GAGE12D

Summary

GAGE12D (G antigen 12D, HGNC:31904) is a protein-coding gene on chromosome Xp11.23, encoding G antigen 12B/C/D/E (A1L429).

At a glance

• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001127199

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31904
Approved symbol	GAGE12D
Name	G antigen 12D
Location	Xp11.23
Locus type	gene with protein product
Status	Approved
Aliases	OTTHUMG00000024145
Ensembl gene	ENSG00000227488
Ensembl biotype	protein_coding
OMIM	300728
Entrez	100132399

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000405679

RefSeq mRNA: 1 — MANE Select: NM_001127199 NM_001127199

CCDS: CCDS48113

Canonical transcript exons

ENST00000405679 — 5 exons

Exon	Start	End
ENSE00001616954	49543437	49543557
ENSE00001654377	49546380	49546505
ENSE00001814088	49548981	49549094
ENSE00001948843	49541733	49541840
ENSE00002458549	49542880	49542971

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 87.63.

Top tissues by expression

121 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	87.63	gold quality
testis	UBERON:0000473	54.44	gold quality
left testis	UBERON:0004533	51.41	gold quality
right testis	UBERON:0004534	47.86	gold quality
bone marrow cell	CL:0002092	38.51	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
mucosa of stomach	UBERON:0001199	35.85	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	32.95	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	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
prefrontal cortex	UBERON:0000451	29.22	gold quality
duodenum	UBERON:0002114	28.14	gold quality
liver	UBERON:0002107	28.04	gold quality
lymph node	UBERON:0000029	27.57	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	27.28	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.14	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
placenta	UBERON:0001987	25.81	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality
muscle of leg	UBERON:0001383	25.30	silver quality
leukocyte	CL:0000738	24.80	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting GAGE12D, 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-9-3P	99.96	70.88	2068
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-887-5P	98.82	65.90	1347
HSA-MIR-6878-5P	98.49	67.91	2142
HSA-MIR-30C-1-3P	97.80	66.36	1499
HSA-MIR-30C-2-3P	97.80	66.45	1499
HSA-MIR-6788-5P	97.80	66.41	1532

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), GAGE12J (ENSG00000224659), GAGE12H (ENSG00000224902), PAGE2 (ENSG00000234068), GAGE12F (ENSG00000236362), GAGE12C (ENSG00000237671), PAGE2B (ENSG00000238269), GAGE13 (ENSG00000274274), GAGE2E (ENSG00000275113)

Protein

Protein identifiers

G antigen 12B/C/D/E — A1L429 (reviewed: A1L429)

All UniProt accessions (1): A1L429

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_001120671* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008625	GAGE_fam	Family
IPR031320	GAGE	Domain

Pfam: PF05831

UniProt features (5 total): 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-A1L429-F1	63.26	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): chrXp11, MIR6878_5P, MIR30C_2_3P, MIR30C_1_3P, MIR6788_5P, MIR887_5P, MIR6505_3P

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

1205 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GAGE12D	SEL1L2	Q5TEA6	474
GAGE12D	CT45A10	P0DMU9	398
GAGE12D	PNLIPRP3	Q17RR3	393
GAGE12D	FAM180B	Q6P0A1	391
GAGE12D	CT45A5	P0DMU8	390
GAGE12D	FAM168B	A1KXE4	380
GAGE12D	C9J5N1	C9J5N1	371
GAGE12D	AARSD1	Q9BTE6	370
GAGE12D	PLGLB1	Q02325	368
GAGE12D	IQCF2	Q8IXL9	357
GAGE12D	FAM168A	Q92567	353
GAGE12D	CYYR1	Q96J86	348
GAGE12D	SPANXB1	Q9NS25	322
GAGE12D	ADGRG4	Q8IZF6	311
GAGE12D	XAGE1B	Q9HD64	290

IntAct

7 interactions, top by confidence:

A	B	Type	Score
GAGE12B	FLJ13057	psi-mi:“MI:0915”(physical association)	0.560
GAGE12B	GMCL2	psi-mi:“MI:0915”(physical association)	0.560
FLJ13057	GAGE12B	psi-mi:“MI:0915”(physical association)	0.560
GMCL2	GAGE12B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (6): GAGE12B (Two-hybrid), GAGE12B (Two-hybrid), GAGE12C (Positive Genetic), GAGE12B (Positive Genetic), GAGE12D (Positive Genetic), GAGE12E (Positive Genetic)

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

646 predictions. Top by Δscore:

Variant	Effect	Δscore
X:49542878:A:AG	acceptor_gain	1.0000
X:49542879:G:GG	acceptor_gain	1.0000
X:49543413:T:TA	acceptor_gain	1.0000
X:49543416:A:AG	acceptor_gain	1.0000
X:49543417:C:G	acceptor_gain	1.0000
X:49543418:A:AG	acceptor_gain	1.0000
X:49543419:C:G	acceptor_gain	1.0000
X:49543422:A:AG	acceptor_gain	1.0000
X:49543422:ACAC:A	acceptor_gain	1.0000
X:49543423:C:G	acceptor_gain	1.0000
X:49543424:A:AG	acceptor_gain	1.0000
X:49543424:AC:A	acceptor_gain	1.0000
X:49543425:C:CA	acceptor_gain	1.0000
X:49543425:C:G	acceptor_gain	1.0000
X:49543429:T:G	acceptor_gain	1.0000
X:49543524:G:GT	donor_gain	1.0000
X:49543570:G:T	donor_gain	1.0000
X:49546375:TTAA:T	acceptor_loss	1.0000
X:49546376:TAAG:T	acceptor_loss	1.0000
X:49546377:A:AG	acceptor_gain	1.0000
X:49546377:AAG:A	acceptor_gain	1.0000
X:49546377:AAGG:A	acceptor_gain	1.0000
X:49546378:A:AG	acceptor_gain	1.0000
X:49546378:AG:A	acceptor_gain	1.0000
X:49546378:AGG:A	acceptor_gain	1.0000
X:49546379:G:A	acceptor_gain	1.0000
X:49546379:G:GC	acceptor_gain	1.0000
X:49546379:GGG:G	acceptor_gain	1.0000
X:49546379:GGGCC:G	acceptor_gain	1.0000
X:49546502:GAAG:G	donor_gain	1.0000

AlphaMissense

765 scored. Top likely-pathogenic:

dbSNP variants (sampled 227 via entrez): RS1168647813 (X:49543433 C>A), RS1170942005 (X:49543625 C>T), RS1174970546 (X:49543893 G>T), RS1178504441 (X:49543728 T>C), RS1186880266 (X:49543441 A>T), RS1201434712 (X:49543468 C>T), RS1202022865 (X:49543486 A>T), RS1202590981 (X:49547840 T>A), RS1212396201 (X:49543250 C>T), RS1223251647 (X:49543499 A>G), RS1224028183 (X:49543131 T>C), RS1233078770 (X:49547828 ATCATTATAC>A), RS1249276086 (X:49543884 A>G), RS1250199837 (X:49543485 G>C), RS1266655915 (X:49543458 G>A)

Disease associations

OMIM: gene MIM:300728 | 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)

Clinical trials (associated diseases)

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