MI:0915”(physical association)	0.560
GATC	CTAG1A	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	SGTB	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	SMG9	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	LAMTOR1	psi-mi:“MI:0915”(physical association)	0.560
BAG6	CTAG1A	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	BEX1	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	UBE2V1	psi-mi:“MI:0915”(physical association)	0.560
ALOX15B	CTAG1A	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	SOHLH1	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	RTN4IP1	psi-mi:“MI:0915”(physical association)	0.560
GTF2I	CTAG1A	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (191): UBQLN1 (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid), CTAG1B (Two-hybrid), CTAG1A (Two-hybrid)

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: O75638, P78358, Q14657, Q9CR70, Q10220

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	3
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1325735	NC_000023.10:g.(153784642_153786697)_(153792726_153814360)del	Pathogenic

SpliceAI

403 predictions. Top by Δscore:

Variant	Effect	Δscore
X:154585311:A:T	donor_gain	0.9900
X:154585473:GTT:G	donor_gain	0.9900
X:154585232:G:GT	donor_gain	0.9800
X:154585262:G:GT	donor_gain	0.9800
X:154585289:G:GT	donor_gain	0.9800
X:154586309:G:T	donor_gain	0.9800
X:154585467:GCT:G	donor_gain	0.9700
X:154585469:T:TG	donor_gain	0.9700
X:154586519:C:G	acceptor_gain	0.9700
X:154586287:G:GG	donor_gain	0.9600
X:154586520:A:AG	acceptor_gain	0.9600
X:154586524:A:AG	acceptor_gain	0.9600
X:154586525:G:GG	acceptor_gain	0.9600
X:154585310:G:GT	donor_gain	0.9500
X:154585469:T:G	donor_gain	0.9500
X:154586283:C:G	donor_gain	0.9500
X:154586292:T:G	donor_gain	0.9500
X:154586525:GCC:G	acceptor_gain	0.9500
X:154586297:G:GT	donor_gain	0.9300
X:154586518:A:AG	acceptor_gain	0.9300
X:154586521:T:G	acceptor_gain	0.9300
X:154586303:G:GT	donor_gain	0.9200
X:154585320:TGCC:T	donor_gain	0.8900
X:154585339:C:A	donor_gain	0.8900
X:154585457:A:T	donor_gain	0.8900
X:154585474:T:G	donor_gain	0.8900
X:154586281:GAC:G	donor_gain	0.8900
X:154586283:C:CG	donor_gain	0.8900
X:154586524:AGCC:A	acceptor_gain	0.8900
X:154586525:GCCG:G	acceptor_gain	0.8900

AlphaMissense

1125 scored. Top likely-pathogenic:

dbSNP variants (sampled 37 via entrez): RS112926777 (X:154583392 T>C), RS1163407242 (X:154586977 C>T), RS1187638489 (X:154587184 C>T), RS1195469678 (X:154587111 T>C), RS1207972651 (X:154587269 C>T), RS1247670864 (X:154587163 T>C), RS1254735150 (X:154587251 A>G), RS1320259716 (X:154586821 G>A), RS1355611764 (X:154587294 T>C), RS1359477005 (X:154586734 T>G), RS1372477485 (X:154585478 ATTCTG>A), RS1373696107 (X:154587100 C>T), RS1397250182 (X:154586959 T>C), RS1426921719 (X:154587114 T>C), RS1457895862 (X:154586978 G>A)

Disease associations

OMIM: gene MIM:300657 | disease phenotypes: MIM:308300

GenCC curated gene-disease

Mondo (1): incontinentia pigmenti (MONDO:0010631)

Orphanet (1): Incontinentia pigmenti (Orphanet:464)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D007184	Incontinentia Pigmenti	C16.131.077.445; C16.131.831.580; C16.320.850.420; C17.800.621.497; C17.800.804.580; C17.800.827.420

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4804257 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
butyraldehyde	increases expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	decreases expression, affects cotreatment	1
Benzo(a)pyrene	decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Silicon Dioxide	increases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases 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_A0WA	A549-A2-ESO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00976586	Not specified	COMPLETED	Role of Pseudogene in Incontinentia Pigmenti, and Its Potential Treatment
NCT05954416	Not specified	RECRUITING	FARD (RaDiCo Cohort) (RaDiCo-FARD)