MAGEB3

gene
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Also known as CT3.5

Summary

MAGEB3 (MAGE family member B3, HGNC:6810) is a protein-coding gene on chromosome Xp21.2, encoding Melanoma-associated antigen B3 (O15480).

This gene is a MAGE-B subfamily member of the MAGE gene family. MAGE family member proteins direct the expression of tumor antigens recognized on a human melanoma by autologous cytolytic T lymphocytes. There are two known clusters of MAGE genes on chromosome X. The members of the MAGE-A subfamily are located in the Xq28 region, while the members of the MAGE-B subfamily are clustered in the Xp21 region.

Source: NCBI Gene 4114 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 40 total — 2 pathogenic
  • MANE Select transcript: NM_002365

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6810
Approved symbolMAGEB3
NameMAGE family member B3
LocationXp21.2
Locus typegene with protein product
StatusApproved
AliasesCT3.5
Ensembl geneENSG00000198798
Ensembl biotypeprotein_coding
OMIM300152
Entrez4114

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000361644, ENST00000620842

RefSeq mRNA: 2 — MANE Select: NM_002365 NM_001386865, NM_002365

CCDS: CCDS14220

Canonical transcript exons

ENST00000361644 — 5 exons

ExonStartEnd
ENSE000014794473023282730232916
ENSE000014794503023065730230817
ENSE000016298913023326230233363
ENSE000017398103023151730231618
ENSE000022517403023586430237495

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 76.04.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.04silver quality
right testisUBERON:000453467.78gold quality
left testisUBERON:000453364.75gold quality
testisUBERON:000047364.59gold quality
corpus epididymisUBERON:000435964.55gold quality
cauda epididymisUBERON:000436057.22silver quality
caput epididymisUBERON:000435856.99gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099156.31gold quality
lower lobe of lungUBERON:000894954.44silver quality
adult organismUBERON:000702353.52silver quality
pancreatic ductal cellCL:000207952.32silver quality
Brodmann (1909) area 46UBERON:000648351.87gold quality
buccal mucosa cellCL:000233650.96gold quality
epithelial cell of pancreasCL:000008349.87gold quality
blood vessel layerUBERON:000479749.29gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
hair follicleUBERON:000207349.18gold quality
quadriceps femorisUBERON:000137749.14gold quality
olfactory bulbUBERON:000226448.92gold quality
thymusUBERON:000237048.90gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
oviduct epitheliumUBERON:000480448.81gold quality
vastus lateralisUBERON:000137948.80gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
left ventricle myocardiumUBERON:000656648.24gold quality
orbitofrontal cortexUBERON:000416748.20gold quality
upper arm skinUBERON:000426348.06gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting MAGEB3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-196A-1-3P99.9972.152772
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-449699.8868.892236
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-442299.7272.072908
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-4735-5P99.4368.491780
HSA-MIR-302A-5P99.3968.211913
HSA-MIR-6830-5P99.0168.731884
HSA-MIR-138-2-3P98.9168.331643
HSA-MIR-477398.3567.301710
HSA-MIR-561-5P98.2568.131365
HSA-MIR-1212098.0568.441768
HSA-MIR-483-3P97.7764.95731
HSA-MIR-467897.5968.31902
HSA-MIR-5699-5P97.3667.031014
HSA-MIR-584-5P95.8268.05848

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriondnl2ENSDARG00000058212
rattus_norvegicusMageb3ENSRNOG00000038269
drosophila_melanogasterMAGEFBGN0037481

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), MAGEE1 (ENSG00000198934), MAGEA12 (ENSG00000213401), MAGEB1 (ENSG00000214107), MAGEA3 (ENSG00000221867), MAGEB6B (ENSG00000232030), MAGEL2 (ENSG00000254585), MAGEA9B (ENSG00000267978), MAGEA2 (ENSG00000268606)

Protein

Protein identifiers

Melanoma-associated antigen B3O15480 (reviewed: O15480)

Alternative names: MAGE-B3 antigen

All UniProt accessions (1): O15480

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in testis.

RefSeq proteins (2): NP_001373794, NP_002356* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002190MHD_domDomain
IPR021072MAGE_NDomain
IPR037445MAGEFamily
IPR041898MAGE_WH1Homologous_superfamily
IPR041899MAGE_WH2Homologous_superfamily

Pfam: PF01454, PF12440

UniProt features (6 total): sequence variant 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15480-F175.340.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, chrXp21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, DCA_UP.V1_DN, KRAS.PROSTATE_UP.V1_UP, MIR548E_5P, MIR1250_3P, MIR6835_3P, MIR4773, MIR12120, MIR4735_5P, MIR5699_5P, GSE13411_NAIVE_VS_SWITCHED_MEMORY_BCELL_UP

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 (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

194 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MAGEB3BCLAF3A2AJT9512
MAGEB3NR0B1P51843461
MAGEB3ANKRD45Q5TZF3422
MAGEB3KIAA1210Q9ULL0418
MAGEB3ZNF518AQ6AHZ1390
MAGEB3FTHL17Q9BXU8331
MAGEB3IL1RAPL1Q9NZN1330
MAGEB3GAR1Q9NY12321
MAGEB3ZNF135P52742317
MAGEB3LUZP4Q9P127305
MAGEB3TASLQ9HAI6302
MAGEB3EBPLQ9BY08300
MAGEB3CELF5Q8N6W0287
MAGEB3ZC4H2Q9NQZ6272
MAGEB3GAGE4P0DSO3271

IntAct

10 interactions, top by confidence:

ABTypeScore
MAGEB3PPP1R7psi-mi:“MI:0915”(physical association)0.560
MAGEB3JPH3psi-mi:“MI:0915”(physical association)0.560
MAGEB3PPP1R7psi-mi:“MI:0914”(association)0.560
MAGEA1MAGEB3psi-mi:“MI:0914”(association)0.530
MAGEA1ANKHD1psi-mi:“MI:0914”(association)0.350
MAGEB3MYH7Bpsi-mi:“MI:0914”(association)0.350

BioGRID (8): MAGEB3 (Affinity Capture-MS), PPP1R7 (Affinity Capture-MS), MAGEB3 (Affinity Capture-MS), PPP1R7 (Affinity Capture-MS), CD200R1 (Affinity Capture-MS), PPP1R7 (Affinity Capture-MS), MAGEB3 (Affinity Capture-MS), CHERP (Cross-Linking-MS (XL-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

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance32
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
2424934NC_000023.10:g.(?28807451)(31241248_?)delPathogenic
564805GRCh37/hg19 Xp22.11-21.1(chrX:24650157-31844543)x2Pathogenic

SpliceAI

476 predictions. Top by Δscore:

VariantEffectΔscore
X:30230818:G:GGdonor_gain0.9900
X:30235858:CTCCA:Cacceptor_loss0.9900
X:30235859:TCCA:Tacceptor_loss0.9900
X:30235860:CCAGG:Cacceptor_loss0.9900
X:30235861:CA:Cacceptor_loss0.9900
X:30235862:A:AGacceptor_gain0.9900
X:30235862:A:Cacceptor_loss0.9900
X:30235862:AG:Aacceptor_gain0.9900
X:30235862:AGGT:Aacceptor_gain0.9900
X:30235863:G:GAacceptor_gain0.9900
X:30235863:GG:Gacceptor_gain0.9900
X:30235863:GGT:Gacceptor_gain0.9900
X:30235863:GGTG:Gacceptor_gain0.9900
X:30235863:GGTGC:Gacceptor_gain0.9900
X:30230816:GA:Gdonor_gain0.9800
X:30230805:G:GGdonor_gain0.9700
X:30230810:GTTCT:Gdonor_gain0.9700
X:30230811:TTCTT:Tdonor_gain0.9700
X:30230800:GCGAA:Gdonor_gain0.9400
X:30230802:G:GTdonor_gain0.9400
X:30232825:A:Gacceptor_gain0.9400
X:30232826:GGCA:Gacceptor_gain0.9400
X:30230812:TCTTG:Tdonor_gain0.9300
X:30230814:TTGA:Tdonor_gain0.9100
X:30230815:TGA:Tdonor_gain0.9100
X:30230816:GAG:Gdonor_gain0.9100
X:30232915:AG:Adonor_loss0.9000
X:30232916:GG:Gdonor_loss0.9000
X:30232917:GTGA:Gdonor_loss0.9000
X:30232918:TGAGC:Tdonor_loss0.9000

AlphaMissense

2310 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:30236747:T:AW275R0.970
X:30236747:T:CW275R0.970
X:30236795:T:CF291L0.961
X:30236797:T:AF291L0.961
X:30236797:T:GF291L0.961
X:30236742:T:CF273S0.960
X:30236750:G:CG276R0.960
X:30236645:T:CF241L0.959
X:30236647:T:AF241L0.959
X:30236647:T:GF241L0.959
X:30236414:T:CF164L0.955
X:30236416:T:AF164L0.955
X:30236416:T:GF164L0.955
X:30236600:T:CF226L0.953
X:30236602:C:AF226L0.953
X:30236602:C:GF226L0.953
X:30236779:G:CK285N0.953
X:30236779:G:TK285N0.953
X:30236749:G:CW275C0.943
X:30236749:G:TW275C0.943
X:30236741:T:CF273L0.938
X:30236743:C:AF273L0.938
X:30236743:C:GF273L0.938
X:30236801:G:CA293P0.934
X:30236694:A:CY257S0.925
X:30236697:T:CL258P0.925
X:30236751:G:AG276D0.915
X:30236706:G:CR261P0.914
X:30236693:T:CY257H0.911
X:30236638:C:AH238Q0.910

dbSNP variants (sampled 300 via entrez): RS1000534614 (X:30234211 G>A), RS1001404124 (X:30235758 A>C,T), RS1002125262 (X:30236153 G>T), RS1002431738 (X:30230033 G>A), RS1003256405 (X:30231960 C>A), RS1003699400 (X:30232969 C>A), RS1004122809 (X:30237582 C>T), RS1004152502 (X:30237308 A>T), RS1004153623 (X:30232467 A>C), RS1005769779 (X:30232387 G>A), RS1006063419 (X:30234948 C>G), RS1006114444 (X:30234451 C>T), RS1007469543 (X:30233805 G>A), RS1007497620 (X:30230737 C>T), RS1007780972 (X:30237040 T>C)

Disease associations

OMIM: gene MIM:300152 | disease phenotypes: MIM:310200

GenCC curated gene-disease

Mondo (1): Duchenne muscular dystrophy (MONDO:0010679)

Orphanet (1): Duchenne muscular dystrophy (Orphanet:98896)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D020388Muscular Dystrophy, DuchenneC05.651.534.500.300; C10.668.491.175.500.300; C16.320.322.562; C16.320.577.300

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.

ChemicalActions (top 5)PubMed papers
CGP 52608affects binding, increases reaction1
licochalcone Bincreases expression1
Benzo(a)pyreneaffects methylation1
Tretinoinincreases expression1
Aflatoxin B1decreases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00606775PHASE4UNKNOWNThe Preventive Efficacy of Carvedilol on Cardiac Dysfunction in Duchenne Muscular Dystrophy
NCT00819845PHASE4UNKNOWNRamipril Versus Carvedilol in Duchenne and Becker Patients
NCT01422200PHASE4COMPLETEDFlu Vaccine Study in Neuromuscular Patients 2011
NCT01999075PHASE4COMPLETEDStacking Exercises Aid the Decline in FVC and Sick Time
NCT04687020PHASE4ACTIVE_NOT_RECRUITINGLong-term Use of Viltolarsen in Boys With Duchenne Muscular Dystrophy in Clinical Practice (VILT-502)
NCT04708314PHASE4TERMINATEDAn Open-Label Study of Golodirsen in Non-Ambulant Patients With Duchenne Muscular Dystrophy
NCT05412394PHASE4RECRUITINGOnce Weekly Infant Corticosteroid Trial for DMD
NCT06713135PHASE4ACTIVE_NOT_RECRUITINGA Study on Safety and Effectiveness of Long-term Treatment With Vamorolone in Boys With Duchenne Muscular Dystrophy
NCT07542314PHASE4NOT_YET_RECRUITINGStudy to Evaluate the Safety and Effectiveness of ELEVIDYS in Participants With Duchenne Muscular Dystrophy Treated in a Post-Marketing Setting
NCT00004646PHASE3COMPLETEDPhase III Randomized, Double-Blind Study of Prednisone for Duchenne Muscular Dystrophy
NCT00110669PHASE3COMPLETEDHigh-dose Prednisone in Duchenne Muscular Dystrophy
NCT00308113PHASE3TERMINATEDCoQ10 and Prednisone in Non-Ambulatory DMD
NCT00839033PHASE3TERMINATEDEvaluation of a Mechanical Device During Acute Respiratory Failure in Patients With Neuromuscular Disorders
NCT01247207PHASE3COMPLETEDStudy of Ataluren in Previously Treated Participants With Nonsense Mutation Dystrophinopathy (nmDBMD)
NCT01557400PHASE3COMPLETEDStudy of Ataluren for Previously Treated Participants With Nonsense Mutation Duchenne/Becker Muscular Dystrophy (nmDBMD) in Europe, Israel, Australia, and Canada
NCT01603407PHASE3COMPLETEDFinding the Optimum Regimen for Duchenne Muscular Dystrophy
NCT01648634PHASE3COMPLETEDNebivolol for the Prevention of Left Ventricular Systolic Dysfunction in Patients With Duchenne Muscular Dystrophy
NCT02255552PHASE3COMPLETEDStudy of Eteplirsen in DMD Patients
NCT02354352PHASE3COMPLETEDTherapeutic Potential for Aldosterone Inhibition in Duchenne Muscular Dystrophy
NCT02500381PHASE3COMPLETEDStudy of SRP-4045 (Casimersen) and SRP-4053 (Golodirsen) in Participants With Duchenne Muscular Dystrophy (DMD)
NCT02814019PHASE3TERMINATEDA Phase III Double-blind Study With Idebenone in Patients With Duchenne Muscular Dystrophy (DMD) Taking Glucocorticoid Steroids
NCT02851797PHASE3COMPLETEDClinical Study to Evaluate the Efficacy and Safety of Givinostat in Ambulant Patients With Duchenne Muscular Dystrophy
NCT03354039PHASE3COMPLETEDTamoxifen in Duchenne Muscular Dystrophy
NCT03532542PHASE3TERMINATEDAn Extension Study to Evaluate Casimersen or Golodirsen in Patients With Duchenne Muscular Dystrophy
NCT03603288PHASE3TERMINATEDPhase III Study With Idebenone in Patients With Duchenne Muscular Dystrophy (SIDEROS-E)
NCT03642145PHASE3WITHDRAWNA Study of Deflazacort (Emflaza®) in Participants With Duchenne Muscular Dystrophy (DMD)
NCT03917719PHASE3TERMINATEDAn Open-Label Extension Study of Edasalonexent in Boys With Duchenne Muscular Dystrophy
NCT04060199PHASE3COMPLETEDStudy to Assess the Efficacy and Safety of Viltolarsen in Ambulant Boys With DMD (RACER53)
NCT04281485PHASE3ACTIVE_NOT_RECRUITINGStudy to Evaluate the Safety and Efficacy of PF-06939926 for the Treatment of Duchenne Muscular Dystrophy
NCT04371666PHASE3TERMINATEDPhase 3 Trial of Pamrevlumab or Placebo With Systemic Corticosteroids in Participants With Non-ambulatory Duchenne Muscular Dystrophy (DMD)
NCT04587908PHASE3ACTIVE_NOT_RECRUITINGA Phase 3 Study of TAS-205 in Patients With Duchenne Muscular Dystrophy(REACH-DMD)
NCT04632940PHASE3TERMINATEDPhase 3 Trial of Pamrevlumab or Placebo in Combination With Systemic Corticosteroids in Participants With Ambulatory DMD
NCT04768062PHASE3UNKNOWNStudy to Assess the Safety and Efficacy of Viltolarsen in Ambulant Boys With DMD (RACER53-X)
NCT05096221PHASE3COMPLETEDA Gene Transfer Therapy Study to Evaluate the Safety and Efficacy of Delandistrogene Moxeparvovec (SRP-9001) in Participants With Duchenne Muscular Dystrophy (DMD)
NCT05689164PHASE3TERMINATEDA Study to Understand the Long-term Safety and Effects of an Experimental Gene Therapy for Duchenne Muscular Dystrophy.
NCT05881408PHASE3ACTIVE_NOT_RECRUITINGA Gene Transfer Therapy Study to Evaluate the Safety and Efficacy of Delandistrogene Moxeparvovec (SRP-9001) in Non-Ambulatory and Ambulatory Participants With Duchenne Muscular Dystrophy (DMD)
NCT05933057PHASE3RECRUITINGEfficacy, Safety and Tolerability of Givinostat in Non-ambulant Patients With Duchenne Muscular Dystrophy
NCT05967351PHASE3ENROLLING_BY_INVITATIONA Long-term Follow-up Study of Participants Who Received Delandistrogene Moxeparvovec (SRP-9001) in a Previous Clinical Study
NCT07160634PHASE3RECRUITINGA Study of SGT-003 Gene Therapy in Ambulant Males With Duchenne Muscular Dystrophy (IMPACT DUCHENNE)
NCT07587242PHASE3NOT_YET_RECRUITINGA Phase 3 Study to Evaluate the Safety and Efficacy of AOC 1044 (Also Referred to as Delpacibart Zotadirsen) in Participants With DMD With Gene Mutations Amenable to Exon 44 Skipping
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Duchenne muscular dystrophy