GMEB2

gene
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Also known as P79PIFKIAA1269PIF79

Summary

GMEB2 (glucocorticoid modulatory element binding protein 2, HGNC:4371) is a protein-coding gene on chromosome 20q13.33, encoding Glucocorticoid modulatory element-binding protein 2 (Q9UKD1). Trans-acting factor that binds to glucocorticoid modulatory elements (GME) present in the TAT (tyrosine aminotransferase) promoter and increases sensitivity to low concentrations of glucocorticoids.

This gene is a member of KDWK gene family. The product of this gene associates with GMEB1 protein, and the complex is essential for parvovirus DNA replication. Study of rat homolog implicates the role of this gene in modulation of transactivation by the glucocorticoid receptor bound to glucocorticoid response elements. This gene appears to use multiple polyadenylation sites.

Source: NCBI Gene 26205 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 77 total — 1 likely-pathogenic
  • MANE Select transcript: NM_012384

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4371
Approved symbolGMEB2
Nameglucocorticoid modulatory element binding protein 2
Location20q13.33
Locus typegene with protein product
StatusApproved
AliasesP79PIF, KIAA1269, PIF79
Ensembl geneENSG00000101216
Ensembl biotypeprotein_coding
OMIM607451
Entrez26205

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 retained_intron

ENST00000266068, ENST00000370069, ENST00000370077, ENST00000889842, ENST00000889843, ENST00000889844, ENST00000936808, ENST00000936809, ENST00000951328

RefSeq mRNA: 1 — MANE Select: NM_012384 NM_012384

CCDS: CCDS13528

Canonical transcript exons

ENST00000370077 — 10 exons

ExonStartEnd
ENSE000006634976360474363604840
ENSE000014174776362695663627101
ENSE000014516826361926763619454
ENSE000038437726358760563590729
ENSE000042833706359775763597860
ENSE000042833716359202263592144
ENSE000042833726360296563603092
ENSE000042833736359253363592670
ENSE000042833746359301163593082
ENSE000042833766359561063595767

Expression profiles

Bgee: expression breadth ubiquitous, 269 present calls, max score 93.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.5436 / max 193.3725, expressed in 1795 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
18839211.42601787
1883911.1176426

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183193.87gold quality
buccal mucosa cellCL:000233688.22gold quality
thymusUBERON:000237086.94gold quality
mucosa of urinary bladderUBERON:000125986.71silver quality
ileal mucosaUBERON:000033186.23gold quality
pancreatic ductal cellCL:000207986.17silver quality
granulocyteCL:000009484.33gold quality
right lobe of thyroid glandUBERON:000111983.96gold quality
tibialis anteriorUBERON:000138583.78gold quality
bloodUBERON:000017883.59gold quality
cartilage tissueUBERON:000241883.50gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.43gold quality
left lobe of thyroid glandUBERON:000112083.13gold quality
tendon of biceps brachiiUBERON:000818883.06gold quality
thyroid glandUBERON:000204682.89gold quality
oocyteCL:000002382.85gold quality
dorsal motor nucleus of vagus nerveUBERON:000287082.65gold quality
endothelial cellCL:000011581.90gold quality
saphenous veinUBERON:000731881.76gold quality
pylorusUBERON:000116681.42gold quality
upper leg skinUBERON:000426281.35gold quality
tracheaUBERON:000312681.34gold quality
inferior olivary complexUBERON:000212781.19gold quality
tongue squamous epitheliumUBERON:000691981.11silver quality
olfactory bulbUBERON:000226481.02gold quality
amniotic fluidUBERON:000017380.94gold quality
lower esophagus mucosaUBERON:003583480.92gold quality
cerebellar vermisUBERON:000472080.77silver quality
apex of heartUBERON:000209880.67gold quality
skin of hipUBERON:000155480.60gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no2.28

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA0862.1GMEB2GMEB

JASPAR matrix evidence (PMIDs): PMID:11743720

miRNA regulators (miRDB)

73 targeting GMEB2, 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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-9-5P100.0072.282361
HSA-MIR-5193100.0067.261744
HSA-MIR-4692100.0067.322066
HSA-MIR-451499.9967.101870
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-314899.9775.066478
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-464899.9167.00710
HSA-MIR-659-3P99.8570.691620
HSA-MIR-76599.8468.242442
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-379-3P99.6969.601524
HSA-MIR-411-3P99.6969.631524
HSA-MIR-509399.6769.262291
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-1915-3P99.5866.791988

Literature-anchored findings (GeneRIF, showing 1)

  • 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)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriogmeb2ENSDARG00000093240
mus_musculusGmeb2ENSMUSG00000038705
rattus_norvegicusGmeb2ENSRNOG00000013339
caenorhabditis_elegansWBGENE00007732
caenorhabditis_elegansWBGENE00008092
caenorhabditis_elegansWBGENE00010010
caenorhabditis_elegansWBGENE00015285

Paralogs (1): GMEB1 (ENSG00000162419)

Protein

Protein identifiers

Glucocorticoid modulatory element-binding protein 2Q9UKD1 (reviewed: Q9UKD1)

Alternative names: DNA-binding protein p79PIF, Parvovirus initiation factor p79

All UniProt accessions (1): Q9UKD1

UniProt curated annotations — full annotation on UniProt →

Function. Trans-acting factor that binds to glucocorticoid modulatory elements (GME) present in the TAT (tyrosine aminotransferase) promoter and increases sensitivity to low concentrations of glucocorticoids. Also binds to the transferrin receptor promoter. Essential auxiliary factor for the replication of parvoviruses.

Subunit / interactions. Homodimer, and heterodimer of GMEB1 and GMEB2. GMEB1 and GMEB2 form the parvovirus initiator complex (PIF). Interacts with the glucocorticoid receptor (NR3C1). May interact with CREB-binding protein (CBP).

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed in peripheral blood lymphocytes and fetal liver. Expressed preferentially in reproductive and/or developmentally important cells, such as testis, placenta, bone marrow and fetal tissues.

RefSeq proteins (1): NP_036516* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF01342, PF25892

UniProt features (17 total): binding site 8, sequence conflict 3, cross-link 2, chain 1, domain 1, modified residue 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UKD1-F161.980.30

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): 175; 110; 136; 140; 143; 154; 167; 171

Post-translational modifications (3): 373, 155, 155

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 92 (showing top): BLALOCK_ALZHEIMERS_DISEASE_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GCM_NF2, CTTTGTA_MIR524, YOSHIMURA_MAPK8_TARGETS_UP, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, HOLLEMAN_DAUNORUBICIN_B_ALL_DN, HOLLEMAN_DAUNORUBICIN_ALL_DN, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HMG20B_TARGET_GENES, NR1I2_TARGET_GENES, RBM34_TARGET_GENES, SFMBT1_TARGET_GENES

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), transcription by RNA polymerase II (GO:0006366)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), identical protein binding (GO:0042802), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
DNA-templated transcription1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
protein binding1
cation binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
DNA binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

1050 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GMEB2TFRCP02786648
GMEB2ARFRP1Q13795597
GMEB2FNDC11Q9BVV2550
GMEB2HSPB2Q16082548
GMEB2ZGPATQ8N5A5529
GMEB2HSPB1P04792525
GMEB2STMN3Q9NZ72515
GMEB2NR3C1P04150501
GMEB2HSPB3Q12988496
GMEB2TYSND1Q2T9J0490
GMEB2BTBD3Q9Y2F9462
GMEB2TATP17735454
GMEB2PXMP4Q9Y6I8446
GMEB2NELFBQ8WX92437
GMEB2ZNF341Q9BYN7408

IntAct

83 interactions, top by confidence:

ABTypeScore
ATXN1GMEB2psi-mi:“MI:0915”(physical association)0.670
SDC2PDPK1psi-mi:“MI:0914”(association)0.640
GMEB2MXRA8psi-mi:“MI:0915”(physical association)0.560
ZMYND19GMEB2psi-mi:“MI:0915”(physical association)0.560
GMEB2GMEB2psi-mi:“MI:0915”(physical association)0.560
CEP19GMEB2psi-mi:“MI:0915”(physical association)0.560
MAP1LC3CGMEB2psi-mi:“MI:0915”(physical association)0.560
TRAF3GMEB2psi-mi:“MI:0915”(physical association)0.560
FHL2GMEB2psi-mi:“MI:0915”(physical association)0.560
PIN1GMEB2psi-mi:“MI:0915”(physical association)0.560
POGZGMEB2psi-mi:“MI:0915”(physical association)0.560
LMO3GMEB2psi-mi:“MI:0915”(physical association)0.560
POU6F2GMEB2psi-mi:“MI:0915”(physical association)0.560
CDC7GMEB2psi-mi:“MI:0915”(physical association)0.560
LMO2GMEB2psi-mi:“MI:0915”(physical association)0.560
MXRA8GMEB2psi-mi:“MI:0915”(physical association)0.560
GMEB2TTF2psi-mi:“MI:0915”(physical association)0.560
MOB1AGMEB2psi-mi:“MI:0915”(physical association)0.560
CD44PDPK1psi-mi:“MI:0914”(association)0.530
GMEB1GMEB2psi-mi:“MI:0915”(physical association)0.500
CBFA2T3GMEB2psi-mi:“MI:0915”(physical association)0.370
CD44TCAF2psi-mi:“MI:0914”(association)0.350
SDC2METTL8psi-mi:“MI:0914”(association)0.350
SDC1ARVCFpsi-mi:“MI:0914”(association)0.350
GMEB1MATN4psi-mi:“MI:0914”(association)0.350
IL7RFAM171A2psi-mi:“MI:0914”(association)0.350

BioGRID (67): GMEB2 (Affinity Capture-RNA), GMEB2 (Affinity Capture-RNA), GMEB2 (Affinity Capture-RNA), GMEB2 (Proximity Label-MS), GMEB2 (Affinity Capture-MS), GMEB2 (Affinity Capture-MS), GMEB2 (Affinity Capture-MS), GMEB2 (Affinity Capture-MS), GMEB2 (Affinity Capture-MS), GMEB2 (Two-hybrid), GMEB2 (Two-hybrid), GMEB2 (Two-hybrid), POU6F2 (Two-hybrid), MOB1A (Two-hybrid), FHL2 (Two-hybrid)

ESM2 similar proteins: A2RSY1, F1R7R1, O54972, O75069, O75151, O88873, P0CH95, P49140, P58929, Q02225, Q06455, Q13233, Q1LY51, Q24767, Q2VPU4, Q2YDD2, Q3KR73, Q499B3, Q4VGL6, Q5F3B1, Q5PQS6, Q5TC82, Q60416, Q60698, Q61909, Q62415, Q62739, Q66IV1, Q6F6B3, Q6NUC6, Q6NYU6, Q7Z3K3, Q80TJ7, Q80W04, Q8BZH4, Q8CHY6, Q8CID0, Q8K2L8, Q8NEM7, Q8TEK3

Diamond homologs: O43439, O54972, O70374, O75081, O75398, O77562, O88450, O88873, P23497, P58929, Q06455, Q13342, Q3KRF1, Q5F3B1, Q61909, Q8BVK9, Q921C6, Q9H930, Q9HB58, Q9IAB2, Q9UKD1, Q9Z1T5, Q24180, Q18171, Q2HJ87, Q9JL60, Q9QUZ8, Q9Y692, Q99388, Q9N1Q5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 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
Extracellular matrix organization510.9×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance62
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1326329GRCh37/hg19 20q13.33(chr20:61826780-62660844)Likely pathogenic

SpliceAI

2175 predictions. Top by Δscore:

VariantEffectΔscore
20:63590725:CAGGG:Cacceptor_gain1.0000
20:63590726:AGGG:Aacceptor_gain1.0000
20:63590727:GGG:Gacceptor_gain1.0000
20:63590728:GG:Gacceptor_gain1.0000
20:63590728:GGC:Gacceptor_loss1.0000
20:63590730:C:CCacceptor_gain1.0000
20:63590730:CTG:Cacceptor_loss1.0000
20:63590731:T:Aacceptor_loss1.0000
20:63592126:T:Cacceptor_gain1.0000
20:63592142:CAT:Cacceptor_gain1.0000
20:63592142:CATCT:Cacceptor_gain1.0000
20:63592145:C:CCacceptor_gain1.0000
20:63592146:T:Cacceptor_gain1.0000
20:63592146:T:TCacceptor_gain1.0000
20:63592527:TCTCA:Tdonor_loss1.0000
20:63592528:CTCA:Cdonor_loss1.0000
20:63592529:TCACC:Tdonor_loss1.0000
20:63592530:CA:Cdonor_loss1.0000
20:63592531:A:ATdonor_loss1.0000
20:63592649:C:CTacceptor_gain1.0000
20:63592649:C:Tacceptor_gain1.0000
20:63592652:C:CTacceptor_gain1.0000
20:63592666:GTCAT:Gacceptor_gain1.0000
20:63592667:TCAT:Tacceptor_gain1.0000
20:63592668:CAT:Cacceptor_gain1.0000
20:63592668:CATC:Cacceptor_gain1.0000
20:63592669:AT:Aacceptor_gain1.0000
20:63592671:C:CCacceptor_gain1.0000
20:63592672:T:Gacceptor_loss1.0000
20:63592673:G:Cacceptor_gain1.0000

AlphaMissense

3429 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:63595698:G:CS177R1.000
20:63595698:G:TS177R1.000
20:63595700:T:GS177R1.000
20:63595704:G:CC175W1.000
20:63595705:C:AC175F1.000
20:63595705:C:GC175S1.000
20:63595705:C:TC175Y1.000
20:63595706:A:GC175R1.000
20:63595706:A:TC175S1.000
20:63595716:G:CC171W1.000
20:63595717:C:GC171S1.000
20:63595717:C:TC171Y1.000
20:63595718:A:GC171R1.000
20:63595718:A:TC171S1.000
20:63595737:G:CF164L1.000
20:63595737:G:TF164L1.000
20:63595738:A:GF164S1.000
20:63595739:A:GF164L1.000
20:63595757:C:GD158H1.000
20:63595767:C:AR154S1.000
20:63595767:C:GR154S1.000
20:63597757:C:AR154M1.000
20:63597757:C:GR154T1.000
20:63597760:A:GL153P1.000
20:63597760:A:TL153H1.000
20:63597762:C:AM152I1.000
20:63597762:C:GM152I1.000
20:63597762:C:TM152I1.000
20:63597778:C:GR147P1.000
20:63597779:G:TR147S1.000

dbSNP variants (sampled 300 via entrez): RS1000041142 (20:63612965 T>A), RS1000060214 (20:63623892 A>C), RS1000080615 (20:63600549 C>G), RS1000099795 (20:63617707 C>T), RS1000136866 (20:63600858 G>A,C), RS1000152286 (20:63606873 A>T), RS1000228666 (20:63623019 C>T), RS1000255626 (20:63595329 G>A), RS1000262887 (20:63606553 T>A), RS1000441719 (20:63614363 G>A,C), RS1000450322 (20:63628912 G>A), RS1000453276 (20:63594372 G>A), RS1000485696 (20:63605959 GA>G,GAA), RS1000613544 (20:63599570 C>T), RS1000673083 (20:63628107 G>C)

Disease associations

OMIM: gene MIM:607451 | disease phenotypes: MIM:121200, MIM:613720

GenCC curated gene-disease

Mondo (2): seizures, benign familial neonatal, 1 (MONDO:0007365), developmental and epileptic encephalopathy, 7 (MONDO:0013387)

Orphanet (2): Self-limited neonatal epilepsy (Orphanet:1949), KCNQ2-related developmental and epileptic encephalopathy (Orphanet:439218)

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001942_22Prostate cancer4.000000e-16
GCST010002_71Refractive error1.000000e-14
GCST010796_2607Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-09
GCST010796_2608Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08
GCST010796_2609Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-09
GCST010796_2610Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-09
GCST010796_2611Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-09
GCST010796_2612Electrocardiogram morphology (amplitude at temporal datapoints)6.000000e-09
GCST90002405_409Reticulocyte count3.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004327electrocardiography
EFO:0007986reticulocyte count

MeSH disease descriptors (1)

DescriptorNameTree numbers
C567743Epilepsy, Benign Neonatal, 1, And-Or Myokymia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects expression5
Arsenicaffects methylation, increases abundance, increases expression2
GSK-J4increases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
sodium arsenatedecreases expression1
trichostatin Adecreases expression1
sodium arseniteincreases abundance, increases expression1
coumarinaffects phosphorylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
jinfukangaffects cotreatment, decreases expression1
Vorinostatdecreases expression1
Benzeneincreases expression1
Benzo(a)pyreneaffects methylation1
Carbamazepineaffects expression1
Cisplatinaffects cotreatment, decreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Doxorubicindecreases expression1
Methyl Methanesulfonateincreases expression1
Smokedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Cyclosporineincreases expression1
Aflatoxin B1decreases methylation1

Clinical trials (associated diseases)

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