EPC2

gene
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Also known as DKFZP566F2124

Summary

EPC2 (enhancer of polycomb 2, HGNC:24543) is a protein-coding gene on chromosome 2q23.1, encoding Enhancer of polycomb homolog 2 (Q52LR7). May play a role in transcription or DNA repair. It is a selective cancer dependency (DepMap: 27.2% of cell lines).

Involved in positive regulation of double-strand break repair via homologous recombination and regulation of cell cycle. Part of NuA4 histone acetyltransferase complex and nucleosome.

Source: NCBI Gene 26122 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 103 total — 4 pathogenic, 2 likely-pathogenic
  • Cancer dependency (DepMap): dependent in 27.2% of screened cell lines
  • MANE Select transcript: NM_015630

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24543
Approved symbolEPC2
Nameenhancer of polycomb 2
Location2q23.1
Locus typegene with protein product
StatusApproved
AliasesDKFZP566F2124
Ensembl geneENSG00000135999
Ensembl biotypeprotein_coding
OMIM611000
Entrez26122

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000258484, ENST00000397424, ENST00000409654, ENST00000449013, ENST00000457184, ENST00000491099, ENST00000902236, ENST00000902237

RefSeq mRNA: 1 — MANE Select: NM_015630 NM_015630

CCDS: CCDS46422

Canonical transcript exons

ENST00000258484 — 14 exons

ExonStartEnd
ENSE00001153925148786305148787569
ENSE00001153931148743622148743767
ENSE00001689981148644751148645170
ENSE00001758796148753927148754133
ENSE00003595825148690214148690373
ENSE00004282159148784668148785001
ENSE00004282160148764955148765146
ENSE00004282161148781644148781780
ENSE00004282162148769151148769240
ENSE00004282163148761782148761930
ENSE00004282164148783597148783756
ENSE00004282165148762670148762802
ENSE00004282166148771044148771387
ENSE00004282167148770792148770937

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 95.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.2969 / max 669.3664, expressed in 1811 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
2295722.29691811

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
germinal epithelium of ovaryUBERON:000130495.73gold quality
calcaneal tendonUBERON:000370195.44gold quality
ganglionic eminenceUBERON:000402394.44gold quality
ventricular zoneUBERON:000305393.98gold quality
cortical plateUBERON:000534393.74gold quality
endothelial cellCL:000011593.20silver quality
sural nerveUBERON:001548893.20gold quality
bone marrow cellCL:000209291.63gold quality
tendonUBERON:000004391.37gold quality
corpus callosumUBERON:000233691.19gold quality
amniotic fluidUBERON:000017390.45gold quality
monocyteCL:000057689.98gold quality
ovaryUBERON:000099289.79gold quality
thymusUBERON:000237089.79gold quality
leukocyteCL:000073889.69gold quality
gingival epitheliumUBERON:000194989.68silver quality
left ovaryUBERON:000211989.63gold quality
middle temporal gyrusUBERON:000277189.56gold quality
smooth muscle tissueUBERON:000113589.02gold quality
visceral pleuraUBERON:000240188.99gold quality
parietal pleuraUBERON:000240088.86gold quality
superficial temporal arteryUBERON:000161488.83gold quality
bone marrowUBERON:000237188.77gold quality
right ovaryUBERON:000211888.69gold quality
Brodmann (1909) area 23UBERON:001355488.52gold quality
urethraUBERON:000005788.50gold quality
popliteal arteryUBERON:000225088.36gold quality
pericardiumUBERON:000240788.35gold quality
tibial arteryUBERON:000761088.35gold quality
saphenous veinUBERON:000731888.34gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.44
E-HCAD-5no2.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

177 targeting EPC2, 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-4262100.0073.263931
HSA-MIR-4668-3P100.0068.742635
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-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-3646100.0073.565283
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3924100.0072.092394
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-186-5P99.9970.833707
HSA-MIR-366299.9973.825684
HSA-MIR-548AW99.9972.573559
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-1213699.9872.815713
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 27.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • EPC1 and EPC2 are components of a complex that directly or indirectly serves to prevent MYC accumulation and AML cell apoptosis, thus sustaining oncogenic potential (PMID:24166297)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioepc2ENSDARG00000007485
mus_musculusEpc2ENSMUSG00000069495
rattus_norvegicusEpc2ENSRNOG00000029447
rattus_norvegicusAC142154.1ENSRNOG00000050758
drosophila_melanogasterE(Pc)FBGN0000581
caenorhabditis_elegansWBGENE00007030

Paralogs (1): EPC1 (ENSG00000120616)

Protein

Protein identifiers

Enhancer of polycomb homolog 2Q52LR7 (reviewed: Q52LR7)

Alternative names: EPC-like

All UniProt accessions (5): C9J1X4, E7ETK1, E9PBA8, Q52LR7, H7C0K5

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in transcription or DNA repair.

Subcellular location. Nucleus.

Similarity. Belongs to the enhancer of polycomb family.

RefSeq proteins (1): NP_056445* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009607Enhancer_polycomb_CDomain
IPR019542Enhancer_polycomb-like_NDomain
IPR024943Enhancer_polycombFamily

Pfam: PF06752, PF10513

UniProt features (14 total): cross-link 4, region of interest 3, compositionally biased region 3, modified residue 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q52LR7-F158.350.15

Functional residue map

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

Post-translational modifications (6): 195, 324, 362, 538, 754, 135

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 239 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GOBP_REGULATION_OF_DNA_RECOMBINATION, ACTACCT_MIR196A_MIR196B, GCM_GSPT1, TGCACTT_MIR519C_MIR519B_MIR519A, GCM_ZNF198, GTTAAAG_MIR302B, TGACCTY_ERR1_Q2, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR_VIA_HOMOLOGOUS_RECOMBINATION, CHANDRAN_METASTASIS_DN, GOBP_REGULATION_OF_DNA_REPAIR, ATGTTAA_MIR302C, CTAGGAA_MIR384, CATTTCA_MIR203

GO Biological Process (9): DNA repair (GO:0006281), chromatin organization (GO:0006325), regulation of transcription by RNA polymerase II (GO:0006357), regulation of apoptotic process (GO:0042981), positive regulation of DNA-templated transcription (GO:0045893), regulation of cell cycle (GO:0051726), positive regulation of double-strand break repair via homologous recombination (GO:1905168), regulation of double-strand break repair (GO:2000779), DNA damage response (GO:0006974)

GO Molecular Function (0):

GO Cellular Component (5): nucleosome (GO:0000786), nucleus (GO:0005634), piccolo histone acetyltransferase complex (GO:0032777), NuA4 histone acetyltransferase complex (GO:0035267), histone acetyltransferase complex (GO:0000123)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
chromatin2
DNA metabolic process1
DNA damage response1
cellular component organization1
transcription by RNA polymerase II1
apoptotic process1
regulation of programmed cell death1
DNA-templated transcription1
positive regulation of RNA biosynthetic process1
cell cycle1
regulation of cellular process1
double-strand break repair via homologous recombination1
regulation of double-strand break repair via homologous recombination1
positive regulation of DNA recombination1
positive regulation of double-strand break repair1
regulation of DNA repair1
double-strand break repair1
cellular response to stress1
protein-DNA complex1
intracellular membrane-bounded organelle1
protein-containing complex1
H4/H2A histone acetyltransferase complex1
protein acetyltransferase complex1

Protein interactions and networks

STRING

1442 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EPC2DMAP1Q9NPF5898
EPC2BRD8Q9H0E9860
EPC2MEAF6Q9HAF1838
EPC2EZH2Q15910832
EPC2TRRAPQ9Y4A5788
EPC2ING3Q9NXR8778
EPC2ACTL6AO96019716
EPC2MORF4L1Q9UBU8695
EPC2MRGBPQ9NV56650
EPC2MBTD1Q05BQ5633
EPC2YEATS4O95619618
EPC2EP400Q96L91566
EPC2CAPN14A8MX76557
EPC2RUVBL1P82276551
EPC2KAT5Q92993545

IntAct

117 interactions, top by confidence:

ABTypeScore
RUVBL1ZNHIT1psi-mi:“MI:0914”(association)0.860
MRGBPYEATS4psi-mi:“MI:0914”(association)0.840
RUVBL2ZNHIT1psi-mi:“MI:0914”(association)0.810
YEATS4ZNHIT1psi-mi:“MI:0914”(association)0.790
H2AZ1ZNHIT1psi-mi:“MI:0914”(association)0.770
MED23MED19psi-mi:“MI:2364”(proximity)0.770
TRRAPATXN7psi-mi:“MI:0914”(association)0.740
MBTD1YEATS4psi-mi:“MI:0914”(association)0.730
MORF4L1SIN3Bpsi-mi:“MI:0914”(association)0.730
ACTL6AZNHIT1psi-mi:“MI:0914”(association)0.720
VPS72ZNHIT1psi-mi:“MI:0914”(association)0.690
H2BC1PPM1Gpsi-mi:“MI:0914”(association)0.640
RUVBL2POLR3Apsi-mi:“MI:0914”(association)0.640
RUVBL1POLR3Apsi-mi:“MI:0914”(association)0.640
MORF4L2YEATS4psi-mi:“MI:0914”(association)0.640
FOXR1YEATS4psi-mi:“MI:0914”(association)0.640
KPNA1TCERG1psi-mi:“MI:0914”(association)0.640
EPC2YEATS4psi-mi:“MI:0914”(association)0.640

BioGRID (124): EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Proximity Label-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EPC2 (Affinity Capture-MS)

ESM2 similar proteins: A3LYI0, A5DLJ8, A5JYW9, A8WSQ9, C5DX31, G4NID8, G5ED89, O14174, O74365, P0C5E6, P0CN58, P0CN59, P18480, P22579, P25644, P32257, P34333, P39927, P50875, P52654, Q06337, Q07684, Q09345, Q09750, Q177A7, Q20374, Q23523, Q23590, Q4VYR7, Q52LR7, Q58NQ4, Q5A2B9, Q5W1J5, Q61X54, Q621Z7, Q66JA8, Q6C7K8, Q6CIN8, Q6CMB8, Q6DJR9

Diamond homologs: P0CN58, P0CN59, Q52LR7, Q5AYR3, Q66JA8, Q6CEV5, Q6DJR9, Q8C0I4, Q9UU94, P43572, Q4I5V3, Q4WDF1, Q6CIN8, Q6FLZ0, Q752Q3, Q7S747, Q8C9X6, Q9H2F5, Q5AAG1, Q6BNX0

SIGNOR signaling

1 interactions.

AEffectBMechanism
EPC2“form complex”“NuA4 complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 108 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
HATs acetylate histones1920.4×1e-17
Chromatin organization1314.3×1e-09
Deposition of new CENPA-containing nucleosomes at the centromere612.9×5e-04
Chromatin modifying enzymes1312.7×3e-09
Formation of the beta-catenin:TCF transactivating complex711.4×3e-04
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks59.9×7e-03
mRNA Polyadenylation67.1×8e-03
Processing of Capped Intron-Containing Pre-mRNA66.7×1e-02

GO biological processes:

GO termPartnersFoldFDR
regulation of double-strand break repair1479.8×1e-21
positive regulation of double-strand break repair via homologous recombination1556.3×1e-20
regulation of DNA replication725.1×9e-07
regulation of DNA repair719.0×6e-06
cellular response to UV514.5×1e-03
regulation of apoptotic process1713.9×8e-13
positive regulation of transcription initiation by RNA polymerase II513.3×2e-03
regulation of cell cycle1611.7×6e-11

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic2
Uncertain significance80
Likely benign0
Benign5

Top pathogenic / likely-pathogenic (6)

Variant IDHGVSClassification
150817GRCh38/hg38 2q23.1-23.2(chr2:148440874-149091788)x1Pathogenic
183383NC_000002.10:g.148447496_149377297delPathogenic
395440GRCh37/hg19 2q23.1-23.3(chr2:148842506-152370040)x1Pathogenic
403692Single allelePathogenic
2506556GRCh37/hg19 2q23.1(chr2:149220152-149633312)Likely pathogenic
562615GRCh37/hg19 2q23.1(chr2:148704099-149545055)x3Likely pathogenic

SpliceAI

2368 predictions. Top by Δscore:

VariantEffectΔscore
2:148645159:G:GTdonor_gain1.0000
2:148645162:G:GTdonor_gain1.0000
2:148645167:ATCGG:Adonor_loss1.0000
2:148645168:TCGG:Tdonor_loss1.0000
2:148645171:G:GGdonor_gain1.0000
2:148645172:T:Adonor_loss1.0000
2:148690203:A:AGacceptor_gain1.0000
2:148690205:A:AGacceptor_gain1.0000
2:148690206:T:Gacceptor_gain1.0000
2:148690212:A:AGacceptor_gain1.0000
2:148690212:AG:Aacceptor_gain1.0000
2:148690213:G:Aacceptor_loss1.0000
2:148690213:G:GAacceptor_gain1.0000
2:148690213:GG:Gacceptor_gain1.0000
2:148690213:GGA:Gacceptor_gain1.0000
2:148690213:GGAA:Gacceptor_gain1.0000
2:148690213:GGAAC:Gacceptor_gain1.0000
2:148690336:A:Tdonor_gain1.0000
2:148690369:TCAGC:Tdonor_gain1.0000
2:148690370:CAGC:Cdonor_gain1.0000
2:148690371:AGC:Adonor_gain1.0000
2:148690372:GC:Gdonor_gain1.0000
2:148690372:GCG:Gdonor_gain1.0000
2:148690374:G:GGdonor_gain1.0000
2:148690374:GTAA:Gdonor_loss1.0000
2:148690375:T:TCdonor_loss1.0000
2:148690378:G:GGdonor_gain1.0000
2:148743620:A:AGacceptor_gain1.0000
2:148743621:G:Aacceptor_loss1.0000
2:148743621:G:GAacceptor_gain1.0000

AlphaMissense

5334 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:148645033:T:CF6L1.000
2:148645034:T:CF6S1.000
2:148645034:T:GF6C1.000
2:148645035:C:AF6L1.000
2:148645035:C:GF6L1.000
2:148645036:C:GR7G1.000
2:148645037:G:AR7Q1.000
2:148645049:T:AL11Q1.000
2:148645051:G:CD12H1.000
2:148645067:T:CL17P1.000
2:148645124:G:CR36P1.000
2:148645130:T:AV38E1.000
2:148645139:T:CM41T1.000
2:148645139:T:GM41R1.000
2:148645142:C:AP42H1.000
2:148645145:C:TT43I1.000
2:148645147:G:AG44R1.000
2:148645147:G:CG44R1.000
2:148645147:G:TG44W1.000
2:148645148:G:AG44E1.000
2:148645151:T:AM45K1.000
2:148645151:T:CM45T1.000
2:148645151:T:GM45R1.000
2:148645152:G:AM45I1.000
2:148645152:G:CM45I1.000
2:148645152:G:TM45I1.000
2:148645162:G:AE49K1.000
2:148645164:G:CE49D1.000
2:148645164:G:TE49D1.000
2:148690216:A:CE52D1.000

dbSNP variants (sampled 300 via entrez): RS1000010253 (2:148750373 A>G), RS1000022907 (2:148710093 A>C), RS1000056117 (2:148662009 T>C), RS1000080929 (2:148700934 T>A,G), RS1000100366 (2:148671473 G>T), RS1000100970 (2:148657143 T>G), RS1000122373 (2:148712492 A>G), RS1000122556 (2:148783958 C>T), RS1000125016 (2:148715148 C>G), RS1000159075 (2:148717275 A>G), RS1000181493 (2:148764117 A>G), RS1000184935 (2:148648032 C>T), RS1000207971 (2:148717446 G>T), RS1000275882 (2:148724258 C>G), RS1000292709 (2:148689066 A>T)

Disease associations

OMIM: gene MIM:611000 | disease phenotypes: MIM:156200

GenCC curated gene-disease

Mondo (1): intellectual disability, autosomal dominant 1 (MONDO:0007974)

Orphanet (1): 2q23.1 microdeletion syndrome (Orphanet:228402)

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST000189_10Protein quantitative trait loci4.000000e-06
GCST000900_1Alzheimer’s disease biomarkers1.000000e-06
GCST000900_4Alzheimer’s disease biomarkers1.000000e-06
GCST006397_6Relative amplitude of rest-activity cycles3.000000e-06
GCST006803_46Schizophrenia8.000000e-07
GCST007201_29Schizophrenia8.000000e-09
GCST007272_35Pulse pressure3.000000e-25
GCST007272_39Pulse pressure6.000000e-24
GCST007576_44Chronotype2.000000e-09
GCST007847_107Type 2 diabetes5.000000e-09
GCST009391_1617Metabolite levels9.000000e-06
GCST010118_16Type 2 diabetes1.000000e-09

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004811interleukin-8 measurement
EFO:0004760t-tau measurement
EFO:0004670beta-amyloid 1-42 measurement
EFO:0005763pulse pressure measurement
EFO:0008328chronotype measurement
EFO:0010378phosphatidylcholine 34:4 measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C566947Mental Retardation, Autosomal Dominant 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects expression5
trichostatin Adecreases expression, affects expression, affects cotreatment3
sodium arsenitedecreases expression2
Formaldehydedecreases expression, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
TAK-243decreases sumoylation1
TL8-506affects cotreatment, increases expression1
propionaldehydedecreases expression1
arseniteaffects binding, decreases reaction1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydedecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Leflunomideincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Amiodaroneincreases expression1
Arsenicaffects methylation1
Caffeineaffects phosphorylation1
Dimethyl Sulfoxideincreases expression1
Doxorubicindecreases expression1
Methyl Methanesulfonateincreases expression1
Testosteronedecreases expression1

Clinical trials (associated diseases)

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