MAGEA9B

Summary

MAGEA9B (MAGE family member A9B, HGNC:31909) is a protein-coding gene on chromosome Xq28, encoding Melanoma-associated antigen 9 (P43362). Not known, though may play a role in embryonal development and tumor transformation or aspects of tumor progression.

MAGEA9B is a duplication of the MAGEA9 gene (MIM 300342) on chromosome Xq28. The 2 copies are separated by about 194 kb (Hartz, 2009).

Source: NCBI Gene 728269 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001080790

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31909
Approved symbol	MAGEA9B
Name	MAGE family member A9B
Location	Xq28
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000267978
Ensembl biotype	protein_coding
OMIM	300764
Entrez	728269

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000593349, ENST00000594744, ENST00000595065, ENST00000602102, ENST00000950133

RefSeq mRNA: 1 — MANE Select: NM_001080790 NM_001080790

CCDS: CCDS35423

Canonical transcript exons

ENST00000595065 — 4 exons

Exon	Start	End
ENSE00003000368	149587394	149587459
ENSE00003043214	149581653	149583244
ENSE00003151235	149583547	149583633
ENSE00003161603	149583320	149583388

Expression profiles

Bgee: expression breadth broad, 34 present calls, max score 86.72.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.15	gold quality
right testis	UBERON:0004534	75.02	gold quality
testis	UBERON:0000473	73.73	gold quality
left testis	UBERON:0004533	73.41	gold quality
placenta	UBERON:0001987	50.22	gold quality
sural nerve	UBERON:0015488	45.00	silver quality
cortical plate	UBERON:0005343	42.55	gold quality
bone marrow cell	CL:0002092	40.71	gold quality
ganglionic eminence	UBERON:0004023	39.89	gold quality
urinary bladder	UBERON:0001255	39.32	gold quality
lymph node	UBERON:0000029	37.37	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
right coronary artery	UBERON:0001625	36.02	gold quality
tonsil	UBERON:0002372	35.73	gold quality
vermiform appendix	UBERON:0001154	35.31	gold quality
granulocyte	CL:0000094	35.23	gold quality
right lung	UBERON:0002167	34.87	gold quality
duodenum	UBERON:0002114	34.70	gold quality
bone marrow	UBERON:0002371	34.07	gold quality
right uterine tube	UBERON:0001302	33.47	gold quality
muscle of leg	UBERON:0001383	32.90	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
prefrontal cortex	UBERON:0000451	31.23	silver quality
leukocyte	CL:0000738	30.98	gold quality
monocyte	CL:0000576	30.75	gold quality
islet of Langerhans	UBERON:0000006	30.31	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
blood	UBERON:0000178	29.45	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	10.86
E-ANND-3	no	0.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting MAGEA9B, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-31-5P	98.58	68.35	1239
HSA-MIR-6780A-3P	98.42	67.49	1518
HSA-MIR-556-5P	97.75	66.17	473
HSA-MIR-134-5P	97.11	66.52	976
HSA-MIR-3118	97.11	66.58	984
HSA-MIR-4433B-5P	95.91	66.56	727
HSA-MIR-550B-3P	95.43	67.73	599

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	ndnl2	ENSDARG00000058212
drosophila_melanogaster	MAGE	FBGN0037481

Paralogs (37): MAGEC2 (ENSG00000046774), TRO (ENSG00000067445), MAGEB2 (ENSG00000099399), MAGED2 (ENSG00000102316), MAGEB4 (ENSG00000120289), MAGEA9 (ENSG00000123584), MAGEA10 (ENSG00000124260), MAGEA4 (ENSG00000147381), MAGED4 (ENSG00000154545), MAGEC1 (ENSG00000155495), MAGEA8 (ENSG00000156009), MAGEC3 (ENSG00000165509), MAGEB6 (ENSG00000176746), MAGEB18 (ENSG00000176774), MAGEF1 (ENSG00000177383), MAGEB10 (ENSG00000177689), MAGED1 (ENSG00000179222), NDN (ENSG00000182636), MAGEB17 (ENSG00000182798), MAGEA2B (ENSG00000183305), NSMCE3 (ENSG00000185115), MAGEA11 (ENSG00000185247), MAGEE2 (ENSG00000186675), MAGED4B (ENSG00000187243), MAGEH1 (ENSG00000187601), MAGEB5 (ENSG00000188408), MAGEB16 (ENSG00000189023), MAGEA6 (ENSG00000197172), MAGEA1 (ENSG00000198681), MAGEB3 (ENSG00000198798), MAGEE1 (ENSG00000198934), MAGEA12 (ENSG00000213401), MAGEB1 (ENSG00000214107), MAGEA3 (ENSG00000221867), MAGEB6B (ENSG00000232030), MAGEL2 (ENSG00000254585), MAGEA2 (ENSG00000268606)

Protein

Protein identifiers

Melanoma-associated antigen 9 — P43362 (reviewed: P43362)

Alternative names: Cancer/testis antigen 1.9, MAGE-9 antigen

All UniProt accessions (4): P43362, A0A075B794, A0A075B798, A0A075B7A9

UniProt curated annotations — full annotation on UniProt →

Function. Not known, though may play a role in embryonal development and tumor transformation or aspects of tumor progression.

Tissue specificity. Expressed in many tumors of several types, such as melanoma, head and neck squamous cell carcinoma, lung carcinoma and breast carcinoma, but not in normal tissues except for testes and placenta.

RefSeq proteins (1): NP_001074259* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002190	MHD_dom	Domain
IPR021072	MAGE_N	Domain
IPR037445	MAGE	Family
IPR041898	MAGE_WH1	Homologous_superfamily
IPR041899	MAGE_WH2	Homologous_superfamily

Pfam: PF01454, PF12440

UniProt features (9 total): sequence conflict 3, compositionally biased region 2, chain 1, domain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P43362-F1	77.17	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN, GOMF_HISTONE_DEACETYLASE_BINDING, chrXq28, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, MIR6780A_3P, PULVER_FOREY_PERTURB_ACCUMULATION_G1_S, PULVER_FOREY_PERTURB_ATTRITION_G2_M, GOBP_NEGATIVE_REGULATION_OF_RNA_BIOSYNTHETIC_PROCESS

GO Biological Process (1): negative regulation of transcription by RNA polymerase II (GO:0000122)

GO Molecular Function (2): histone deacetylase binding (GO:0042826), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
enzyme binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGEA9B	CTAG2	O75638	594
MAGEA9B	CTAG1A	P78358	541
MAGEA9B	HSFX4	A0A1B0GTS1	446
MAGEA9B	TMEM86A	Q8N2M4	433
MAGEA9B	MAGEC1	O60732	411
MAGEA9B	GET3	O43681	405
MAGEA9B	TMEM185A	Q8NFB2	398
MAGEA9B	TSPAN2	O60636	396
MAGEA9B	EOLA1	Q8TE69	393
MAGEA9B	VIPR1	P32241	370
MAGEA9B	EOLA2	Q96DE9	365
MAGEA9B	SSX1	Q16384	360
MAGEA9B	CXorf51A	A0A1B0GTR3	356
MAGEA9B	OR4D5	Q8NGN0	348
MAGEA9B	SPACA5B	Q96QH8	326

IntAct

20 interactions, top by confidence:

A	B	Type	Score
MAGEA9	APPL1	psi-mi:“MI:0915”(physical association)	0.740
APPL1	MAGEA9	psi-mi:“MI:0915”(physical association)	0.740
MAGEA4	MAGEB16	psi-mi:“MI:0914”(association)	0.530
NSA2	TYW5	psi-mi:“MI:0914”(association)	0.530
MAGEA10	POTEF	psi-mi:“MI:0914”(association)	0.530
MAGEA1	MAGEB3	psi-mi:“MI:0914”(association)	0.530
MAGEA1	ANKHD1	psi-mi:“MI:0914”(association)	0.350
MAGEA9	CIBAR1	psi-mi:“MI:0914”(association)	0.350
MAGEA9	MED19	psi-mi:“MI:0914”(association)	0.350
SAP30BP	TYW5	psi-mi:“MI:0914”(association)	0.350
MAGEA1	ANKRD17	psi-mi:“MI:0914”(association)	0.350
COMMD10	MAGEA9	psi-mi:“MI:0914”(association)	0.350
CRH	CST4	psi-mi:“MI:0914”(association)	0.350

BioGRID (225): APPL1 (Two-hybrid), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), RNF40 (Affinity Capture-MS), ZFC3H1 (Affinity Capture-MS), EAPP (Affinity Capture-MS), FAM91A1 (Affinity Capture-MS), MAGEA9B (Affinity Capture-MS), HELZ2 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YX57, A1A5P9, A2A368, A2A9R3, A8MXT2, B2KFW1, O15479, O15480, O15481, O15553, P0C6Y7, P10073, P17040, P25233, P43355, P43356, P43357, P43358, P43360, P43362, P43363, P43364, P43366, Q13342, Q16666, Q4R998, Q5PPP4, Q5RD14, Q6AY37, Q6PCZ4, Q8BQR7, Q8IWY8, Q8IX06, Q8N660, Q8N7X4, Q8TD90, Q96DU7, Q96LZ2, Q96M61, Q99608

Diamond homologs: A0A0J9YX57, A1A5P9, A2A368, A2A9R3, A6NCF6, A6QLI5, A8MXT2, O15479, O15480, O15481, O60732, P25233, P43355, P43356, P43357, P43358, P43360, P43361, P43362, P43363, P43364, P43365, P43366, Q12816, Q4R998, Q5PPP4, Q5RFC2, Q6AY37, Q6ITT4, Q6PCZ4, Q8BQR7, Q8N7X4, Q8TD90, Q8TD91, Q96JG8, Q96LZ2, Q96M61, Q96MG7, Q99608, Q9BE18

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

522 predictions. Top by Δscore:

Variant	Effect	Δscore
X:149583240:CAGGC:C	acceptor_gain	1.0000
X:149583318:A:AC	donor_gain	1.0000
X:149583319:C:CC	donor_gain	1.0000
X:149583319:CAGGT:C	donor_gain	1.0000
X:149583243:GCC:G	acceptor_loss	0.9900
X:149583245:C:CC	acceptor_gain	0.9900
X:149583246:T:C	acceptor_loss	0.9900
X:149583319:CAG:C	donor_gain	0.9800
X:149583242:GGC:G	acceptor_gain	0.9700
X:149583388:CCT:C	acceptor_loss	0.9700
X:149583389:CT:C	acceptor_loss	0.9700
X:149583319:CA:C	donor_gain	0.9600
X:149583243:GC:G	acceptor_gain	0.9500
X:149583244:CC:C	acceptor_gain	0.9500
X:149583313:GACT:G	donor_loss	0.9500
X:149583314:ACTT:A	donor_loss	0.9500
X:149583315:CTTAC:C	donor_loss	0.9500
X:149583316:TTACA:T	donor_loss	0.9500
X:149583317:TAC:T	donor_loss	0.9500
X:149583318:A:T	donor_loss	0.9500
X:149583319:C:CA	donor_loss	0.9500
X:149583319:CAGG:C	donor_gain	0.9500
X:149583241:AGGC:A	acceptor_gain	0.9400
X:149583312:TGAC:T	donor_loss	0.9400
X:149583160:CTCCT:C	acceptor_gain	0.9000
X:149585500:C:A	donor_gain	0.9000
X:149587389:CTTAC:C	donor_loss	0.9000
X:149587391:T:TA	donor_loss	0.9000
X:149587392:A:C	donor_loss	0.9000
X:149583389:C:CC	acceptor_gain	0.8900

AlphaMissense

2078 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1156301914 (X:149582056 T>C), RS1156627620 (X:149586369 T>C,G), RS1156715060 (X:149584778 GC>G,GCC,GCCC), RS1158051483 (X:149581189 G>C), RS1158421680 (X:149585916 C>A,G,T), RS1158521325 (X:149583596 A>G), RS1159228993 (X:149583584 C>T), RS1159656016 (X:149586770 C>G,T), RS1159756287 (X:149585838 G>A,C), RS1162554328 (X:149586275 T>A,C), RS1163475817 (X:149584641 G>A), RS1163581619 (X:149581813 T>C), RS1163840665 (X:149586211 T>G), RS1165090422 (X:149585801 G>A), RS1165131662 (X:149584063 G>A)

Disease associations

OMIM: gene MIM:300764 | 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Decitabine	affects expression	1
Benztropine	affects cotreatment, decreases expression	1
Cuprizone	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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