MAGEB6B

Summary

MAGEB6B (MAGE family member B6B, HGNC:28824) is a protein-coding gene on chromosome Xp21.3, encoding Melanoma-associated antigen B6B (A0A0J9YX57).

Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 392433 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001396029

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28824
Approved symbol	MAGEB6B
Name	MAGE family member B6B
Location	Xp21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000232030
Ensembl biotype	protein_coding
Entrez	392433

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000416929

RefSeq mRNA: 1 — MANE Select: NM_001396029 NM_001396029

CCDS: CCDS94582

Canonical transcript exons

ENST00000416929 — 1 exons

Exon	Start	End
ENSE00003978252	26160601	26162410

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 38.19.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	38.19	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
granulocyte	CL:0000094	36.52	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
right testis	UBERON:0004534	34.80	gold quality
testis	UBERON:0000473	33.85	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
left testis	UBERON:0004533	33.27	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.58	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
leukocyte	CL:0000738	27.23	gold quality
tonsil	UBERON:0002372	27.05	gold quality
urinary bladder	UBERON:0001255	26.71	gold quality
monocyte	CL:0000576	26.59	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
blood	UBERON:0000178	25.90	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
muscle of leg	UBERON:0001383	24.86	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

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), 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), MAGEL2 (ENSG00000254585), MAGEA9B (ENSG00000267978), MAGEA2 (ENSG00000268606)

Protein

Protein identifiers

Melanoma-associated antigen B6B — A0A0J9YX57 (reviewed: A0A0J9YX57)

All UniProt accessions (1): A0A0J9YX57

RefSeq proteins (1): NP_001382958* (*=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 5, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A0J9YX57-F1	67.58	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chrXp21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ZNF274_TARGET_GENES, GOBP_NEGATIVE_REGULATION_OF_RNA_BIOSYNTHETIC_PROCESS

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

140 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGEB6B	OR12D2	P58182	507
MAGEB6B	MYO15B	Q96JP2	480
MAGEB6B	FBLL1	A6NHQ2	439
MAGEB6B	SLC25A51	Q9H1U9	400
MAGEB6B	ADAM21	Q9UKJ8	394
MAGEB6B	SLC35A4	Q96G79	391
MAGEB6B	DPY19L2	Q6NUT2	369
MAGEB6B	HERC2	O95714	367
MAGEB6B	TEX13A	Q9BXU3	325
MAGEB6B	NDUFV3	P56181	305
MAGEB6B	CD8B2	A6NJW9	302
MAGEB6B	SPACA9	Q96E40	291
MAGEB6B	TMEM183A	Q8IXX5	269
MAGEB6B	ZBTB45	Q96K62	255
MAGEB6B	PLEKHM1	Q9Y4G2	253

IntAct

0 interactions, top by confidence:

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

199 predictions. Top by Δscore:

Variant	Effect	Δscore
X:26161524:G:GT	donor_gain	0.7900
X:26161436:A:AG	donor_gain	0.7700
X:26161402:C:G	donor_gain	0.7100
X:26161497:C:T	donor_gain	0.6700
X:26161499:ACC:A	donor_gain	0.6600
X:26161516:G:GT	donor_gain	0.6600
X:26161533:G:GA	donor_gain	0.6100
X:26161482:G:GT	donor_gain	0.6000
X:26161537:C:A	donor_gain	0.6000
X:26161510:G:GT	donor_gain	0.5900
X:26161615:GATAA:G	donor_gain	0.5900
X:26161587:G:GT	donor_gain	0.5800
X:26161620:G:GG	donor_gain	0.5500
X:26161449:G:GT	donor_gain	0.5300
X:26161480:T:A	donor_gain	0.5300
X:26161516:G:T	donor_gain	0.5200
X:26161524:G:T	donor_gain	0.5100
X:26161421:G:GT	donor_gain	0.5000
X:26161437:T:G	donor_gain	0.5000
X:26161395:C:A	donor_gain	0.4900
X:26161515:GGAG:G	donor_gain	0.4900
X:26161616:A:G	donor_gain	0.4900
X:26161358:A:C	acceptor_gain	0.4800
X:26161377:C:T	donor_gain	0.4800
X:26161417:G:GT	donor_gain	0.4800
X:26161421:G:T	donor_gain	0.4800
X:26161600:G:GT	donor_gain	0.4800
X:26161514:AGGAG:A	donor_loss	0.4700
X:26161518:GGTC:G	donor_loss	0.4700
X:26161519:G:A	donor_loss	0.4700

AlphaMissense

2621 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:26161670:T:C	F357S	0.971
X:26161675:T:A	W359R	0.970
X:26161675:T:C	W359R	0.970
X:26161355:T:C	L252S	0.964
X:26161707:G:C	K369N	0.961
X:26161707:G:T	K369N	0.961
X:26161669:T:C	F357L	0.957
X:26161671:C:A	F357L	0.957
X:26161671:C:G	F357L	0.957
X:26161677:G:C	W359C	0.953
X:26161677:G:T	W359C	0.953
X:26161678:G:C	G360R	0.951
X:26161217:T:C	L206P	0.945
X:26161228:T:C	F210L	0.924
X:26161230:T:A	F210L	0.924
X:26161230:T:G	F210L	0.924
X:26161685:G:C	R362P	0.915
X:26161729:G:C	A377P	0.915
X:26161718:T:C	L373P	0.914
X:26161217:T:G	L206R	0.911
X:26161676:G:C	W359S	0.910
X:26161670:T:G	F357C	0.909
X:26161310:T:C	L237P	0.908
X:26161384:T:G	Y262D	0.906
X:26161634:G:C	R345P	0.904
X:26161679:G:A	G360D	0.903
X:26161780:G:C	A394P	0.903
X:26161679:G:T	G360V	0.901
X:26161342:T:C	F248L	0.899
X:26161344:T:A	F248L	0.899

dbSNP variants (sampled 300 via entrez): RS1005148307 (X:26159806 C>A), RS1005180965 (X:26160410 C>G,T), RS1008986795 (X:26160921 G>C), RS1010988215 (X:26161925 T>A), RS1011964671 (X:26159228 C>A,T), RS1012455304 (X:26159694 C>T), RS1014182358 (X:26158949 A>G), RS1015496318 (X:26162081 G>T), RS1015553492 (X:26162543 C>A), RS1016532567 (X:26160453 T>A,C), RS1022242206 (X:26161036 C>A,G,T), RS1023288021 (X:26158768 G>A), RS1023783422 (X:26159242 C>G), RS1028142388 (X:26162841 T>C), RS1028530535 (X:26162189 C>T)

Disease associations

OMIM: gene `` | 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ICG 001	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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