ENC1

gene
On this page

Also known as PIG10ENC-1TP53I10KLHL37

Summary

ENC1 (ectodermal-neural cortex 1, HGNC:3345) is a protein-coding gene on chromosome 5q13.3, encoding Ectoderm-neural cortex protein 1 (O14682). Actin-binding protein involved in the regulation of neuronal process formation and in differentiation of neural crest cells.

This gene encodes a member of the kelch-related family of actin-binding proteins. The encoded protein plays a role in the oxidative stress response as a regulator of the transcription factor Nrf2, and expression of this gene may play a role in malignant transformation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 8507 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 40 total
  • MANE Select transcript: NM_003633

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3345
Approved symbolENC1
Nameectodermal-neural cortex 1
Location5q13.3
Locus typegene with protein product
StatusApproved
AliasesPIG10, ENC-1, TP53I10, KLHL37
Ensembl geneENSG00000171617
Ensembl biotypeprotein_coding
OMIM605173
Entrez8507

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 18 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000302351, ENST00000508331, ENST00000509127, ENST00000509284, ENST00000510316, ENST00000618628, ENST00000651128, ENST00000875692, ENST00000875693, ENST00000875694, ENST00000875695, ENST00000875696, ENST00000875697, ENST00000875698, ENST00000875699, ENST00000875700, ENST00000875701, ENST00000875702, ENST00000928979

RefSeq mRNA: 4 — MANE Select: NM_003633 NM_001256574, NM_001256575, NM_001256576, NM_003633

CCDS: CCDS4021, CCDS58958

Canonical transcript exons

ENST00000302351 — 3 exons

ExonStartEnd
ENSE000011280617462740974629992
ENSE000011716157463468474636498
ENSE000032446497464030774640728

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 99.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.1902 / max 1865.4284, expressed in 1690 samples.

FANTOM5 promoters (19 alternative TSS)

Promoter IDTPM avgSamples expressed
6207830.05811600
6207511.21631568
620771.6111344
620761.0718289
620790.4183115
620810.3049131
620820.252586
620870.242888
620740.177080
620730.161766

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
Brodmann (1909) area 10UBERON:001354199.88gold quality
frontal poleUBERON:000279599.86gold quality
middle temporal gyrusUBERON:000277199.67gold quality
ganglionic eminenceUBERON:000402399.54gold quality
orbitofrontal cortexUBERON:000416799.41gold quality
Brodmann (1909) area 46UBERON:000648399.25gold quality
superior frontal gyrusUBERON:000266199.21gold quality
CA1 field of hippocampusUBERON:000388199.20gold quality
ventricular zoneUBERON:000305399.02gold quality
parietal lobeUBERON:000187298.92gold quality
postcentral gyrusUBERON:000258198.76gold quality
cortical plateUBERON:000534398.35gold quality
Brodmann (1909) area 23UBERON:001355498.32gold quality
entorhinal cortexUBERON:000272898.20gold quality
prefrontal cortexUBERON:000045198.16gold quality
dorsolateral prefrontal cortexUBERON:000983498.13gold quality
frontal lobeUBERON:001652597.92gold quality
frontal cortexUBERON:000187097.91gold quality
neocortexUBERON:000195097.69gold quality
occipital lobeUBERON:000202197.69gold quality
cerebral cortexUBERON:000095697.67gold quality
Brodmann (1909) area 9UBERON:001354097.64gold quality
middle frontal gyrusUBERON:000270297.56gold quality
adult organismUBERON:000702397.52gold quality
primary visual cortexUBERON:000243697.10gold quality
cingulate cortexUBERON:000302796.76gold quality
embryoUBERON:000092296.74gold quality
anterior cingulate cortexUBERON:000983596.74gold quality
temporal lobeUBERON:000187196.64gold quality
Ammon’s hornUBERON:000195496.37gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-HCAD-30yes2192.51
E-HCAD-56yes1174.27
E-GEOD-109979yes1099.45
E-MTAB-8894yes1082.84
E-HCAD-25yes913.48
E-HCAD-5yes807.07
E-MTAB-10018yes173.85
E-HCAD-35yes58.25
E-CURD-114yes10.41
E-ANND-3yes7.09
E-ENAD-27yes6.68

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTNNB1, NFE2L2, TCF4, TCF7L2

miRNA regulators (miRDB)

143 targeting ENC1, 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-513A-5P100.0069.772465
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-5692A100.0074.406850
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-9-5P100.0072.282361
HSA-MIR-4481100.0066.421669
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-453499.9966.581907
HSA-MIR-548P99.9872.253784
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-60799.9773.625593
HSA-MIR-568899.9673.234504
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-185-3P99.9567.011743
HSA-MIR-808299.9567.271170
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-539-5P99.9370.302855
HSA-MIR-338-5P99.9272.342951
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-464899.9167.00710

Literature-anchored findings (GeneRIF, showing 12)

  • results suggest that upregulation of ENC-1 contributes to the development of HCL and provides new information on the possible dysregulation of ENC-1 including expression of a novel antisense gene, ENC-1AS (PMID:15459180)
  • NRP/B enhances oxidative stress responses in breast cancer cells via the Nrf2 pathway, identifying a novel role of nuclear matrix protein(s) in oxidative stress responses. (PMID:17875699)
  • NRP/B mutations impair Nrf2-dependent NQO1 induction in primary brain tumors. (PMID:18981988)
  • ENC1 functions as a negative regulator of Nrf2 through suppressing Nrf2 protein translation. (PMID:19424503)
  • ENC1 interacts with the phosphorylated p62 to impair autophagic degradation of mutant huntingtin protein aggregates. (PMID:26637326)
  • we identified ENC1 and UNC5C as genes with convergent genetic, epigenetic, and transcriptomic evidence supporting a potential role in the dissociation of cognition and neuropathology in an aging population. (PMID:28441426)
  • The low expression of ENC1 was associated with favorable prognosis in ovarian cancer patients. And the knockdown of ENC1 can significantly inhibit ovarian cancer cell proliferation, migration, and invasion. (PMID:30125994)
  • Ectodermal-neural cortex 1 as a novel biomarker predicts poor prognosis and induces metastasis in breast cancer by promoting Wnt/beta-catenin pathway. (PMID:32618411)
  • Ectodermalneural cortex 1 affects the biological function of lung cancer through the MAPK pathway. (PMID:33693958)
  • Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma. (PMID:34362881)
  • The emerging role of ectodermal neural cortex 1 in cancer. (PMID:38177640)
  • Comprehensive pan-cancer analysis reveals ENC1 as a promising prognostic biomarker for tumor microenvironment and therapeutic responses. (PMID:39455818)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioenc1ENSDARG00000035398
mus_musculusEnc1ENSMUSG00000041773
rattus_norvegicusEnc1ENSRNOG00000016541
drosophila_melanogastergprsFBGN0024232

Paralogs (2): KLHL25 (ENSG00000183655), BTBD17 (ENSG00000204347)

Protein

Protein identifiers

Ectoderm-neural cortex protein 1O14682 (reviewed: O14682)

Alternative names: Kelch-like protein 37, Nuclear matrix protein NRP/B, p53-induced gene 10 protein

All UniProt accessions (3): D6R9D7, O14682, Q53XS2

UniProt curated annotations — full annotation on UniProt →

Function. Actin-binding protein involved in the regulation of neuronal process formation and in differentiation of neural crest cells. Down-regulates transcription factor NF2L2/NRF2 by decreasing the rate of protein synthesis and not via a ubiquitin-mediated proteasomal degradation mechanism.

Subunit / interactions. Binds to RB1. Hypophosphorylated RB1 associates with ENC1 during neuronal differentiation, while hyperphosphorylated RB1 associates with ENC1 in undifferentiating cells. Part of a complex that contains CUL3, RBX1 and ENC1. Interacts indirectly with KEAP1.

Subcellular location. Nucleus matrix. Cytoplasm. Cytoskeleton.

Tissue specificity. Detected in fetal brain tissue, moderate expression in fetal heart, lung and kidney. Highly expressed in adult brain, particularly high in the hippocampus and amygdala, and spinal cord. Detectable in adult pancreas. May be down-regulated in neuroblastoma tumors.

Post-translational modifications. Ubiquitinated by E3 ubiquitin ligase complex formed by CUL3 and RBX1 and probably targeted for proteasome-independent degradation. Quinone-induced oxidative stress increases its ubiquitination.

Induction. By p53/TP53.

Isoforms (2)

UniProt IDNamesCanonical?
O14682-11yes
O14682-22

RefSeq proteins (4): NP_001243503, NP_001243504, NP_001243505, NP_003624* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR006652Kelch_1Repeat
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR011705BACKDomain
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR017096BTB-kelch_proteinFamily
IPR030562ENC1_BTB_POZ_domDomain
IPR047097ENC1_BACKDomain

Pfam: PF00651, PF01344, PF07707, PF24681

UniProt features (18 total): sequence conflict 8, repeat 6, chain 1, domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O14682-F188.220.62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 450 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GSE45365_NK_CELL_VS_BCELL_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEUROGENESIS, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, RODRIGUES_NTN1_TARGETS_DN, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION

GO Biological Process (7): nervous system development (GO:0007399), proteasomal ubiquitin-independent protein catabolic process (GO:0010499), positive regulation of neuron projection development (GO:0010976), protein ubiquitination (GO:0016567), negative regulation of translation (GO:0017148), obsolete proteolysis involved in protein catabolic process (GO:0051603), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (2): actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (8): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), nuclear matrix (GO:0016363), Cul3-RING ubiquitin ligase complex (GO:0031463), neuronal cell body (GO:0043025)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
nuclear lumen2
system development1
proteasomal protein catabolic process1
regulation of neuron projection development1
neuron projection development1
positive regulation of cell projection organization1
protein modification by small protein conjugation1
translation1
regulation of translation1
negative regulation of gene expression1
negative regulation of protein metabolic process1
regulation of metabolic process1
primary metabolic process1
cytoskeletal protein binding1
binding1
chromosome1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
intracellular membraneless organelle1
cullin-RING ubiquitin ligase complex1
somatodendritic compartment1
cell body1

Protein interactions and networks

STRING

1008 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ENC1HEXBP07686912
ENC1OGAO60502650
ENC1SNX33Q8WV41642
ENC1PLAGL2Q9UPG8500
ENC1GM2AP17900492
ENC1LARS1Q9P2J5490
ENC1GPR85P60893483
ENC1SQSTM1Q13501476
ENC1RAG1P15918474
ENC1TM9SF4Q92544473
ENC1SOX15P35717456
ENC1BRD4O60885445
ENC1TBR1Q16650437
ENC1RBBP8NLQ8NC74424
ENC1ZIC1Q15915414

IntAct

39 interactions, top by confidence:

ABTypeScore
KLHL25ENC1psi-mi:“MI:0914”(association)0.640
CUL3ENC1psi-mi:“MI:0914”(association)0.640
KLHL9ENC1psi-mi:“MI:0914”(association)0.640
ENC1SQSTM1psi-mi:“MI:0915”(physical association)0.560
ENC1SQSTM1psi-mi:“MI:0403”(colocalization)0.560
HTTENC1psi-mi:“MI:0914”(association)0.540
HTTENC1psi-mi:“MI:0915”(physical association)0.540
ENC1HTTpsi-mi:“MI:0403”(colocalization)0.540
ENC1PLIN5psi-mi:“MI:0914”(association)0.530
CAPN2MYO9Apsi-mi:“MI:0914”(association)0.530
HSP90AB1ENC1psi-mi:“MI:0915”(physical association)0.400
SPG11ENC1psi-mi:“MI:0915”(physical association)0.370
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
CUL3KLHL2psi-mi:“MI:0914”(association)0.350
ENC1CUL1psi-mi:“MI:0914”(association)0.350
FBXL17ENC1psi-mi:“MI:0914”(association)0.350
BACH2ENC1psi-mi:“MI:0914”(association)0.350
ENC1IGKCpsi-mi:“MI:0914”(association)0.350
ACKR3PDE2Apsi-mi:“MI:0914”(association)0.350
ALDH3B1ENC1psi-mi:“MI:0914”(association)0.350
BACH1ENC1psi-mi:“MI:0914”(association)0.350
CD80RIMOC1psi-mi:“MI:0914”(association)0.350
CXCR3RIMOC1psi-mi:“MI:0914”(association)0.350
DNAJA2ENC1psi-mi:“MI:0914”(association)0.350

BioGRID (48): ENC1 (Biochemical Activity), SQSTM1 (Affinity Capture-Western), ENC1 (Affinity Capture-Western), KLHL25 (Affinity Capture-MS), ENC1 (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), PLIN5 (Affinity Capture-MS), ENC1 (Affinity Capture-RNA), ENC1 (Affinity Capture-Western), ENC1 (Affinity Capture-Western), ENC1 (Reconstituted Complex), ENC1 (Affinity Capture-MS), ENC1 (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), PLIN5 (Affinity Capture-MS)

ESM2 similar proteins: A2AAX3, A2AUC9, B3DIV9, D2HEW7, D3ZA50, D3ZZC3, E9QJ30, G3X9X1, O14682, O35709, O60662, Q08BL9, Q0D2A9, Q1LYM6, Q2TBA0, Q2WGJ6, Q3B7M1, Q4KLM4, Q53GT1, Q56A24, Q5EB39, Q5RCQ9, Q5RDY3, Q5RGB8, Q5U504, Q5U575, Q5ZJU2, Q66HD2, Q6DEL7, Q6DFF7, Q6GQU2, Q6NYM1, Q6Q7X9, Q6TFL4, Q6V595, Q8BRG6, Q8BWA5, Q8CA72, Q8IY47, Q8N4N3

Diamond homologs: A0JMG1, A1YEX3, B0WWP2, B3DIV9, B3M9V8, B3NDN0, B4GRJ2, B4HIK1, B4J045, B4L0G9, B4LIG6, B4MXW3, B4PD06, B4QLQ2, B7U179, D3Z8N4, D4A2K4, E0CZ16, E7F6F9, F1LZF0, F1MBP6, O14682, O22286, O35709, O43791, O81432, O95198, P0DMR5, P0DMR6, P24278, P28575, P34568, P58544, P58545, Q08DK3, Q08DS0, Q0D2A9, Q0IHH9, Q0VCW1, Q16RL8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 35 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
Neddylation612.4×5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance33
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

698 predictions. Top by Δscore:

VariantEffectΔscore
5:74637566:TATG:Tdonor_gain1.0000
5:74637567:ATGA:Adonor_gain1.0000
5:74629988:GTGAG:Gacceptor_gain0.9900
5:74629989:TGAG:Tacceptor_gain0.9900
5:74636496:CTC:Cacceptor_gain0.9900
5:74637563:A:ACdonor_gain0.9900
5:74637564:C:CCdonor_gain0.9900
5:74637567:A:ACdonor_gain0.9900
5:74640305:A:ACdonor_gain0.9900
5:74640306:C:CCdonor_gain0.9900
5:74640306:CAG:Cdonor_gain0.9900
5:74629990:GAG:Gacceptor_gain0.9800
5:74629990:GAGC:Gacceptor_loss0.9800
5:74629991:AGCTG:Aacceptor_loss0.9800
5:74629992:GCTG:Gacceptor_loss0.9800
5:74629993:C:CAacceptor_loss0.9800
5:74629993:C:CCacceptor_gain0.9800
5:74629994:T:Aacceptor_loss0.9800
5:74629998:A:ACacceptor_gain0.9800
5:74636497:TCC:Tacceptor_loss0.9800
5:74636499:CTAA:Cacceptor_loss0.9800
5:74636500:T:Aacceptor_loss0.9800
5:74631701:A:Cdonor_gain0.9700
5:74634679:CTTA:Cdonor_loss0.9700
5:74634680:TTAC:Tdonor_loss0.9700
5:74634681:T:TAdonor_loss0.9700
5:74636494:CACTC:Cacceptor_gain0.9700
5:74636499:C:CCacceptor_gain0.9700
5:74640306:CA:Cdonor_gain0.9700
5:74637482:A:Cdonor_gain0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000043316 (5:74630556 C>T), RS1000055772 (5:74634442 A>G), RS1000085521 (5:74641939 A>C), RS1000152309 (5:74628949 C>G,T), RS1000163647 (5:74628505 A>G), RS1000394207 (5:74638351 A>G), RS1001090845 (5:74640844 G>C), RS1001224357 (5:74642304 A>G), RS1001365894 (5:74629295 G>A), RS1001463162 (5:74633218 C>G,T), RS1001584565 (5:74629679 T>C), RS1001634103 (5:74640890 A>G), RS1002246542 (5:74640891 G>C,T), RS1002322744 (5:74629301 A>G), RS1002371634 (5:74627834 C>A)

Disease associations

OMIM: gene MIM:605173 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST003542_148Night sleep phenotypes8.000000e-06
GCST003989_32Chin dimples5.000000e-12
GCST004025_5Systemic juvenile idiopathic arthritis5.000000e-07
GCST004291_3Residual cognition8.000000e-06
GCST006444_15Bone mineral density (hip)5.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0003925cognition
EFO:0022597aging
EFO:0007702hip bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Estradiolaffects expression, affects cotreatment, decreases expression, increases expression5
Valproic Acidaffects expression, decreases expression, decreases methylation, increases expression5
Cyclosporineaffects cotreatment, decreases expression5
bisphenol Aaffects expression, decreases expression4
trichostatin Aaffects methylation, increases expression, affects cotreatment, affects expression4
sodium arseniteaffects methylation, decreases expression, increases abundance, increases expression4
Resveratrolaffects cotreatment, decreases expression, increases expression4
Tretinoindecreases expression, increases expression4
Aflatoxin B1affects expression, increases expression, increases methylation4
Benzo(a)pyreneincreases expression, increases methylation3
Formaldehydedecreases expression, increases expression3
methylmercuric chlorideincreases expression2
Vorinostatdecreases expression, increases expression2
Acetaminophendecreases expression, increases expression2
Doxorubicinincreases expression2
Ethinyl Estradioldecreases expression, affects expression2
Hydrogen Peroxideaffects expression, increases expression2
Lipopolysaccharidesaffects expression, affects cotreatment, decreases expression, affects reaction2
Progesteroneaffects cotreatment, decreases expression2
Silicon Dioxideincreases expression2
Tamoxifenincreases expression, affects expression, affects cotreatment, decreases expression2
Tunicamycindecreases expression2
Raloxifene Hydrochloridedecreases expression, increases expression, affects expression, affects cotreatment2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4increases expression1
3,19-(2-bromobenzylidene)andrographolidedecreases expression, decreases response to substance1
urushioldecreases expression1
triphenyl phosphateaffects expression1
alpha-pinenedecreases expression, increases abundance, affects cotreatment1
pirinixic acidaffects binding, decreases expression, increases activity1

Clinical trials (associated diseases)

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