MAGEB1

Summary

MAGEB1 (MAGE family member B1, HGNC:6808) is a protein-coding gene on chromosome Xp21.2, encoding Melanoma-associated antigen B1 (P43366).

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. This gene is localized in the DSS (dosage-sensitive sex reversal) critical region, and expressed in testis and in a significant fraction of tumors of various histological types. This gene and other MAGEB members are clustered on chromosome Xp22-p21. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene, however, the full length nature of some variants has not been defined.

Source: NCBI Gene 4112 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_177404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6808
Approved symbol	MAGEB1
Name	MAGE family member B1
Location	Xp21.2
Locus type	gene with protein product
Status	Approved
Aliases	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1
Ensembl gene	ENSG00000214107
Ensembl biotype	protein_coding
OMIM	300097
Entrez	4112

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000378981, ENST00000397548, ENST00000397550, ENST00000929323, ENST00000929324

RefSeq mRNA: 3 — MANE Select: NM_177404 NM_002363, NM_177404, NM_177415

CCDS: CCDS14222

Canonical transcript exons

ENST00000397548 — 2 exons

Exon	Start	End
ENSE00001529172	30247146	30247256
ENSE00003849384	30250434	30252040

Expression profiles

Bgee: expression breadth broad, 15 present calls, max score 85.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4481 / max 30.9502, expressed in 67 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195850	0.3699	64
195851	0.0594	29
195849	0.0189	3

Top tissues by expression

278 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	85.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.00	gold quality
right testis	UBERON:0004534	81.90	gold quality
left testis	UBERON:0004533	80.61	gold quality
testis	UBERON:0000473	80.07	gold quality
secondary oocyte	CL:0000655	67.59	gold quality
buccal mucosa cell	CL:0002336	58.15	gold quality
adult organism	UBERON:0007023	58.15	gold quality
ileal mucosa	UBERON:0000331	53.15	silver quality
pancreatic ductal cell	CL:0002079	49.82	silver quality
epithelial cell of pancreas	CL:0000083	49.43	gold quality
deltoid	UBERON:0001476	49.32	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
quadriceps femoris	UBERON:0001377	49.27	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
thymus	UBERON:0002370	48.90	gold quality
choroid plexus epithelium	UBERON:0003911	48.89	gold quality
myocardium	UBERON:0002349	48.87	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
vastus lateralis	UBERON:0001379	48.70	gold quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	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
oviduct epithelium	UBERON:0004804	48.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting MAGEB1, 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-3064-3P	100.00	70.09	1254
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-26A-1-3P	99.64	66.81	788
HSA-MIR-26A-2-3P	99.64	66.82	786
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-377-3P	99.37	70.18	1905
HSA-MIR-520G-3P	98.91	67.38	1914
HSA-MIR-520H	98.91	67.38	1914
HSA-MIR-1294	98.91	69.26	1030
HSA-MIR-9986	98.91	69.28	1024
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-676-5P	98.49	68.87	1492
HSA-MIR-561-5P	98.25	68.13	1365
HSA-MIR-138-1-3P	98.25	67.89	867
HSA-MIR-4432	97.80	67.87	705
HSA-MIR-4642	97.52	67.60	916
HSA-MIR-216B-5P	97.16	66.76	1126
HSA-MIR-6888-5P	95.89	63.78	831

Literature-anchored findings (GeneRIF, showing 1)

• Results show that hypertonic culture medium differentially induces the expression of melanoma antigens B1 and B2 (MAGE-B1, -B2) in different human tumor cell lines. (PMID:12018852)

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), MAGEA3 (ENSG00000221867), MAGEB6B (ENSG00000232030), MAGEL2 (ENSG00000254585), MAGEA9B (ENSG00000267978), MAGEA2 (ENSG00000268606)

Protein

Protein identifiers

Melanoma-associated antigen B1 — P43366 (reviewed: P43366)

Alternative names: Cancer/testis antigen 3.1, DSS-AHC critical interval MAGE superfamily 10, MAGE-B1 antigen, MAGE-XP antigen

All UniProt accessions (1): P43366

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed only in testis.

RefSeq proteins (3): NP_002354, NP_796379, NP_803134 (=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 (32 total): helix 12, sequence conflict 6, compositionally biased region 4, strand 3, region of interest 2, turn 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6R7T	X-RAY DIFFRACTION	2.68

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P43366-F1	74.66	0.39

Antibody-complex structures (SAbDab): 1 — 6R7T

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, MODULE_99, chrXp21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, KRAS.AMP.LUNG_UP.V1_UP, ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP, MIR4482_3P, MIR1290, MIR20A_3P, MIR3064_3P, MIR561_5P, MIR6888_5P

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

GO Molecular Function (0):

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
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

370 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGEB1	NR0B1	P51843	631
MAGEB1	GAGE4	P0DSO3	571
MAGEB1	C12orf54	Q6X4T0	570
MAGEB1	TRIM41	Q8WV44	495
MAGEB1	PAGE3	Q5JUK9	474
MAGEB1	CTAG2	O75638	434
MAGEB1	SPANXA1	Q9NS26	434
MAGEB1	SSX5	O60225	423
MAGEB1	FTHL17	Q9BXU8	408
MAGEB1	PAGE1	O75459	379
MAGEB1	SMC5	Q8IY18	377
MAGEB1	PAGE4	O60829	374
MAGEB1	FAM47B	Q8NA70	370
MAGEB1	CTAG1A	P78358	370
MAGEB1	SPANXC	Q9NY87	370
MAGEB1	SPANXD	Q9BXN6	370
MAGEB1	CT47A11	Q5JQC4	370

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SRPK2	MAGEB1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
MAGEB1	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440

BioGRID (11): MDM4 (Affinity Capture-Western), MAGEB1 (Synthetic Lethality), MAGEB1 (Biochemical Activity), MAGEB1 (Protein-peptide), MAGEB1 (Reconstituted Complex), MAGEB1 (Biochemical Activity), NSMCE4A (Affinity Capture-Western), EID3 (Affinity Capture-Western), EID2 (Affinity Capture-Western), MAGEB1 (Biochemical Activity), MAGEB1 (Biochemical Activity)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

579 predictions. Top by Δscore:

Variant	Effect	Δscore
X:30246378:TTC:T	donor_gain	1.0000
X:30246284:TGCA:T	acceptor_loss	0.9900
X:30246286:CA:C	acceptor_loss	0.9900
X:30246287:A:AG	acceptor_gain	0.9900
X:30246288:G:GG	acceptor_gain	0.9900
X:30246391:AGGGT:A	donor_loss	0.9900
X:30246392:GG:G	donor_gain	0.9900
X:30246393:GG:G	donor_gain	0.9900
X:30246394:G:T	donor_loss	0.9900
X:30246395:T:TC	donor_loss	0.9900
X:30246397:AGTTA:A	donor_loss	0.9900
X:30250428:CTTCA:C	acceptor_loss	0.9900
X:30250429:TTCA:T	acceptor_loss	0.9900
X:30250430:TCAG:T	acceptor_loss	0.9900
X:30250431:CAG:C	acceptor_loss	0.9900
X:30250432:A:T	acceptor_loss	0.9900
X:30246288:GGTT:G	acceptor_gain	0.9800
X:30250433:GGT:G	acceptor_gain	0.9800
X:30246287:AG:A	acceptor_gain	0.9700
X:30246287:AGGTT:A	acceptor_gain	0.9700
X:30246288:GG:G	acceptor_gain	0.9700
X:30246288:GGTTG:G	acceptor_gain	0.9700
X:30246368:G:GT	donor_gain	0.9700
X:30250432:A:AG	acceptor_gain	0.9700
X:30250433:G:GG	acceptor_gain	0.9700
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

AlphaMissense

2280 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:30251307:T:A	W272R	0.988
X:30251307:T:C	W272R	0.988
X:30250974:T:C	F161L	0.987
X:30250976:T:A	F161L	0.987
X:30250976:T:G	F161L	0.987
X:30251302:T:C	F270S	0.983
X:30251339:G:C	K282N	0.980
X:30251339:G:T	K282N	0.980
X:30251309:G:C	W272C	0.978
X:30251309:G:T	W272C	0.978
X:30251301:T:C	F270L	0.976
X:30251303:C:A	F270L	0.976
X:30251303:C:G	F270L	0.976
X:30251355:T:C	F288L	0.976
X:30251357:T:A	F288L	0.976
X:30251357:T:G	F288L	0.976
X:30251310:G:C	G273R	0.971
X:30251160:T:C	F223L	0.966
X:30251162:C:A	F223L	0.966
X:30251162:C:G	F223L	0.966
X:30251412:G:C	A307P	0.964
X:30251257:T:C	L255P	0.963
X:30251391:T:C	F300L	0.960
X:30251393:C:A	F300L	0.960
X:30251393:C:G	F300L	0.960
X:30251350:T:A	L286H	0.954
X:30250987:T:C	L165S	0.951
X:30251218:G:C	R242P	0.950
X:30251308:G:C	W272S	0.950
X:30251319:G:C	A276P	0.949

dbSNP variants (sampled 300 via entrez): RS1000880990 (X:30244767 G>A), RS1001011777 (X:30247676 C>T), RS1001080251 (X:30248313 A>G), RS1001350459 (X:30250338 A>G), RS1001584787 (X:30251515 G>A,T), RS1002199287 (X:30243615 T>C), RS1002735153 (X:30244997 A>T), RS1002796080 (X:30246026 G>A), RS1003174531 (X:30245602 C>T), RS1003233952 (X:30243820 G>A), RS1003430996 (X:30252257 AAAG>A), RS1003967762 (X:30246745 G>A,T), RS1004938848 (X:30247817 T>C), RS1005546202 (X:30251767 A>G), RS1006054158 (X:30250044 C>T)

Disease associations

OMIM: gene MIM:300097 | disease phenotypes: MIM:300679

GenCC curated gene-disease

Mondo (1): chromosome Xp21 deletion syndrome (MONDO:0010399)

Orphanet (1): Xp21 deletion syndrome (Orphanet:261476)

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

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

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment, affects response to substance	1
CGP 52608	affects binding, increases reaction	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Catechin	affects cotreatment, decreases expression	1
Endosulfan	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Valproic Acid	affects expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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