GMEB1

gene
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Also known as P96PIFPIF96

Summary

GMEB1 (glucocorticoid modulatory element binding protein 1, HGNC:4370) is a protein-coding gene on chromosome 1p35.3, encoding Glucocorticoid modulatory element-binding protein 1 (Q9Y692). Acts as a DNA-binding transcriptional regulator involved in modulating the expression of genes responsive to glucocorticoid signaling.

This gene encodes a member of KDWK gene family which associates with GMEB2 protein. The GMEB1-GMEB2 complex is essential for parvovirus DNA replication. Studies in rat for a similar gene suggest that this gene’s role is to modulate the transactivation of the glucocorticoid receptor when it is bound to glucocorticoid response elements. Three alternative spliced transcript variants encoding different isoforms exist.

Source: NCBI Gene 10691 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 66 total
  • MANE Select transcript: NM_001319674

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4370
Approved symbolGMEB1
Nameglucocorticoid modulatory element binding protein 1
Location1p35.3
Locus typegene with protein product
StatusApproved
AliasesP96PIF, PIF96
Ensembl geneENSG00000162419
Ensembl biotypeprotein_coding
OMIM604409
Entrez10691

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 25 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000294409, ENST00000361872, ENST00000373816, ENST00000480454, ENST00000853890, ENST00000853891, ENST00000853892, ENST00000853893, ENST00000853894, ENST00000853895, ENST00000853896, ENST00000853897, ENST00000853898, ENST00000853899, ENST00000940222, ENST00000940223, ENST00000940224, ENST00000940225, ENST00000940226, ENST00000940227, ENST00000940228, ENST00000941581, ENST00000941582, ENST00000941583, ENST00000941584, ENST00000941585

RefSeq mRNA: 3 — MANE Select: NM_001319674 NM_001319674, NM_006582, NM_024482

CCDS: CCDS327, CCDS328

Canonical transcript exons

ENST00000373816 — 10 exons

ExonStartEnd
ENSE000012047582866878428668839
ENSE000012047682868358328683740
ENSE000014360962869010428690186
ENSE000014616552871407328719353
ENSE000034688172871052028710642
ENSE000035804282870419228704329
ENSE000036157712869294228693045
ENSE000036276842870243828702569
ENSE000036644542869158528691709
ENSE000036718902869692728697084

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 86.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.5088 / max 71.7681, expressed in 1772 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
18277.41631755
18261.0925731

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011586.44gold quality
secondary oocyteCL:000065585.72gold quality
buccal mucosa cellCL:000233684.86silver quality
cortical plateUBERON:000534384.72gold quality
tibiaUBERON:000097983.84gold quality
visceral pleuraUBERON:000240182.89gold quality
ganglionic eminenceUBERON:000402382.46gold quality
monocyteCL:000057682.37gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.29gold quality
leukocyteCL:000073882.25gold quality
mononuclear cellCL:000084282.21gold quality
parietal pleuraUBERON:000240082.19gold quality
amniotic fluidUBERON:000017382.11gold quality
germinal epithelium of ovaryUBERON:000130482.09gold quality
bloodUBERON:000017881.56gold quality
calcaneal tendonUBERON:000370181.55gold quality
pleuraUBERON:000097781.07gold quality
tendonUBERON:000004380.34gold quality
esophagus squamous epitheliumUBERON:000692080.11gold quality
oocyteCL:000002379.88gold quality
palpebral conjunctivaUBERON:000181279.77gold quality
stromal cell of endometriumCL:000225579.63gold quality
islet of LangerhansUBERON:000000679.05gold quality
ventricular zoneUBERON:000305378.98gold quality
gingival epitheliumUBERON:000194978.85gold quality
epithelium of nasopharynxUBERON:000195178.69gold quality
nasopharynxUBERON:000172878.68gold quality
eyeUBERON:000097078.65gold quality
bone marrowUBERON:000237177.95gold quality
triceps brachiiUBERON:000150977.42gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-MTAB-6058no262.22
E-ANND-3no4.76

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
PER2
TAT

miRNA regulators (miRDB)

43 targeting GMEB1, 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-4481100.0066.421669
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-4745-5P99.9865.951028
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-464899.9167.00710
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-129999.7771.242389
HSA-MIR-509399.6769.262291
HSA-MIR-6832-3P99.5270.441726
HSA-MIR-6833-5P99.5068.931161
HSA-MIR-520A-5P99.3566.721632
HSA-MIR-525-5P99.3566.851615
HSA-MIR-504-3P99.3067.181745
HSA-MIR-6878-3P99.2464.23920
HSA-MIR-442699.1766.741949
HSA-MIR-6734-3P99.1566.271627
HSA-MIR-93598.8269.361072

Literature-anchored findings (GeneRIF, showing 6)

  • consensus DNA recognition motif for two KDWK transcription factors identifies flexible-length, CpG-methylation sensitive cognate binding sites in the majority of human promoters (PMID:11743720)
  • 1.55 A resolution crystal structure of a central portion of GMEB1, encompassing its SAND domain (PMID:12702733)
  • GMEB1 is capable of binding to the prodomain of caspase-2; findings indicated that GMEB1 might be an endogenous inhibitory protein that selectively interacts with prodomain of caspase-2 to disrupt the autoactivation (PMID:15555560)
  • GMEB1 is an endogenous regulator that selectively binds to initiator procaspases and inhibits caspase-induced apoptosis (PMID:16497673)
  • GMEB1 effectively attenuated caspase activation and apoptosis caused by these stresses in human neuroblastoma SK-N-MC cells, indicating that it functions as a potent inhibitor of caspase activation and apoptosis in response to oxidative stress. (PMID:18455874)
  • Our findings show the de-ubiquitinase USP40 regulates the ubiquitination and degradation of CFLARL; and GMEB1 acts as a bridge protein for USP40 and CFLARL. Mechanistically, we found GMEB1 inhibits the activation of CASP8 by modulating ubiquitination and degradation of CFLARL (PMID:31046799)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriogmeb1ENSDARG00000062060
mus_musculusGmeb1ENSMUSG00000028901
rattus_norvegicusGmeb1ENSRNOG00000010910
caenorhabditis_elegansWBGENE00007732
caenorhabditis_elegansWBGENE00008092
caenorhabditis_elegansWBGENE00010010
caenorhabditis_elegansWBGENE00015285

Paralogs (1): GMEB2 (ENSG00000101216)

Protein

Protein identifiers

Glucocorticoid modulatory element-binding protein 1Q9Y692 (reviewed: Q9Y692)

Alternative names: DNA-binding protein p96PIF, Parvovirus initiation factor p96

All UniProt accessions (2): B1AT47, Q9Y692

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a DNA-binding transcriptional regulator involved in modulating the expression of genes responsive to glucocorticoid signaling. Specifically binds AT-rich DNA motifs known as glucocorticoid modulatory elements (GMEs), repressing or enhancing transcription depending on cellular context. Forms heterodimeric complexes with GMEB2, which enhances its DNA-binding specificity and transcriptional activity. This complex plays a critical role in the repression of glucocorticoid receptor (GR/NR3C1) transcriptional activity, acting as a negative modulator of glucocorticoid signaling. Regulates dopamine-enriched midbrain genes, including tyrosine hydroxylase/TH and the dopamine transporter SLC6A3, essential for dopamine signaling. Also binds the transferrin receptor promoter. In the cytoplasm, inhibits caspase activation and neuronal apoptosis by stabilizing CFLARL and blocking pro-caspase 8 activation.

Subunit / interactions. Homodimer, and heterodimer with GMEB2. GMEB1 and GMEB2 form the parvovirus initiator complex (PIF). Interacts with the glucocorticoid receptor (NR3C1) and NCOA2/TIF2. May interact with HSP27 and CREB-binding protein (CBP). Interacts with USP40 and CFLAR; these interactions allow USP40-mediated CFLAR deubiquitination. Interacts with TRAF3; this interaction enhances the anti-apoptotic activity of GMEB1.

Subcellular location. Nucleus. Cytoplasm.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y692-11yes
Q9Y692-22

RefSeq proteins (3): NP_001306603, NP_006573, NP_077808 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000770SAND_domDomain
IPR010919SAND-like_dom_sfHomologous_superfamily
IPR059099GMEB1/2/Spe-44_domDomain

Pfam: PF01342, PF25892

UniProt features (30 total): binding site 8, strand 5, helix 5, sequence conflict 3, initiator methionine 1, chain 1, modified residue 1, splice variant 1, sequence variant 1, domain 1, turn 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1OQJX-RAY DIFFRACTION1.55

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y692-F157.890.26

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 170; 174; 178; 113; 139; 143; 146; 157

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 126 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, chr1p35, GOMF_HEAT_SHOCK_PROTEIN_BINDING, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY, ATF2_S_UP.V1_DN, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ATF5_TARGET_GENES, CBX7_TARGET_GENES, E2F2_TARGET_GENES, GLI3_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of apoptotic process (GO:0043066), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (12): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), protein-macromolecule adaptor activity (GO:0030674), identical protein binding (GO:0042802), metal ion binding (GO:0046872), Hsp27 protein binding (GO:0051008), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
cellular anatomical structure3
regulation of DNA-templated transcription2
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II2
protein binding2
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
positive regulation of DNA-templated transcription1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
molecular adaptor activity1
cation binding1
heat shock protein binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
transcription cis-regulatory region binding1
transcription regulator activity1
binding1
DNA binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1

Protein interactions and networks

STRING

790 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GMEB1TFRCP02786647
GMEB1HSPB2Q16082605
GMEB1HSPB1P04792557
GMEB1HSPB3Q12988553
GMEB1AIREO43918462
GMEB1NRIP1P48552460
GMEB1YIPF1Q9Y548450
GMEB1TATP17735415
GMEB1TRIM54Q9BYV2394
GMEB1HIBADHP31937379
GMEB1ITGB5P18084375
GMEB1NR3C1P04150358
GMEB1SF3A2Q15428347
GMEB1UBE2IP50550347
GMEB1ZBTB11O95625343

IntAct

48 interactions, top by confidence:

ABTypeScore
SDC2PDPK1psi-mi:“MI:0914”(association)0.640
SSRP1H3C1psi-mi:“MI:0914”(association)0.610
CD44PDPK1psi-mi:“MI:0914”(association)0.530
TRAF3GMEB1psi-mi:“MI:0915”(physical association)0.510
GMEB1GMEB2psi-mi:“MI:0915”(physical association)0.500
GPC1SNAP23psi-mi:“MI:0915”(physical association)0.400
GPC1GANABpsi-mi:“MI:0915”(physical association)0.400
GMEB1NSpsi-mi:“MI:0915”(physical association)0.370
NS1GMEB1psi-mi:“MI:0915”(physical association)0.370
NS2GMEB1psi-mi:“MI:0915”(physical association)0.370
NSGMEB1psi-mi:“MI:0915”(physical association)0.370
GMEB1psi-mi:“MI:0915”(physical association)0.370
GMEB1UBE2Ipsi-mi:“MI:0915”(physical association)0.370
IFNA14GMEB1psi-mi:“MI:0915”(physical association)0.370
GMEB1SMAD3psi-mi:“MI:0915”(physical association)0.370
ATF7IPGMEB1psi-mi:“MI:0915”(physical association)0.370
SMAD1GMEB1psi-mi:“MI:0915”(physical association)0.370
GMEB1SNIP1psi-mi:“MI:0915”(physical association)0.370

BioGRID (61): GMEB1 (Two-hybrid), GMEB1 (Two-hybrid), GMEB1 (Two-hybrid), GMEB1 (Reconstituted Complex), GMEB1 (Affinity Capture-Western), GMEB2 (Affinity Capture-MS), GMEB1 (Affinity Capture-MS), GMEB1 (Affinity Capture-MS), MATN4 (Affinity Capture-MS), DHRS2 (Affinity Capture-MS), WDR54 (Affinity Capture-MS), GMEB1 (Affinity Capture-MS), GMEB1 (Affinity Capture-MS), GMEB1 (Two-hybrid), GMEB1 (Affinity Capture-Western)

ESM2 similar proteins: A0JMF8, B1WAV2, F2Z3T4, O02818, O77627, O88873, O93602, P05411, P05412, P05627, P12981, P15336, P16951, P17325, P18870, P22415, P31367, P48381, P54864, P56432, P58929, P79703, Q00969, Q04073, Q07956, Q07957, Q0V989, Q0V9K5, Q16656, Q24312, Q2HJ87, Q2TAL8, Q32NR3, Q4R3I8, Q4V872, Q502P7, Q58A65, Q5EAP5, Q5FWL0, Q61069

Diamond homologs: O75398, O77562, O88450, O88873, P58929, Q18171, Q24180, Q2HJ87, Q3KRF1, Q8BVK9, Q921C6, Q9JL60, Q9QUZ8, Q9UKD1, Q9Y692, Q9Z1T5, P23497, Q13342, A9CPT4, Q09415, Q9BXT4, Q9H930, Q9N1Q5, Q9VU41, Q9HB58, Q99388, A2A8L1, D3ZD32, F4KBP5, O15164, O16102, O43918, O96028, O97159, Q09698, Q12830, Q14839, Q5SPL2, Q64127, Q6E2N3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 48 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
Diseases associated with glycosaminoglycan metabolism5119.0×5e-08
Attachment and Entry593.9×1e-07
Defective B4GALT7 causes EDS, progeroid type589.2×1e-07
Defective B3GAT3 causes JDSSDHD589.2×1e-07
Defective B3GALT6 causes EDSP2 and SEMDJL1589.2×1e-07
HS-GAG degradation577.6×2e-07
Respiratory syncytial virus (RSV) attachment and entry577.6×2e-07
Initiation of coagulation cascade574.3×2e-07

GO biological processes:

GO termPartnersFoldFDR
cell migration69.0×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance55
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1422 predictions. Top by Δscore:

VariantEffectΔscore
1:28668836:GACG:Gdonor_gain1.0000
1:28668838:CGG:Cdonor_loss1.0000
1:28668840:G:GGdonor_gain1.0000
1:28683582:GCA:Gacceptor_gain1.0000
1:28690072:A:AGacceptor_gain1.0000
1:28690073:G:GGacceptor_gain1.0000
1:28690073:GTTT:Gacceptor_gain1.0000
1:28691576:T:Aacceptor_gain1.0000
1:28691583:A:AGacceptor_gain1.0000
1:28691584:G:GCacceptor_gain1.0000
1:28691584:GA:Gacceptor_gain1.0000
1:28691584:GAT:Gacceptor_gain1.0000
1:28691584:GATA:Gacceptor_gain1.0000
1:28691584:GATAC:Gacceptor_gain1.0000
1:28691709:GGTAA:Gdonor_loss1.0000
1:28691710:GTA:Gdonor_loss1.0000
1:28691711:T:Adonor_loss1.0000
1:28692934:A:AGacceptor_gain1.0000
1:28692935:C:Gacceptor_gain1.0000
1:28692938:TTA:Tacceptor_loss1.0000
1:28692939:TA:Tacceptor_loss1.0000
1:28692940:A:AGacceptor_gain1.0000
1:28692941:G:GGacceptor_gain1.0000
1:28692941:GT:Gacceptor_gain1.0000
1:28692941:GTT:Gacceptor_gain1.0000
1:28692941:GTTC:Gacceptor_gain1.0000
1:28692941:GTTCA:Gacceptor_gain1.0000
1:28693042:TCAGG:Tdonor_loss1.0000
1:28693043:CAGG:Cdonor_loss1.0000
1:28693046:G:GAdonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000005795 (1:28668261 A>T), RS1000015565 (1:28705882 C>T), RS1000079220 (1:28706217 G>A,C,T), RS1000137848 (1:28715138 C>G), RS1000154731 (1:28673366 C>T), RS1000241276 (1:28686476 A>C,G), RS1000243431 (1:28673121 C>G,T), RS1000260096 (1:28690953 C>A,G,T), RS1000283385 (1:28693135 T>C), RS1000297301 (1:28699629 C>G), RS1000417269 (1:28668901 C>A,G,T), RS1000469180 (1:28667920 G>T), RS1000511847 (1:28715416 G>A), RS1000519712 (1:28704007 C>G,T), RS1000604722 (1:28668085 T>C)

Disease associations

OMIM: gene MIM:604409 | 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
GCST90002379_3Basophil count4.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005090basophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression3
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases stability2
Tretinoinincreases expression2
aristolochic acid Idecreases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chloridedecreases expression1
manganese chlorideincreases abundance, affects cotreatment, decreases expression1
benzo(e)pyrenedecreases methylation1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
monomethylarsonous aciddecreases expression1
abrineincreases expression1
(+)-JQ1 compounddecreases expression1
Leflunomideincreases expression1
Acetaminophendecreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Doxorubicindecreases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Methapyrilenedecreases methylation1
Rotenonedecreases expression1
Smokedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Tunicamycindecreases expression1
Urethaneincreases expression1
Cyclosporineincreases expression1
Cadmium Chloridedecreases expression1

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.