MAGEB4

Summary

MAGEB4 (MAGE family member B4, HGNC:6811) is a protein-coding gene on chromosome Xp21.2, encoding Melanoma-associated antigen B4 (O15481).

This gene is a member of the MAGEB gene family. The members of this family have their entire coding sequences located in the last exon, and the encoded proteins show 50 to 68% sequence identity to each other. The promoters and first exons of the MAGEB genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The MAGEB genes are clustered on chromosome Xp22-p21. This gene sequence ends in the first intron of MAGEB1, another family member. This gene is expressed in testis.

Source: NCBI Gene 4115 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_002367

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6811
Approved symbol	MAGEB4
Name	MAGE family member B4
Location	Xp21.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC33144, CT3.6
Ensembl gene	ENSG00000120289
Ensembl biotype	protein_coding
OMIM	300153
Entrez	4115

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000378982

RefSeq mRNA: 1 — MANE Select: NM_002367 NM_002367

CCDS: CCDS14221

Canonical transcript exons

ENST00000378982 — 1 exons

Exon	Start	End
ENSE00001479432	30242000	30244187

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 71.89.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0265 / max 16.9649, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195848	0.0127	4
195847	0.0106	4
195846	0.0031	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	71.89	gold quality
right testis	UBERON:0004534	71.78	gold quality
left testis	UBERON:0004533	70.71	gold quality
testis	UBERON:0000473	69.55	gold quality
cauda epididymis	UBERON:0004360	52.19	gold quality
oviduct epithelium	UBERON:0004804	49.60	gold quality
caput epididymis	UBERON:0004358	49.52	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
hair follicle	UBERON:0002073	49.18	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
myocardium	UBERON:0002349	48.87	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
quadriceps femoris	UBERON:0001377	48.78	gold quality
epithelial cell of pancreas	CL:0000083	48.64	gold quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality
vastus lateralis	UBERON:0001379	48.25	gold quality
left ventricle myocardium	UBERON:0006566	48.24	gold quality
orbitofrontal cortex	UBERON:0004167	48.20	gold quality
upper arm skin	UBERON:0004263	48.06	gold quality
cervix epithelium	UBERON:0004801	48.04	gold quality
tongue squamous epithelium	UBERON:0006919	47.92	gold quality
mucosa of urinary bladder	UBERON:0001259	47.80	gold quality
metanephric glomerulus	UBERON:0004736	47.45	gold quality
thymus	UBERON:0002370	47.42	gold quality
kidney epithelium	UBERON:0004819	47.39	gold quality
nephron tubule	UBERON:0001231	47.30	gold quality
diaphragm	UBERON:0001103	47.05	gold quality
gluteal muscle	UBERON:0002000	47.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting MAGEB4, 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-513A-5P	100.00	69.77	2465
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-3529-3P	99.90	73.55	3045

Literature-anchored findings (GeneRIF, showing 2)

• The whole exome analysis of a consanguineous Turkish family revealed MAGEB4 as a possible new X-linked cause of inherited male infertility. This study provides the first clue to the physiological function of a MAGE protein. (PMID:28401488)
• High MAGEB4 expression is associated with Transitional Cell Carcinoma of Bladder. (PMID:29058301)

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), 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), MAGEA9B (ENSG00000267978), MAGEA2 (ENSG00000268606)

Protein

Protein identifiers

Melanoma-associated antigen B4 — O15481 (reviewed: O15481)

Alternative names: MAGE-B4 antigen

All UniProt accessions (1): O15481

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in testis.

RefSeq proteins (1): NP_002358* (*=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 (10 total): compositionally biased region 4, region of interest 2, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O15481-F1	75.43	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, chrXp21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, RELA_DN.V1_UP, MIR3658, MIR3529_3P, MIR551B_5P, MIR513A_3P_MIR513C_3P, MIR4482_3P, MIR3133, MIR4799_5P, MIR4318, MIR136_5P, MIR5187_3P

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

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

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

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
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGEB4	TEX11	Q8IYF3	484
MAGEB4	TEX15	Q9BXT5	484
MAGEB4	NR0B1	P51843	479
MAGEB4	ZMYND15	Q9H091	475
MAGEB4	DNAH6	Q9C0G6	453
MAGEB4	TSGA10	Q9BZW7	434
MAGEB4	MEGF8	Q7Z7M0	431
MAGEB4	XAGE3	Q8WTP9	431
MAGEB4	C4orf51	C9J302	420
MAGEB4	ACTL7A	Q9Y615	419
MAGEB4	SYCE1	Q8N0S2	403
MAGEB4	CGB2	Q6NT52	396
MAGEB4	SPANXN4	Q5MJ08	394
MAGEB4	TDRD9	Q8NDG6	391
MAGEB4	SSX7	Q7RTT5	373

IntAct

151 interactions, top by confidence:

A	B	Type	Score
ROCK1	MAGEB4	psi-mi:“MI:0915”(physical association)	0.740
MAGEB4	ROCK1	psi-mi:“MI:0915”(physical association)	0.740
MAGEB4	MED21	psi-mi:“MI:0915”(physical association)	0.720
MAGEB4	KANK2	psi-mi:“MI:0915”(physical association)	0.720
MAGEB4	USHBP1	psi-mi:“MI:0915”(physical association)	0.720
KANK2	MAGEB4	psi-mi:“MI:0915”(physical association)	0.720
USHBP1	MAGEB4	psi-mi:“MI:0915”(physical association)	0.720
MAGEB4	KRT38	psi-mi:“MI:0915”(physical association)	0.670
KRT38	MAGEB4	psi-mi:“MI:0915”(physical association)	0.670
MAGEB4	TNR	psi-mi:“MI:0915”(physical association)	0.560
MAGEB4	HGS	psi-mi:“MI:0915”(physical association)	0.560
WDR62	MAGEB4	psi-mi:“MI:0915”(physical association)	0.560
MAGEA8	MAGEB4	psi-mi:“MI:0915”(physical association)	0.560
RUNDC3A	MAGEB4	psi-mi:“MI:0915”(physical association)	0.560
MAGEB4	CCDC136	psi-mi:“MI:0915”(physical association)	0.560
FERD3L	MAGEB4	psi-mi:“MI:0915”(physical association)	0.560
MAGEB4	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
MAGEB4	ZNF341	psi-mi:“MI:0915”(physical association)	0.560
MAGEB4	USP25	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (76): MAGEB4 (Two-hybrid), ROCK1 (Two-hybrid), TNR (Two-hybrid), KRT38 (Two-hybrid), HGS (Two-hybrid), MED21 (Two-hybrid), RUNDC3A (Two-hybrid), KANK2 (Two-hybrid), USP25 (Two-hybrid), CCDC136 (Two-hybrid), USHBP1 (Two-hybrid), LZTS2 (Two-hybrid), ZNF341 (Two-hybrid), FERD3L (Two-hybrid), WDR62 (Two-hybrid)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	3
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

68 predictions. Top by Δscore:

Variant	Effect	Δscore
X:30243792:TG:T	donor_gain	0.9600
X:30243793:G:GT	donor_gain	0.9600
X:30243798:CTGAG:C	donor_loss	0.9600
X:30243801:AGG:A	donor_loss	0.9600
X:30243802:GGTAT:G	donor_loss	0.9600
X:30243803:G:C	donor_loss	0.9600
X:30243804:T:A	donor_loss	0.9600
X:30243797:TCTG:T	donor_gain	0.9500
X:30244170:G:GT	donor_gain	0.9000
X:30243800:G:GT	donor_gain	0.8800
X:30243864:G:T	donor_gain	0.8800
X:30243793:GA:G	donor_gain	0.8700
X:30243794:AA:A	donor_gain	0.8700
X:30244187:A:G	donor_gain	0.8500
X:30243803:G:GG	donor_gain	0.7500
X:30243897:G:GG	donor_gain	0.6900
X:30243805:A:T	donor_loss	0.6800
X:30243900:T:A	donor_gain	0.5900
X:30243795:A:AG	donor_gain	0.5800
X:30243796:G:GG	donor_gain	0.5800
X:30243798:CTGA:C	donor_gain	0.5800
X:30243896:T:TG	donor_gain	0.5800
X:30244026:TTGGA:T	donor_gain	0.5600
X:30242303:TGGCA:T	acceptor_gain	0.5400
X:30243799:TGAG:T	donor_gain	0.5300
X:30243800:GAGG:G	donor_gain	0.5300
X:30243864:G:GT	donor_gain	0.4900
X:30243800:GAG:G	donor_gain	0.4800
X:30242284:C:A	acceptor_gain	0.4500
X:30242283:G:GA	acceptor_gain	0.4400

AlphaMissense

2266 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:30242944:T:C	F270S	0.985
X:30242619:T:C	F162L	0.984
X:30242621:T:A	F162L	0.984
X:30242621:T:G	F162L	0.984
X:30242949:T:A	W272R	0.983
X:30242949:T:C	W272R	0.983
X:30242751:A:C	S206R	0.980
X:30242753:T:A	S206R	0.980
X:30242753:T:G	S206R	0.980
X:30242981:G:C	K282N	0.978
X:30242981:G:T	K282N	0.978
X:30242997:T:C	F288L	0.978
X:30242999:T:A	F288L	0.978
X:30242999:T:G	F288L	0.978
X:30242847:T:C	F238L	0.976
X:30242849:T:A	F238L	0.976
X:30242849:T:G	F238L	0.976
X:30242802:T:C	F223L	0.973
X:30242804:C:A	F223L	0.973
X:30242804:C:G	F223L	0.973
X:30242952:G:C	G273R	0.972
X:30242951:G:C	W272C	0.971
X:30242951:G:T	W272C	0.971
X:30242943:T:C	F270L	0.964
X:30242945:C:A	F270L	0.964
X:30242945:C:G	F270L	0.964
X:30242860:G:C	R242P	0.959
X:30242798:G:C	W221C	0.958
X:30242798:G:T	W221C	0.958
X:30242899:T:A	L255Q	0.954

dbSNP variants (sampled 300 via entrez): RS1002199287 (X:30243615 T>C), RS1002902061 (X:30240982 C>T), RS1002975656 (X:30241447 A>T), RS1003233952 (X:30243820 G>A), RS1004929009 (X:30240829 T>C), RS1006144454 (X:30241635 G>A), RS1006526304 (X:30241158 T>C), RS1007694816 (X:30241658 A>G), RS1008284741 (X:30243747 C>T), RS1008731723 (X:30244335 T>C), RS1012953703 (X:30241069 T>C), RS1015053152 (X:30240897 A>C,G), RS1015391683 (X:30243760 G>A), RS1016086739 (X:30240726 T>C), RS1017081793 (X:30242816 G>C,T)

Disease associations

OMIM: gene MIM:300153 | 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

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression	2
CGP 52608	affects binding, increases reaction	1
Acetaminophen	decreases expression	1
Mercury	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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