MAGEB6

Summary

MAGEB6 (MAGE family member B6, HGNC:23796) is a protein-coding gene on chromosome Xp21.3, encoding Melanoma-associated antigen B6 (Q8N7X4).

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 expressed in testis, and in a significant fraction of tumors of various histological types. The MAGEB genes are clustered on chromosome Xp22-p21.

Source: NCBI Gene 158809 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_173523

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23796
Approved symbol	MAGEB6
Name	MAGE family member B6
Location	Xp21.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40242, MAGE-B6, MAGEB6A, CT3.4
Ensembl gene	ENSG00000176746
Ensembl biotype	protein_coding
OMIM	300467
Entrez	158809

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000379034

RefSeq mRNA: 1 — MANE Select: NM_173523 NM_173523

CCDS: CCDS14217

Canonical transcript exons

ENST00000379034 — 2 exons

Exon	Start	End
ENSE00001479550	26193786	26195646
ENSE00001479551	26192440	26192527

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 83.38.

Top tissues by expression

240 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	83.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.40	gold quality
right testis	UBERON:0004534	63.02	gold quality
left testis	UBERON:0004533	61.52	gold quality
testis	UBERON:0000473	61.10	gold quality
lower lobe of lung	UBERON:0008949	60.69	silver quality
sperm	CL:0000019	51.36	silver quality
adult organism	UBERON:0007023	43.97	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality
oviduct epithelium	UBERON:0004804	40.03	gold quality
mammary duct	UBERON:0001765	39.98	gold quality
mucosa of sigmoid colon	UBERON:0004993	39.95	gold quality
deltoid	UBERON:0001476	39.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting MAGEB6, 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-511-3P	99.99	68.85	1467
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-4318	99.38	66.94	1505
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-3190-5P	98.87	64.89	1345

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	ndnl2	ENSDARG00000058212
mus_musculus	Mageb1	ENSMUSG00000062162
mus_musculus	Mageb2	ENSMUSG00000073069
mus_musculus	Mageb3	ENSMUSG00000074881
mus_musculus	Gm5071	ENSMUSG00000078123
mus_musculus	Mageb6b1	ENSMUSG00000094861
mus_musculus	Mageb6b2	ENSMUSG00000096072
rattus_norvegicus	Mageb4	ENSRNOG00000022806
rattus_norvegicus	Mageb6b1	ENSRNOG00000022848
rattus_norvegicus	Magebl1	ENSRNOG00000043508
rattus_norvegicus	Mageb6l1	ENSRNOG00000051281
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), 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 B6 — Q8N7X4 (reviewed: Q8N7X4)

Alternative names: Cancer/testis antigen 3.4, MAGE-B6 antigen

All UniProt accessions (1): Q8N7X4

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in testis. Not expressed in other normal tissues, but is expressed in tumors of different histological origins.

RefSeq proteins (1): NP_775794* (*=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 (8 total): compositionally biased region 4, chain 1, domain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7X4-F1	70.53	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): HATADA_METHYLATED_IN_LUNG_CANCER_DN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, chrXp21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, MIR520D_5P, MIR524_5P, MIR4803, MIR3609, MIR548AH_5P, MIR6515_3P, MIR4275, MIR501_5P, MIR2276_3P, MIR4318

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:

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

Protein interactions and networks

STRING

360 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGEB6	CENPA	P49450	602
MAGEB6	MAGEC1	O60732	525
MAGEB6	HOXD9	P28356	517
MAGEB6	A0A1W2PQG5	A0A1W2PQG5	473
MAGEB6	CSAG2	Q9Y5P2	447
MAGEB6	OR1I1	O60431	431
MAGEB6	CT55	Q8WUE5	430
MAGEB6	SSX7	Q7RTT5	422
MAGEB6	SPANXA1	Q9NS26	419
MAGEB6	ACTL8	Q9H568	396
MAGEB6	SPANXN4	Q5MJ08	393
MAGEB6	SPANXN3	Q5MJ09	375
MAGEB6	ZNF165	P49910	371
MAGEB6	XAGE3	Q8WTP9	370
MAGEB6	MAGEC3	Q8TD91	367

IntAct

64 interactions, top by confidence:

A	B	Type	Score
MAGEB6	PHC2	psi-mi:“MI:0915”(physical association)	0.560
HACL1	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
PHC2	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
APBA2	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
SUPV3L1	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
ROBO1	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	AGTR1	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	CLN3	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	EEF1D	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	F8	psi-mi:“MI:0915”(physical association)	0.560
FMR1	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	HSP90AB1	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	PRDX1	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	SERPINA1	psi-mi:“MI:0915”(physical association)	0.560
ST3GAL3	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
BRK1	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
ARHGAP25	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	DNM1L	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	CCT8	psi-mi:“MI:0915”(physical association)	0.560
MAGEB6	TPPP	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (12): MAGEB6 (Two-hybrid), MAGEB6 (Two-hybrid), MAGEB6 (Affinity Capture-MS), MAGEB6 (Affinity Capture-MS), MAGEB6 (Affinity Capture-MS), MAGEB6 (Two-hybrid), MAGEB6 (Two-hybrid), MAGEB6 (Two-hybrid), MAGEB6 (Proximity Label-MS), MAGEB6 (Affinity Capture-MS), MAGEB6 (Two-hybrid), MAGEB6 (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

154 predictions. Top by Δscore:

Variant	Effect	Δscore
X:26193781:TCCA:T	acceptor_loss	0.9400
X:26193782:CCAG:C	acceptor_loss	0.9400
X:26193783:CA:C	acceptor_loss	0.9400
X:26193784:AGG:A	acceptor_loss	0.9400
X:26193784:A:AG	acceptor_gain	0.9200
X:26193785:G:GG	acceptor_gain	0.9200
X:26192524:CTTG:C	donor_loss	0.9000
X:26192528:GTGG:G	donor_loss	0.9000
X:26192529:T:A	donor_loss	0.9000
X:26192531:GGTAT:G	donor_loss	0.9000
X:26192530:GG:G	donor_loss	0.8900
X:26192532:GT:G	donor_loss	0.8900
X:26193631:T:TA	acceptor_gain	0.8900
X:26192533:T:G	donor_loss	0.8700
X:26192528:G:GG	donor_gain	0.8600
X:26193785:GGT:G	acceptor_gain	0.8400
X:26193781:T:G	acceptor_gain	0.8100
X:26193780:A:AG	acceptor_gain	0.8000
X:26193631:TGAG:T	acceptor_gain	0.7900
X:26193632:G:GC	acceptor_gain	0.7500
X:26192498:G:GT	donor_gain	0.7200
X:26193630:CTGAG:C	acceptor_gain	0.7200
X:26193633:A:T	acceptor_gain	0.7200
X:26193631:TG:T	acceptor_gain	0.7000
X:26192733:CCCAG:C	donor_loss	0.6900
X:26192734:CCAG:C	donor_loss	0.6900
X:26192735:CAGGT:C	donor_loss	0.6900
X:26192736:AGG:A	donor_loss	0.6900
X:26192737:GGTC:G	donor_loss	0.6900
X:26192738:G:GA	donor_loss	0.6900

AlphaMissense

2629 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:26194916:T:C	F357S	0.975
X:26194915:T:C	F357L	0.964
X:26194917:C:A	F357L	0.964
X:26194917:C:G	F357L	0.964
X:26194921:T:A	W359R	0.961
X:26194921:T:C	W359R	0.961
X:26194953:G:C	K369N	0.958
X:26194953:G:T	K369N	0.958
X:26194588:T:C	F248L	0.952
X:26194590:T:A	F248L	0.952
X:26194590:T:G	F248L	0.952
X:26194923:G:C	W359C	0.952
X:26194923:G:T	W359C	0.952
X:26194924:G:C	G360R	0.946
X:26194601:T:C	L252S	0.940
X:26194880:G:C	R345P	0.929
X:26194916:T:G	F357C	0.923
X:26194474:T:C	F210L	0.912
X:26194476:T:A	F210L	0.912
X:26194476:T:G	F210L	0.912
X:26194853:T:C	L336S	0.907
X:26194630:T:G	Y262D	0.903
X:26194931:G:C	R362P	0.903
X:26194553:T:C	I236T	0.902
X:26194925:G:T	G360V	0.899
X:26195026:G:C	A394P	0.896
X:26194867:T:C	Y341H	0.893
X:26194924:G:T	G360C	0.892
X:26194544:T:G	F233C	0.891
X:26194868:A:C	Y341S	0.890

dbSNP variants (sampled 300 via entrez): RS1000354382 (X:26191443 C>A,T), RS1000382548 (X:26191734 G>T), RS1003726090 (X:26191844 G>A), RS1003778297 (X:26192357 G>A,C), RS1005709267 (X:26192395 C>G,T), RS1005804569 (X:26190979 T>C), RS1006195580 (X:26192707 G>A), RS1010946240 (X:26195807 C>A), RS1011620018 (X:26194600 T>C), RS1012529115 (X:26191747 T>G), RS1012580987 (X:26192267 CAGAT>C), RS1014379943 (X:26191116 C>A,T), RS1014680104 (X:26191333 T>C), RS1016060428 (X:26194771 G>A), RS1017117787 (X:26192748 G>A)

Disease associations

OMIM: gene MIM:300467 | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
coumarin	increases phosphorylation	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	increases expression, affects cotreatment	1
jinfukang	affects cotreatment, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Folic Acid	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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