MAGEA6

gene
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Also known as CT1.6MAGE3BMAGE-3b

Summary

MAGEA6 (MAGE family member A6, HGNC:6804) is a protein-coding gene on chromosome Xq28, encoding Melanoma-associated antigen 6 (P43360). Activator of ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases that acts as a repressor of autophagy.

This gene is a member of the MAGEA gene family. The members of this family encode proteins with 50 to 80% sequence identity to each other. The promoters and first exons of the MAGEA genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The MAGEA genes are clustered at chromosomal location Xq28. They have been implicated in some hereditary disorders, such as dyskeratosis congenita. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 4105 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 61 total
  • MANE Select transcript: NM_005363

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6804
Approved symbolMAGEA6
NameMAGE family member A6
LocationXq28
Locus typegene with protein product
StatusApproved
AliasesCT1.6, MAGE3B, MAGE-3b
Ensembl geneENSG00000197172
Ensembl biotypeprotein_coding
OMIM300176
Entrez4105

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000329342, ENST00000412733, ENST00000457643, ENST00000616035, ENST00000923265

RefSeq mRNA: 2 — MANE Select: NM_005363 NM_005363, NM_175868

CCDS: CCDS76050

Canonical transcript exons

ENST00000329342 — 3 exons

ExonStartEnd
ENSE00001691201152769654152769689
ENSE00001753927152767796152767861
ENSE00001853660152766136152767715

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 87.79.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.79gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.10gold quality
right testisUBERON:000453472.99gold quality
testisUBERON:000047371.76gold quality
left testisUBERON:000453370.68gold quality
placentaUBERON:000198743.25silver quality
bone marrow cellCL:000209237.98gold quality
sural nerveUBERON:001548837.24gold quality
colonic epitheliumUBERON:000039737.20gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
ganglionic eminenceUBERON:000402335.49gold quality
smooth muscle tissueUBERON:000113534.00gold quality
muscle tissueUBERON:000238533.54gold quality
skeletal muscle tissueUBERON:000113433.38gold quality
bone marrowUBERON:000237132.67gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
liverUBERON:000210731.33gold quality
bloodUBERON:000017830.65gold quality
muscle of legUBERON:000138329.88gold quality
stromal cell of endometriumCL:000225529.87gold quality
right coronary arteryUBERON:000162529.62silver quality
gastrocnemiusUBERON:000138829.31gold quality
urinary bladderUBERON:000125529.08gold quality
prefrontal cortexUBERON:000045129.04gold quality
right lobe of liverUBERON:000111428.88gold quality
heart left ventricleUBERON:000208428.78gold quality
cortex of kidneyUBERON:000122528.24gold quality
endocervixUBERON:000045828.16gold quality
duodenumUBERON:000211428.14gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-11yes89.79
E-ANND-3no0.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting MAGEA6, 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-371B-5P99.9975.344759
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-590-3P99.9674.346478
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-449699.8868.892236
HSA-MIR-137-3P99.8774.742401
HSA-MIR-450399.8571.451869
HSA-MIR-383-3P99.8565.841359
HSA-MIR-44899.7972.372103
HSA-MIR-4694-3P99.7969.532640
HSA-MIR-56799.6368.571219
HSA-MIR-426199.5970.303415
HSA-MIR-216A-5P99.5068.021288
HSA-MIR-513C-5P99.5068.421730
HSA-MIR-514B-5P99.5068.191766
HSA-MIR-147B-5P99.4570.622432
HSA-MIR-372-5P99.4169.112299
HSA-MIR-6507-5P99.3670.462524
HSA-MIR-442799.3470.331854
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-31-5P98.5868.351239
HSA-MIR-1212098.0568.441768
HSA-MIR-526B-5P97.4167.991074
HSA-MIR-5586-3P95.5167.00805
HSA-MIR-550B-3P95.4367.73599
HSA-MIR-430195.0065.22554

Literature-anchored findings (GeneRIF, showing 17)

  • Disease-associated bias in T helper type 1 (Th1)/Th2 CD4(+) T cell responses against MAGE-6 in HLA-DRB10401(+) patients with renal cell carcinoma or melanoma. (PMID:12208877)
  • MAGE-6 encodes HLA-DRbeta1*0401-presented epitopes recognized by CD4+ T cells from patients with melanoma or renal cell carcinoma (PMID:12631591)
  • Multiple simultaneous detection of MAGE-A [subtypes] more specific and sensitive than detection of single MAGE-A antigen for the diagnostic and prognostic evaluation of oral squamous cell carcinoma (PMID:18197853)
  • Report MAGEA1-A6 expression in sputum suggests presence of lung cancer cells or precancerous cells. (PMID:22134685)
  • To identify novel CTL epitopes from MAGE-A6 and MAGE-A12 antigens. (PMID:22707303)
  • MAGEA3/6 positivity was associated with significantly better disease-free survival. (PMID:25564441)
  • Study describes a widespread mechanism to suppress AMPK through its ubiquitination and degradation by the cancer-specific MAGE-A3/6-TRIM28 ubiquitin ligase. MAGE-A3 and MAGE-A6 are highly similar proteins normally expressed only in the male germline but frequently re-activated in human cancers. (PMID:25679763)
  • MageA6 and MageA11 form a protein complex resulting in the stabilization of MageA11 and consequently the enhancement of androgen receptor activity. (PMID:28542476)
  • MAGEA6 promotes glioma cell survival possibly via targeting AMPKalpha1. (PMID:29024810)
  • MAGEA6 knockdown by targeted-shRNA induced AMPK stabilization and activation, which led to mTOR complex 1 (mTORC1) in-activation and RCC cell death/apoptosis. (PMID:29448247)
  • Data indicate that miR-1273g represses melanoma antigen family A 3/melanoma antigen family A 6 (MAGEA3/6 )expression in colorectal cancer (CRC) cells and tissues, which may suggest a cancer-specific therapeutic. (PMID:30056111)
  • data indicate that the activation of CT-GABRA3 is correlated with that of MAGEA6. Therefore, MAGEA6 is linked with CT-GABRA3 through a bidirectional promoter. (PMID:31593956)
  • High MAGEA6 expression is associated with recurrence in Gastric Cancer. (PMID:31704814)
  • Lnc-THOR silencing inhibits human glioma cell survival by activating MAGEA6-AMPK signaling. (PMID:31727877)
  • Differential expression of MAGEA6 toggles autophagy to promote pancreatic cancer progression. (PMID:32270762)
  • Co-expression of cancer-testis antigens of MAGE-A6 and MAGE-A11 is associated with tumor aggressiveness in patients with bladder cancer. (PMID:35022469)
  • Knockdown of MAGE-A6 enhanced the irradiation sensitivity of non-small cell lung cancer cells by activating the AMPK pathway. (PMID:35285568)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
danio_reriondnl2ENSDARG00000058212
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), 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 6P43360 (reviewed: P43360)

Alternative names: Cancer/testis antigen 1.6, MAGE-6 antigen, MAGE3B antigen

All UniProt accessions (3): E7ETG4, E7EUF2, P43360

UniProt curated annotations — full annotation on UniProt →

Function. Activator of ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases that acts as a repressor of autophagy. May enhance ubiquitin ligase activity of TRIM28 and stimulate p53/TP53 ubiquitination by TRIM28. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. May play a role in tumor transformation or aspects of tumor progression. In vitro promotes cell viability in melanoma cell lines.

Subunit / interactions. Interacts with TRIM28.

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.

Post-translational modifications. Ubiquitinated by the DCX(DCAF12) complex specifically recognizes the diglutamate (Glu-Glu) at the C-terminus, leading to its degradation.

RefSeq proteins (2): NP_005354, NP_787064 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002190MHD_domDomain
IPR021072MAGE_NDomain
IPR037445MAGEFamily
IPR041898MAGE_WH1Homologous_superfamily
IPR041899MAGE_WH2Homologous_superfamily

Pfam: PF01454, PF12440

UniProt features (7 total): compositionally biased region 3, chain 1, domain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P43360-F172.600.46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_REGULATION_OF_AUTOPHAGY, HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP, HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP, GOBP_NEGATIVE_REGULATION_OF_AUTOPHAGY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP, HAMAI_APOPTOSIS_VIA_TRAIL_DN, GOBP_NEGATIVE_REGULATION_OF_CATABOLIC_PROCESS, GOMF_HISTONE_DEACETYLASE_BINDING, ALONSO_METASTASIS_NEURAL_UP, HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN, chrXq28

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), negative regulation of autophagy (GO:0010507)

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:

CategoryTerms
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
autophagy1
negative regulation of catabolic process1
regulation of autophagy1
enzyme binding1
binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

398 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MAGEA6CTAG2O75638825
MAGEA6CTAG1AP78358786
MAGEA6CSAG1Q6PB30636
MAGEA6TRIM28Q13263622
MAGEA6ARHGAP44Q17R89472
MAGEA6NPAS4Q8IUM7470
MAGEA6A0A1W2PQG5A0A1W2PQG5445
MAGEA6ANAPC4Q9UJX5438
MAGEA6CDC26Q8NHZ8437
MAGEA6ANAPC7Q9UJX3437
MAGEA6OR52E6Q96RD3431
MAGEA6ANAPC1Q9H1A4422
MAGEA6ANAPC11Q9NYG5419
MAGEA6ZIM2Q9NZV7417
MAGEA6GAGE4P0DSO3377

IntAct

376 interactions, top by confidence:

ABTypeScore
MAGEA6ATPAF2psi-mi:“MI:0915”(physical association)0.810
ATPAF2MAGEA6psi-mi:“MI:0915”(physical association)0.810
TULP3MAGEA6psi-mi:“MI:0915”(physical association)0.780
STAMBPL1MAGEA6psi-mi:“MI:0915”(physical association)0.780
MAGEA6GFOD1psi-mi:“MI:0915”(physical association)0.780
MAGEA6TULP3psi-mi:“MI:0915”(physical association)0.780
MAGEA6STAMBPL1psi-mi:“MI:0915”(physical association)0.780
NCK2MAGEA6psi-mi:“MI:0915”(physical association)0.720
RPL37AMAGEA6psi-mi:“MI:0915”(physical association)0.720
MAGEA6KLHL38psi-mi:“MI:0915”(physical association)0.720
MORN3MAGEA6psi-mi:“MI:0915”(physical association)0.720
MAGEA6EXOC5psi-mi:“MI:0915”(physical association)0.720
MIPOL1MAGEA6psi-mi:“MI:0915”(physical association)0.720
LIN37MAGEA6psi-mi:“MI:0915”(physical association)0.720
MAGEA6BCL7Bpsi-mi:“MI:0915”(physical association)0.720
MAGEA6RASSF4psi-mi:“MI:0915”(physical association)0.720
SH2D4AMAGEA6psi-mi:“MI:0915”(physical association)0.720
LSM2MAGEA6psi-mi:“MI:0915”(physical association)0.720
MAGEA6NCK2psi-mi:“MI:0915”(physical association)0.720

BioGRID (120): MAGEA6 (Two-hybrid), PDE4D (Two-hybrid), RPL37A (Two-hybrid), STX5 (Two-hybrid), TULP3 (Two-hybrid), NCK2 (Two-hybrid), SNX4 (Two-hybrid), BCL7B (Two-hybrid), ATP6V1G1 (Two-hybrid), AKAP9 (Two-hybrid), TXNDC9 (Two-hybrid), BET1 (Two-hybrid), EXOC5 (Two-hybrid), ACOT7 (Two-hybrid), FRMPD1 (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

2 interactions.

AEffectBMechanism
DCAF12“down-regulates quantity by destabilization”MAGEA6binding
Cullin4-RBX1-DDB1“down-regulates quantity by destabilization”MAGEA6polyubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign4
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

555 predictions. Top by Δscore:

VariantEffectΔscore
X:152767790:A:ACdonor_gain1.0000
X:152767791:C:CCdonor_gain1.0000
X:152767794:A:ACdonor_gain1.0000
X:152767795:C:CCdonor_gain1.0000
X:152767795:CAG:Cdonor_gain1.0000
X:152767795:CAGAT:Cdonor_gain1.0000
X:152769651:TA:Tdonor_loss1.0000
X:152769653:C:CTdonor_loss1.0000
X:152767711:CTGGC:Cacceptor_gain0.9900
X:152767713:GGCCT:Gacceptor_loss0.9900
X:152767714:GCCTG:Gacceptor_loss0.9900
X:152767716:C:CCacceptor_gain0.9900
X:152767717:T:Aacceptor_loss0.9900
X:152767788:TTAC:Tdonor_loss0.9900
X:152767789:TACT:Tdonor_loss0.9900
X:152767790:ACTT:Adonor_loss0.9900
X:152767791:CTTA:Cdonor_gain0.9900
X:152767792:TTA:Tdonor_loss0.9900
X:152767793:T:TCdonor_loss0.9900
X:152767794:A:Tdonor_loss0.9900
X:152767795:CA:Cdonor_gain0.9900
X:152767795:CAGA:Cdonor_gain0.9900
X:152769652:A:ACdonor_gain0.9900
X:152769653:C:CCdonor_gain0.9900
X:152769653:CCTTG:Cdonor_gain0.9900
X:152769657:G:Adonor_gain0.9900
X:152767860:ACCT:Aacceptor_loss0.9800
X:152767862:C:CCacceptor_gain0.9800
X:152767863:T:Cacceptor_loss0.9800
X:152767713:GGC:Gacceptor_gain0.9700

AlphaMissense

2052 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:152767165:A:CF162L0.948
X:152767165:A:TF162L0.948
X:152767167:A:GF162L0.948
X:152766839:A:GF271S0.942
X:152766838:G:CF271L0.928
X:152766838:G:TF271L0.928
X:152766840:A:GF271L0.928
X:152766834:A:GW273R0.927
X:152766834:A:TW273R0.927
X:152766832:C:AW273C0.914
X:152766832:C:GW273C0.914
X:152766831:C:GG274R0.894
X:152766875:C:GR259P0.891
X:152767282:C:AK123N0.873
X:152767282:C:GK123N0.873
X:152767247:A:GM135T0.869
X:152766884:A:GL256P0.864
X:152767163:C:AG163V0.864
X:152766830:C:TG274D0.851
X:152767210:A:CF147L0.850
X:152767210:A:TF147L0.850
X:152767212:A:GF147L0.850
X:152766823:C:AR276S0.845
X:152766823:C:GR276S0.845
X:152766839:A:CF271C0.845
X:152767178:A:GL158S0.838
X:152766884:A:TL256Q0.837
X:152766811:T:AE280D0.829
X:152766811:T:GE280D0.829
X:152766833:C:GW273S0.828

dbSNP variants (sampled 300 via entrez): RS1047232 (X:152766387 A>C,G), RS1047234 (X:152766383 C>A,T), RS1157341385 (X:152771059 A>G), RS1157579855 (X:152769961 C>T), RS1157617735 (X:152767683 T>C), RS1157749045 (X:152766180 C>T), RS1159499064 (X:152770479 G>A), RS1159734005 (X:152768379 C>G), RS1160675613 (X:152770143 C>T), RS1161428356 (X:152770380 T>C), RS1161533488 (X:152771152 C>T), RS1161698114 (X:152769976 G>A), RS1161774599 (X:152768032 G>A), RS1161791731 (X:152766519 CAA>C,CAAA), RS1161914393 (X:152767808 T>C)

Disease associations

OMIM: gene MIM:300176 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST011353_5Serum alkaline phosphatase levels4.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
Decitabineaffects expression2
Mitomycinaffects response to substance, affects binding, decreases expression, increases response to substance2
butyraldehydeincreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
Cisplatinaffects binding, decreases expression, increases response to substance1
Etoposideaffects response to substance1
Fluorouracildecreases expression, affects response to substance1
Gallic Acidincreases expression1
Methotrexateaffects response to substance1
Mitoxantroneaffects response to substance1
Valproic Acidincreases methylation1
Aflatoxin B1decreases methylation1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1WCAbcam HeLa MAGEA6 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.