MYCBP

gene
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Also known as AMY-1

Summary

MYCBP (MYC binding protein, HGNC:7554) is a protein-coding gene on chromosome 1p34.3, encoding c-Myc-binding protein (Q99417). May control the transcriptional activity of MYC.

The protein encoded by this gene binds to the N-terminus of the oncogenic protein C-MYC, enhancing the ability of C-MYC to activate E box-dependent transcription. The encoded protein is normally found in the cytoplasm, but it translocates to the nucleus during S phase of the cell cycle and associates with C-MYC. This protein may be involved in spermatogenesis. This gene can be silenced by microRNA-22. Two transcript variants, one protein-coding and the other probably not protein-coding, have been found for this gene.

Source: NCBI Gene 26292 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Druggable target: yes
  • MANE Select transcript: NM_012333

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7554
Approved symbolMYCBP
NameMYC binding protein
Location1p34.3
Locus typegene with protein product
StatusApproved
AliasesAMY-1
Ensembl geneENSG00000214114
Ensembl biotypeprotein_coding
OMIM606535
Entrez26292

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000397572, ENST00000465771, ENST00000494695, ENST00000495043, ENST00000922069, ENST00000922070, ENST00000922071

RefSeq mRNA: 1 — MANE Select: NM_012333 NM_012333

CCDS: CCDS431

Canonical transcript exons

ENST00000397572 — 5 exons

ExonStartEnd
ENSE000014592493886249338864714
ENSE000019266473887329138873348
ENSE000035027573886756238867610
ENSE000035294363887301838873090
ENSE000036110183886688038867009

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 94.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.5526 / max 642.6341, expressed in 1809 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1184425.55261809

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
olfactory segment of nasal mucosaUBERON:000538694.71gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.68gold quality
monocyteCL:000057691.98gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047391.88gold quality
mononuclear cellCL:000084291.85gold quality
right testisUBERON:000453491.83gold quality
mucosa of transverse colonUBERON:000499191.83gold quality
leukocyteCL:000073891.75gold quality
left testisUBERON:000453391.48gold quality
rectumUBERON:000105290.78gold quality
testisUBERON:000047390.09gold quality
lower esophagus mucosaUBERON:003583489.48gold quality
esophagus mucosaUBERON:000246989.47gold quality
right uterine tubeUBERON:000130288.92gold quality
adrenal tissueUBERON:001830388.66gold quality
granulocyteCL:000009488.20gold quality
body of pancreasUBERON:000115088.17gold quality
islet of LangerhansUBERON:000000688.04gold quality
esophagusUBERON:000104387.70gold quality
pancreasUBERON:000126487.10gold quality
transverse colonUBERON:000115786.57gold quality
right adrenal glandUBERON:000123386.36gold quality
lower esophagusUBERON:001347385.91gold quality
lower esophagus muscularis layerUBERON:003583385.89gold quality
right adrenal gland cortexUBERON:003582785.75gold quality
left adrenal glandUBERON:000123485.69gold quality
body of stomachUBERON:000116185.68gold quality
epithelium of bronchusUBERON:000203185.38gold quality
minor salivary glandUBERON:000183085.20gold quality
oocyteCL:000002385.19gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-134144yes28.06
E-ANND-3yes9.13
E-GEOD-100618no357.24

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTNNB1, LEF1, MYC

miRNA regulators (miRDB)

124 targeting MYCBP, 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-574-5P100.0066.01989
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-8485100.0077.574731
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-450099.9972.722367
HSA-MIR-511-3P99.9968.851467
HSA-MIR-366299.9973.825684
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-568899.9673.234504

Literature-anchored findings (GeneRIF, showing 16)

  • AMY-1 was localized in the mitochondria of HeLa and sperm in association with AKAP149 and S-AKAP84, respectively. These results suggest that AMY-1 plays a role in spermatogenesis (PMID:11483602)
  • identified a novel AMY-1-binding protein, AAT-1, and determied its expression profiles, genes, and cellular localization; results showed that AAT-1 was specifically expressed in the testis throughout spermatogenesis and was also present in mature sperm (PMID:12223483)
  • interacts with S-AKAP84 and AKAP95 in the cytoplasm and the nucleus, respectively, and inhibits enzyme acdtivity by preventing binding of its catalytic subunit to A-kinase-anchoring protein (AKAP) complex (PMID:12414807)
  • AMY-1 coordinates ADP-Ribosylation Factors-mediated membrane trafficking and signaling pathways. (PMID:16866877)
  • An important role for MBP-1 in the altered cell proliferation and energy utilization that occur in response to an altered glucose concentration. (PMID:17595061)
  • Suppression of telomerase activity mediated by PinX1 is involved in the Mad1/c-Myc pathway. (PMID:20544396)
  • miR-22 acts as a tumor suppressor through direct repression of MYCBP expression and subsequent reduction of oncogenic c-Myc activities. (PMID:20562918)
  • c-Myc expression is reduced in pterygium compared with normal conjunctiva. (PMID:22050566)
  • Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression. (PMID:30489189)
  • lnc-XLEC1 had inhibitive effects that may result from its collaboration with MBP-1 (MYCBP). (PMID:30698832)
  • Through activating MYCBP and by sponging miR-574-5p. (PMID:31094023)
  • Data found that MYCBP was highly expressed in hepatocellular carcinoma (HCC) tissues. Its overexpression is correlated with poor prognosis which indicates that MYCBP might play a cancer-promoting role in HCC. Further results found that EYA4 suppressed HCC tumor cell growth by repressing MYCBP by dephosphorylating beta-catenin S552. (PMID:31385398)
  • lncRNA LUNAR1 accelerates colorectal cancer progression by targeting the miR4953p/MYCBP axis. (PMID:33300052)
  • TAZ is indispensable for c-MYC-induced hepatocarcinogenesis. (PMID:34464659)
  • MiR-26b-5p inhibits cell proliferation and EMT by targeting MYCBP in triple-negative breast cancer. (PMID:34895159)
  • Circ_0002669 promotes osteosarcoma tumorigenesis through directly binding to MYCBP and sponging miR-889-3p. (PMID:38570856)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriomycbpENSDARG00000091001
mus_musculusMycbpENSMUSG00000028647
rattus_norvegicusMycbpENSRNOG00000065724

Protein

Protein identifiers

c-Myc-binding proteinQ99417 (reviewed: Q99417)

Alternative names: Associate of Myc 1

All UniProt accessions (2): A0A0D9SEI7, Q99417

UniProt curated annotations — full annotation on UniProt →

Function. May control the transcriptional activity of MYC. Stimulates the activation of E box-dependent transcription by MYC.

Subunit / interactions. Binds via its C-terminal region to the N-terminal region of MYC. Associates with AKAP1/S-AKAP84. Interacts with MYCBPAP. Interacts with CFAP91. Interacts with CFAP65 in a MYCBPAP-dependent manner. Interacts with OTUD4.

Subcellular location. Cytoplasm. Nucleus. Mitochondrion.

Tissue specificity. Highly expressed in heart, placenta, pancreas, skeletal muscle and kidney. Also present at low levels in lung.

Similarity. Belongs to the AMY1 family.

RefSeq proteins (1): NP_036465* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026060AMY1Family

UniProt features (7 total): helix 2, initiator methionine 1, chain 1, sequence conflict 1, strand 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2YY0X-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99417-F186.240.66

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 174 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, TGCGCANK_UNKNOWN, GCANCTGNY_MYOD_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, GOBP_MALE_GAMETE_GENERATION, MODULE_16, CTATGCA_MIR153, CAGCTG_AP4_Q5, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, CCTGTGA_MIR513, chr1p34, AAAGACA_MIR511

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), spermatogenesis (GO:0007283), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (2): transcription coactivator activity (GO:0003713), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA-templated transcription2
intracellular membrane-bounded organelle2
cellular anatomical structure2
regulation of gene expression1
regulation of RNA biosynthetic process1
developmental process involved in reproduction1
male gamete generation1
regulation of DNA-templated transcription1
positive regulation of RNA biosynthetic process1
transcription coregulator activity1
positive regulation of DNA-templated transcription1
binding1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

1289 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MYCBPMYCBPAPQ8TBZ2942
MYCBPMYCP01106918
MYCBPCFAP91Q7Z4T9915
MYCBPAKAP1Q92667891
MYCBPENO1P06733506
MYCBPCRELD1Q96HD1442
MYCBPPLA2G4AP47712439
MYCBPGIPC2Q8TF65436
MYCBPPRKAR2BP31323424
MYCBPMYCBP2O75592410
MYCBPESR1P03372406
MYCBPGADD45GO95257404
MYCBPPTNP21246401
MYCBPPOLR3EQ9NVU0396
MYCBPMXI1P50539392

IntAct

103 interactions, top by confidence:

ABTypeScore
YWHABPIK3C2Apsi-mi:“MI:0914”(association)0.800
ARFGEF2MYCBPpsi-mi:“MI:0915”(physical association)0.790
MYCBPARFGEF1psi-mi:“MI:0915”(physical association)0.790
MYCBPARFGEF2psi-mi:“MI:0915”(physical association)0.790
ARFGEF1MYCBPpsi-mi:“MI:0915”(physical association)0.790
MYCBPARFGEF2psi-mi:“MI:0403”(colocalization)0.790
ARFGEF1MYCBPpsi-mi:“MI:0403”(colocalization)0.790
HEXIM2AHCYL1psi-mi:“MI:0914”(association)0.740
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
KDM5ASIN3Bpsi-mi:“MI:0914”(association)0.640
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
MYCBPMYCBPAPpsi-mi:“MI:0915”(physical association)0.620
MYCBPAPMYCBPpsi-mi:“MI:0915”(physical association)0.620
CFAP91MYCBPpsi-mi:“MI:0915”(physical association)0.610
MYCBPCFAP91psi-mi:“MI:0407”(direct interaction)0.610
CFAP91MYCBPpsi-mi:“MI:0403”(colocalization)0.610
MYCBPCFAP91psi-mi:“MI:0403”(colocalization)0.610
YWHAEPIK3C2Apsi-mi:“MI:0914”(association)0.570
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
YWHAZPIK3C2Apsi-mi:“MI:0914”(association)0.570
AKAP8MYCBPpsi-mi:“MI:0915”(physical association)0.550
MYCBPAKAP8psi-mi:“MI:0914”(association)0.550

BioGRID (138): MYCBP (Affinity Capture-MS), EIF5AL1 (Co-fractionation), MYCBP (Co-fractionation), MYCBP (Co-fractionation), MYCBP (Co-fractionation), MYCBP (Co-fractionation), TPT1 (Co-fractionation), MYCBP (Affinity Capture-MS), MYCBP (Affinity Capture-MS), MYCBP (Affinity Capture-MS), MYCBP (Reconstituted Complex), MYCBP (Affinity Capture-MS), MYCBP (Affinity Capture-MS), MYCBP (Affinity Capture-MS), MYCBP (Affinity Capture-MS)

ESM2 similar proteins: A2XK00, B2RXB2, B5X3I1, C0HMA2, D4A9E1, G0RY74, G0RYE9, O14348, O17453, O75506, O95295, P60192, Q0V9C8, Q0VCF3, Q13503, Q16RX1, Q178E6, Q17NH9, Q2TBP7, Q2TBU8, Q3ZC22, Q4R6N3, Q5R561, Q5R7A8, Q5R8J5, Q5RDI2, Q5RE46, Q5RGJ6, Q5XJ97, Q5ZKJ4, Q68EW7, Q6ASS9, Q6DDT0, Q6DF11, Q6P255, Q7QB45, Q7T338, Q7ZTI5, Q8GW48, Q8K3X8

Diamond homologs: Q2TBP7, Q54I57, Q5R7A8, Q99417, Q9EQS3, Q9VG76

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 111 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria552.1×5e-06
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex546.0×6e-06
SARS-CoV-1 targets host intracellular signalling and regulatory pathways546.0×6e-06
Activation of BH3-only proteins534.0×2e-05
RHO GTPases activate PKNs521.7×1e-04
Intrinsic Pathway for Apoptosis520.1×1e-04
Apoptosis613.8×1e-04
Translocation of SLC2A4 (GLUT4) to the plasma membrane612.7×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

919 predictions. Top by Δscore:

VariantEffectΔscore
1:38867534:AAAG:Adonor_gain1.0000
1:38873016:AC:Adonor_gain1.0000
1:38873017:CC:Cdonor_gain1.0000
1:38873289:A:ACdonor_gain1.0000
1:38873290:C:CCdonor_gain1.0000
1:38864711:CAAG:Cacceptor_gain0.9900
1:38866875:TTTA:Tdonor_loss0.9900
1:38866876:TTA:Tdonor_loss0.9900
1:38866877:TA:Tdonor_loss0.9900
1:38866878:AC:Adonor_loss0.9900
1:38866879:CCTT:Cdonor_loss0.9900
1:38873327:G:Cdonor_gain0.9900
1:38864715:C:CCacceptor_gain0.9800
1:38867547:G:Tdonor_gain0.9800
1:38873013:CTCA:Cdonor_loss0.9800
1:38873014:TCA:Tdonor_loss0.9800
1:38873015:CA:Cdonor_loss0.9800
1:38873016:A:ACdonor_gain0.9800
1:38873016:A:AGdonor_loss0.9800
1:38873017:C:CCdonor_gain0.9800
1:38873285:CCTCA:Cdonor_loss0.9800
1:38873286:CTCA:Cdonor_loss0.9800
1:38873287:TCA:Tdonor_loss0.9800
1:38873288:CACTT:Cdonor_loss0.9800
1:38873289:ACTTT:Adonor_loss0.9800
1:38864714:GC:Gacceptor_loss0.9700
1:38864715:C:CAacceptor_loss0.9700
1:38866877:TAC:Tdonor_loss0.9700
1:38866879:CCTTT:Cdonor_loss0.9700
1:38873012:GCTCA:Gdonor_loss0.9700

AlphaMissense

663 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:38867006:A:CF47L1.000
1:38867006:A:TF47L1.000
1:38867008:A:GF47L1.000
1:38873053:A:GL18S1.000
1:38873064:G:CF14L1.000
1:38873064:G:TF14L1.000
1:38873065:A:GF14S1.000
1:38873066:A:GF14L1.000
1:38867577:G:TP41H0.999
1:38867578:G:AP41S0.999
1:38867598:A:GL34S0.999
1:38867607:A:GL31S0.999
1:38873042:C:AG22W0.999
1:38873053:A:CL18W0.999
1:38873062:C:GR15P0.999
1:38873065:A:CF14C0.999
1:38873075:G:AR11C0.999
1:38873075:G:TR11S0.999
1:38867568:G:TA44D0.998
1:38867577:G:AP41L0.998
1:38867579:T:AK40N0.998
1:38867579:T:GK40N0.998
1:38867596:A:GY35H0.998
1:38873023:G:AT28I0.998
1:38873026:A:GL27P0.998
1:38873041:C:AG22V0.998
1:38873041:C:TG22E0.998
1:38873051:C:TE19K0.998
1:38873052:C:AL18F0.998
1:38873052:C:GL18F0.998

dbSNP variants (sampled 300 via entrez): RS1000003932 (1:38867170 G>A), RS1000060196 (1:38864286 G>C), RS1000657994 (1:38862595 A>G), RS1001491394 (1:38863936 G>C,T), RS1001546920 (1:38866694 C>T), RS1001744444 (1:38871428 T>C), RS1002084368 (1:38874208 A>G), RS1002429876 (1:38868533 A>G), RS1002481204 (1:38862112 T>G), RS1002491833 (1:38872852 G>A), RS1002649774 (1:38865083 G>T), RS1003087400 (1:38873166 C>A,G,T), RS1003403133 (1:38867339 G>C), RS1003488645 (1:38871076 C>T), RS1003684903 (1:38870078 G>A)

Disease associations

OMIM: gene MIM:606535 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003475_2Beard thickness8.000000e-06
GCST005312_27Menopause (age at onset)5.000000e-21

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004704age at menopause

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067196 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
methylmercuric chloridedecreases expression3
bisphenol Adecreases expression, increases expression3
Air Pollutantsaffects cotreatment, increases abundance, increases expression, affects expression3
sodium arsenitedecreases expression, increases expression2
Cisplatindecreases expression, decreases reaction, increases expression2
Ozoneaffects cotreatment, increases expression, increases abundance, affects expression2
Cyclosporinedecreases expression2
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
methylparabendecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chloridedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
methacrylaldehydeincreases expression, increases abundance, affects cotreatment1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, decreases expression1
NSC 689534affects binding, decreases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Copperaffects binding, decreases expression1
Coumestrolaffects cotreatment, increases expression1
Doxorubicinaffects response to substance1
Estradiolincreases expression1
Formaldehydedecreases expression1
Methyl Methanesulfonatedecreases expression1
Phenobarbitalaffects expression1
Piroxicamdecreases expression, decreases reaction1
Silicon Dioxidedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652935BindingBinding affinity to human MYCBP incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.