MAGEB16

Summary

MAGEB16 (MAGE family member B16, HGNC:21188) is a protein-coding gene on chromosome Xp21.1, encoding Melanoma-associated antigen B16 (A2A368).

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

Source: NCBI Gene 139604 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 41 total
• MANE Select transcript: NM_001370158

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21188
Approved symbol	MAGEB16
Name	MAGE family member B16
Location	Xp21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000189023
Ensembl biotype	protein_coding
OMIM	300762
Entrez	139604

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000399985, ENST00000399987, ENST00000399988, ENST00000399989, ENST00000399992

RefSeq mRNA: 4 — MANE Select: NM_001370158 NM_001099921, NM_001370158, NM_001370159, NM_001426398

CCDS: CCDS43927

Canonical transcript exons

ENST00000399988 — 2 exons

Exon	Start	End
ENSE00001541118	35798342	35798418
ENSE00003978144	35802131	35803772

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 90.53.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.24	gold quality
testis	UBERON:0000473	59.46	gold quality
right testis	UBERON:0004534	58.17	gold quality
left testis	UBERON:0004533	57.61	gold quality
bone marrow cell	CL:0002092	38.43	gold quality
granulocyte	CL:0000094	38.13	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	32.90	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
leukocyte	CL:0000738	30.38	gold quality
monocyte	CL:0000576	29.98	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	29.73	gold quality
right uterine tube	UBERON:0001302	29.34	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	27.66	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
right coronary artery	UBERON:0001625	26.93	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
blood	UBERON:0000178	26.43	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting MAGEB16, 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-1193	100.00	65.93	529
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-452-3P	99.01	66.25	1241
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-513B-3P	98.76	68.12	1577
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-7114-5P	98.51	67.87	1349
HSA-MIR-4766-3P	98.48	67.94	1347
HSA-MIR-6837-3P	98.42	66.71	1149
HSA-MIR-10397-3P	97.78	65.70	601
HSA-MIR-5089-3P	97.50	67.82	758
HSA-MIR-34A-3P	96.80	67.70	805
HSA-MIR-135A-3P	94.19	66.09	495

Literature-anchored findings (GeneRIF, showing 1)

• The testis-specific expression of MAGEB16 and Mageb16 is regulated by the methylation status of their promoter regions. (PMID:24219866)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ndnl2	ENSDARG00000058212
mus_musculus	Mageb16	ENSMUSG00000046942
rattus_norvegicus	Mageb16	ENSRNOG00000029408
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), 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 B16 — A2A368 (reviewed: A2A368)

Alternative names: MAGE-B16 antigen

All UniProt accessions (2): A0A0A0MSA3, A2A368

RefSeq proteins (4): NP_001093391, NP_001357087, NP_001357088, NP_001413327 (=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 (12 total): sequence variant 5, compositionally biased region 3, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2A368-F1	75.12	0.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): chrXp21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, MIR466, MIR545_3P, MIR4427, MIR548AV_3P, GSE28237_EARLY_VS_LATE_GC_BCELL_UP, GSE30083_SP1_VS_SP2_THYMOCYTE_DN, GSE30083_SP2_VS_SP3_THYMOCYTE_UP, GSE30083_SP3_VS_SP4_THYMOCYTE_DN, GOBP_NEGATIVE_REGULATION_OF_RNA_BIOSYNTHETIC_PROCESS, GSE7460_CTRL_VS_FOXP3_OVEREXPR_TCONV_1_UP, GSE19888_ADENOSINE_A3R_INH_VS_ACT_WITH_INHIBITOR_PRETREATMENT_IN_MAST_CELL_UP

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

408 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGEB16	FAM209A	Q5JX71	626
MAGEB16	REDIC1	Q86WS4	614
MAGEB16	SPATA31G1	Q5VYM1	595
MAGEB16	OR2L8	Q8NGY9	589
MAGEB16	C9orf43	Q8TAL5	584
MAGEB16	SLC22A24	Q8N4F4	573
MAGEB16	TMCO5A	Q8N6Q1	567
MAGEB16	ZFAND4	Q86XD8	560
MAGEB16	LANCL3	Q6ZV70	538
MAGEB16	OR5AR1	Q8NGP9	533
MAGEB16	TULP2	O00295	532
MAGEB16	PKDREJ	Q9NTG1	531
MAGEB16	SLC22A10	Q63ZE4	512
MAGEB16	SPATA16	Q9BXB7	507
MAGEB16	ZNF117	Q03924	479

IntAct

4 interactions, top by confidence:

A	B	Type	Score
MAGEA4	MAGEB16	psi-mi:“MI:0914”(association)	0.530

BioGRID (3): MAGEB16 (Affinity Capture-MS), MAGEB16 (Affinity Capture-MS), MAGEB16 (Affinity Capture-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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

534 predictions. Top by Δscore:

Variant	Effect	Δscore
X:35802130:GGCA:G	acceptor_gain	0.9900
X:35802126:CTTA:C	acceptor_loss	0.9700
X:35802127:TTA:T	acceptor_loss	0.9700
X:35802128:TAGG:T	acceptor_loss	0.9700
X:35802129:A:AG	acceptor_gain	0.9700
X:35802130:G:GG	acceptor_gain	0.9700
X:35798412:TGTCG:T	donor_gain	0.9600
X:35798413:GTCGA:G	donor_gain	0.9500
X:35802130:GGC:G	acceptor_gain	0.9400
X:35798414:TCGAG:T	donor_gain	0.9300
X:35800569:G:GG	donor_gain	0.9300
X:35800574:GACCC:G	donor_gain	0.9200
X:35800478:A:AG	acceptor_gain	0.8900
X:35800479:G:GG	acceptor_gain	0.8900
X:35802129:AG:A	acceptor_gain	0.8700
X:35802130:GG:G	acceptor_gain	0.8700
X:35802133:AGT:A	acceptor_gain	0.8300
X:35802134:GTG:G	acceptor_gain	0.8300
X:35798402:C:T	donor_gain	0.7700
X:35802134:G:GA	acceptor_gain	0.7600
X:35801315:TCTCA:T	acceptor_loss	0.7300
X:35801316:CTCA:C	acceptor_loss	0.7300
X:35801317:TCA:T	acceptor_loss	0.7300
X:35801318:C:G	acceptor_loss	0.7300
X:35801319:A:G	acceptor_loss	0.7300
X:35801320:G:GT	acceptor_loss	0.7300
X:35802134:GTGA:G	acceptor_gain	0.7300
X:35801309:C:G	acceptor_loss	0.7200
X:35801330:G:GT	acceptor_loss	0.7200
X:35798361:G:GT	donor_gain	0.7100

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000160247 (X:35803842 T>C), RS1000310998 (X:35798104 G>C), RS1001372222 (X:35803528 T>C), RS1001406731 (X:35800785 G>A), RS1001633786 (X:35801367 G>A), RS1001923187 (X:35800452 G>A), RS1002360102 (X:35799032 G>A), RS1003309225 (X:35803579 C>T), RS1004240974 (X:35803776 A>G), RS1005130762 (X:35802218 C>A,T), RS1006099905 (X:35796926 C>G), RS1006846897 (X:35799073 G>A), RS1007523307 (X:35798681 A>G), RS1008111270 (X:35802034 T>A,C,G), RS1008788483 (X:35801006 G>A,T)

Disease associations

OMIM: gene MIM:300762 | 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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression	1

Clinical trials (associated diseases)

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