GAGE12J

Summary

GAGE12J (G antigen 12J, HGNC:17778) is a protein-coding gene on chromosome Xp11.23, encoding G antigen 12J (A6NER3).

At a glance

• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001098406

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17778
Approved symbol	GAGE12J
Name	G antigen 12J
Location	Xp11.23
Locus type	gene with protein product
Status	Approved
Aliases	OTTHUMG00000024137
Ensembl gene	ENSG00000224659
Ensembl biotype	protein_coding
OMIM	300733
Entrez	729396

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000442437

RefSeq mRNA: 1 — MANE Select: NM_001098406 NM_001098406

CCDS: CCDS43939

Canonical transcript exons

ENST00000442437 — 5 exons

Exon	Start	End
ENSE00001628554	49322037	49322144
ENSE00001781026	49326690	49326815
ENSE00001800316	49323743	49323863
ENSE00001948974	49329271	49329384
ENSE00002450766	49323186	49323277

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 95.93.

Top tissues by expression

123 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	95.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.15	gold quality
testis	UBERON:0000473	80.25	gold quality
left testis	UBERON:0004533	79.67	gold quality
right testis	UBERON:0004534	78.68	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
adenohypophysis	UBERON:0002196	36.92	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
right ovary	UBERON:0002118	32.07	gold quality
pituitary gland	UBERON:0000007	31.75	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
urinary bladder	UBERON:0001255	31.06	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
blood	UBERON:0000178	29.74	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
nucleus accumbens	UBERON:0001882	28.72	gold quality
metanephros cortex	UBERON:0010533	28.62	gold quality
duodenum	UBERON:0002114	28.14	gold quality
muscle of leg	UBERON:0001383	28.01	gold quality
lymph node	UBERON:0000029	27.57	gold quality
leukocyte	CL:0000738	27.30	gold quality
gastrocnemius	UBERON:0001388	27.28	gold quality
monocyte	CL:0000576	27.27	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-124263	yes	4398.86
E-CURD-11	yes	359.88
E-MTAB-6308	yes	342.65
E-GEOD-134144	yes	26.62
E-CURD-53	no	1632.58
E-ANND-3	no	0.65

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (22): PAGE1 (ENSG00000068985), PAGE4 (ENSG00000101951), XAGE2 (ENSG00000155622), PAGE5 (ENSG00000158639), XAGE3 (ENSG00000171402), XAGE5 (ENSG00000171405), GAGE2A (ENSG00000189064), PAGE3 (ENSG00000204279), XAGE1A (ENSG00000204379), XAGE1B (ENSG00000204382), GAGE1 (ENSG00000205777), GAGE12G (ENSG00000215269), GAGE10 (ENSG00000215274), GAGE12E (ENSG00000216649), GAGE12H (ENSG00000224902), GAGE12D (ENSG00000227488), PAGE2 (ENSG00000234068), GAGE12F (ENSG00000236362), GAGE12C (ENSG00000237671), PAGE2B (ENSG00000238269), GAGE13 (ENSG00000274274), GAGE2E (ENSG00000275113)

Protein

Protein identifiers

G antigen 12J — A6NER3 (reviewed: A6NER3)

All UniProt accessions (1): A6NER3

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. This gene belongs to a multigene family expressed in a large variety of tumors whereas in normal tissues, expression is restricted to germ cells. These genes organized in clustered repeats, have a high degree of predicted sequence identity, but differ by scattered single nucleotide substitution. Their sequences contain either the antigenic peptide YYWPRPRRY or YRPRPRRY which is recognized by cytotoxic T-cells.

Similarity. Belongs to the GAGE family.

RefSeq proteins (1): NP_001091876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008625	GAGE_fam	Family
IPR031320	GAGE	Domain

Pfam: PF05831

UniProt features (10 total): sequence variant 5, compositionally biased region 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NER3-F1	64.15	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chrXp11

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1185 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GAGE12J	PHGR1	C9JFL3	473
GAGE12J	PNLIPRP3	Q17RR3	419
GAGE12J	MUCL3	Q3MIW9	394
GAGE12J	CT47A11	Q5JQC4	374
GAGE12J	MAGEE1	Q9HCI5	373
GAGE12J	CYYR1	Q96J86	372
GAGE12J	ASTE1	Q2TB18	371
GAGE12J	TMSB4Y	O14604	370
GAGE12J	VWA2	Q5GFL6	370
GAGE12J	MGAT4C	Q9UBM8	370
GAGE12J	SCAND1	P57086	351
GAGE12J	MUC22	E2RYF6	336
GAGE12J	SPRR2E	P22531	324
GAGE12J	HNRNPCL1	O60812	323
GAGE12J	ZNF208	O43345	315

IntAct

114 interactions, top by confidence:

A	B	Type	Score
GAGE12J	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	WHRN	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
APBA3	GAGE12J	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD7	GAGE12J	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	NHERF4	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	MPP2	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	TAX1BP3	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PDZK1	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	LDB3	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PALS2	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	SNTG1	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PICK1	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	FRMPD2	psi-mi:“MI:0407”(direct interaction)	0.440
GRID2IP	GAGE12J	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	ARHGAP21	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	SHANK1	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	TJP1	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PTPN13	psi-mi:“MI:0407”(direct interaction)	0.440
WHRN	GAGE12J	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	PATJ	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	GRIP1	psi-mi:“MI:0407”(direct interaction)	0.440
GAGE12J	LIN7C	psi-mi:“MI:0407”(direct interaction)	0.440

ESM2 similar proteins: A0A0U1RQG5, A1L429, A6NDE8, A6NER3, A6NGK3, E1AZ71, O08664, O60829, O75459, O76087, P0C2W7, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, P52651, P62521, P86478, P86479, P86480, P86481, P86496, Q13066, Q13069, Q13070, Q17QW4, Q28181, Q2T9P9, Q32PA2, Q4V321, Q4V326, Q5JQC4, Q5U2Y8, Q62100, Q63803, Q64256, Q6NT46, Q6X7S9, Q7Z2X7

Diamond homologs: A1L429, A6NDE8, A6NER3, A6NGK3, O75459, O76087, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, Q13066, Q13069, Q13070, Q4V321, Q4V326, Q6NT46, Q8WTP9, Q96GT9, Q9UEU5, Q8WWM1, Q5JUK9, Q5JRK9, Q7Z2X7, Q9HD64

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 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
Ras activation upon Ca2+ influx through NMDA receptor	5	58.3×	8e-07
Unblocking of NMDA receptors, glutamate binding and activation	5	55.5×	8e-07
Negative regulation of NMDA receptor-mediated neuronal transmission	5	55.5×	8e-07
Long-term potentiation	5	48.5×	1e-06
Assembly and cell surface presentation of NMDA receptors	9	46.6×	2e-11
Neurexins and neuroligins	10	40.2×	7e-12
Protein-protein interactions at synapses	6	32.5×	8e-07
Neuronal System	6	5.4×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	88.8×	6e-17
protein localization to synapse	6	63.8×	4e-08
receptor clustering	7	60.7×	4e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	7	48.2×	2e-08
cell-cell adhesion	10	14.1×	2e-07
protein-containing complex assembly	8	12.7×	1e-05
chemical synaptic transmission	7	7.5×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

550 predictions. Top by Δscore:

Variant	Effect	Δscore
X:49323184:A:AG	acceptor_gain	1.0000
X:49323185:G:GG	acceptor_gain	1.0000
X:49323185:GT:G	acceptor_gain	1.0000
X:49323716:A:AG	acceptor_gain	1.0000
X:49323716:ATTT:A	acceptor_gain	1.0000
X:49323717:T:G	acceptor_gain	1.0000
X:49323719:T:TA	acceptor_gain	1.0000
X:49323722:A:AG	acceptor_gain	1.0000
X:49323723:C:G	acceptor_gain	1.0000
X:49323724:A:AG	acceptor_gain	1.0000
X:49323725:C:G	acceptor_gain	1.0000
X:49323728:A:AG	acceptor_gain	1.0000
X:49323728:ACAC:A	acceptor_gain	1.0000
X:49323729:C:G	acceptor_gain	1.0000
X:49323730:A:AG	acceptor_gain	1.0000
X:49323730:AC:A	acceptor_gain	1.0000
X:49323731:C:CA	acceptor_gain	1.0000
X:49323731:C:G	acceptor_gain	1.0000
X:49323735:T:G	acceptor_gain	1.0000
X:49323741:A:AG	acceptor_gain	1.0000
X:49323742:G:GC	acceptor_gain	1.0000
X:49323830:G:GT	donor_gain	1.0000
X:49323845:G:GT	donor_gain	1.0000
X:49323876:G:T	donor_gain	1.0000
X:49326686:TAA:T	acceptor_loss	1.0000
X:49326687:A:AG	acceptor_gain	1.0000
X:49326687:AAG:A	acceptor_gain	1.0000
X:49326687:AAGG:A	acceptor_gain	1.0000
X:49326688:A:AG	acceptor_gain	1.0000
X:49326688:A:G	acceptor_gain	1.0000

AlphaMissense

763 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:49323752:T:C	F32L	0.828
X:49323754:C:A	F32L	0.828
X:49323754:C:G	F32L	0.828
X:49323202:G:C	W3C	0.622
X:49323202:G:T	W3C	0.622

dbSNP variants (sampled 300 via entrez): RS10126890 (X:49324883 G>A), RS10126926 (X:49324861 C>T), RS11091255 (X:49326937 C>G), RS11091256 (X:49327181 T>C,G), RS11091257 (X:49327464 C>T), RS111788301 (X:49320961 T>A), RS1137130 (X:49326707 G>C), RS1156297191 (X:49327342 T>C), RS1156353863 (X:49326692 C>T), RS1156448575 (X:49329395 G>A,C), RS1156661608 (X:49324023 C>G,T), RS1156875698 (X:49325443 A>G), RS1157549804 (X:49322349 G>A,T), RS1157875752 (X:49320483 T>A,C), RS1157921238 (X:49323543 C>T)

Disease associations

OMIM: gene MIM:300733 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression	1
Lipopolysaccharides	affects expression, affects response to substance	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1SL	Abcam HeLa GAGE12J KO	Cancer cell line	Female

Clinical trials (associated diseases)

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