ZNF366

gene
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Also known as FLJ39796

Summary

ZNF366 (zinc finger protein 366, HGNC:18316) is a protein-coding gene on chromosome 5q13.1, encoding Zinc finger protein 366 (Q8N895). Has transcriptional repression activity.

Enables nuclear estrogen receptor binding activity and transcription corepressor activity. Involved in negative regulation of intracellular estrogen receptor signaling pathway; negative regulation of transcription by RNA polymerase II; and response to estrogen. Located in nucleoplasm.

Source: NCBI Gene 167465 — RefSeq curated summary.

At a glance

  • GWAS associations: 23
  • Clinical variants (ClinVar): 145 total
  • MANE Select transcript: NM_152625

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18316
Approved symbolZNF366
Namezinc finger protein 366
Location5q13.1
Locus typegene with protein product
StatusApproved
AliasesFLJ39796
Ensembl geneENSG00000178175
Ensembl biotypeprotein_coding
OMIM610159
Entrez167465

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000318442, ENST00000414109, ENST00000514477, ENST00000867840, ENST00000964997

RefSeq mRNA: 1 — MANE Select: NM_152625 NM_152625

CCDS: CCDS4015

Canonical transcript exons

ENST00000318442 — 5 exons

ExonStartEnd
ENSE000012583497244724372447417
ENSE000012583567245640472456595
ENSE000012583777243990372444291
ENSE000012583867246016572461510
ENSE000020280897250725172507410

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 76.26.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3596 / max 165.5908, expressed in 371 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
620402.3248369
2035850.03489

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548876.26gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047375.58gold quality
colonic epitheliumUBERON:000039773.42gold quality
smooth muscle tissueUBERON:000113573.06gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099172.93gold quality
apex of heartUBERON:000209871.98gold quality
omental fat padUBERON:001041470.68gold quality
peritoneumUBERON:000235870.60gold quality
vermiform appendixUBERON:000115470.39gold quality
heart left ventricleUBERON:000208469.88gold quality
adipose tissue of abdominal regionUBERON:000780869.09gold quality
cardiac ventricleUBERON:000208268.94gold quality
lymph nodeUBERON:000002968.05gold quality
subcutaneous adipose tissueUBERON:000219068.02gold quality
muscle of legUBERON:000138367.88gold quality
monocyteCL:000057667.74gold quality
leukocyteCL:000073867.41gold quality
gall bladderUBERON:000211067.29gold quality
hindlimb stylopod muscleUBERON:000425267.26gold quality
gastrocnemiusUBERON:000138867.16gold quality
body of uterusUBERON:000985366.90gold quality
heartUBERON:000094866.62gold quality
right atrium auricular regionUBERON:000663166.41gold quality
upper lobe of left lungUBERON:000895265.53gold quality
cardiac atriumUBERON:000208165.34gold quality
right lungUBERON:000216765.33gold quality
right lobe of thyroid glandUBERON:000111964.91gold quality
calcaneal tendonUBERON:000370164.75gold quality
upper lobe of lungUBERON:000894864.63gold quality
caecumUBERON:000115363.89gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-9801yes8.36
E-MTAB-6678yes7.54
E-ANND-3yes4.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

135 targeting ZNF366, 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-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4455100.0065.481587
HSA-MIR-186-5P99.9970.833707
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-314899.9775.066478
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-590-3P99.9674.346478
HSA-MIR-568899.9673.234504
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-495-3P99.9672.814197
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-767-5P99.9570.85993
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-335-3P99.9373.364958
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-498-3P99.9171.271114
HSA-MIR-130599.9171.433443
HSA-MIR-806399.9169.763146

Literature-anchored findings (GeneRIF, showing 10)

  • DC-SCRIPT consists of a proline-rich region, 11 C2H2-type zinc fingers, and an acidic region. Localization studies reveal that DC-SCRIPT resides in the nucleus and that nuclear localization is critically dependent on the zinc fingers. (DC-SCRIPT) (PMID:16393996)
  • Results indicate that ZNF366 may play an important role in regulating the expression of genes in response to estrogen. (PMID:17085477)
  • Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study (PMID:19525478)
  • DC-SCRIPT can act as a tumor suppressor in breast cancer development.[review] (PMID:20478364)
  • study provides a higher level of evidence that DC-SCRIPT is indeed an independent, pure prognostic, factor for primary breast cancer and shows that DC-SCRIPT mRNA expression is most informative for either ESR1-positive and/or ESR2-low pT1 tumors (PMID:21122099)
  • DC-SCRIPT is a key regulator of androgen receptor and vitamin d receptor that play an opposite role in prostate cancer etiology and loss of DC-SCRIPT may be involved in the onset of prostate cancer. (PMID:22473304)
  • DC-SCRIPT has a primary role in the regulation of interleukin (IL)-10 production by monocytes. (PMID:22615205)
  • DC-SCRIPT serves an important role in regulating GR function in DCs, corepressing GR-dependent upregulation of the tolerance-inducing transcription factor GILZ. (PMID:23440419)
  • these data show that DC-SCRIPT acts as a novel regulator of CDKN2B and induces cell cycle arrest in ESR1-positive breast cancer cells. (PMID:25663546)
  • These data demonstrate that besides nuclear receptor regulation, DC-SCRIPT also modulates activation of NF-kappaBp65 after TLR activation in human DCs. (PMID:26170389)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioznf366ENSDARG00000040116
mus_musculusZfp366ENSMUSG00000050919
rattus_norvegicusZfp366ENSRNOG00000017249
drosophila_melanogasterCG11902FBGN0028647
drosophila_melanogasterCG11696FBGN0030314
drosophila_melanogasterCG10631FBGN0032817

Paralogs (7): ZNF671 (ENSG00000083814), ZNF710 (ENSG00000140548), ZNF212 (ENSG00000170260), ZNF662 (ENSG00000182983), ZNF667 (ENSG00000198046), ZNF783 (ENSG00000204946), ZNF865 (ENSG00000261221)

Protein

Protein identifiers

Zinc finger protein 366Q8N895 (reviewed: Q8N895)

Alternative names: Dendritic cell-specific transcript protein

All UniProt accessions (2): Q8N895, F8W732

UniProt curated annotations — full annotation on UniProt →

Function. Has transcriptional repression activity. Acts as a corepressor of ESR1; the function seems to involve CTBP1 and histone deacetylases.

Subunit / interactions. Interacts with ESR1 and NRIP1. Interacts (via PXDLS motif) with CTBP1.

Subcellular location. Nucleus.

Tissue specificity. Expressed in immature and mature dendritic cells (DCs). Not detected in other blood cell types.

RefSeq proteins (1): NP_689838* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050636C2H2-ZF_domain-containingFamily

Pfam: PF00096, PF13912

UniProt features (25 total): zinc finger region 11, mutagenesis site 6, region of interest 4, chain 1, short sequence motif 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N895-F157.540.15

Functional residue map

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

Mutagenesis-validated functional residues (6):

PositionPhenotype
590abolishes interaction with ctbp1 and in part relieves transcription repression; when associated with a-592.
592abolishes interaction with ctbp1 and in part relieves transcription repression; when associated with a-590.
593abolishes interaction with ctbp1. abolishes interaction with ctbp1; when associated with a-648.
645decreases interaction with ctbp1; when associated with a-647.
647decreases interaction with ctbp1; when associated with a-645.
648no effect on interaction with ctbp1. abolishes interaction with ctbp1; when associated with a-593.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_ESTROGEN_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_INTRACELLULAR_STEROID_HORMONE_RECEPTOR_SIGNALING_PATHWAY, FOXO4_01, LHX3_01, FOXO1_01, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_HORMONE_MEDIATED_SIGNALING_PATHWAY, CCANNAGRKGGC_UNKNOWN, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_STEROID_HORMONE_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_INTRACELLULAR_ESTROGEN_RECEPTOR_SIGNALING_PATHWAY, GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS, GOBP_RESPONSE_TO_ESTROGEN, OCT1_06

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147), response to estrogen (GO:0043627)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity (GO:0003700), transcription corepressor activity (GO:0003714), zinc ion binding (GO:0008270), nuclear estrogen receptor binding (GO:0030331), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of DNA-templated transcription2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
estrogen receptor signaling pathway1
negative regulation of intracellular steroid hormone receptor signaling pathway1
regulation of intracellular estrogen receptor signaling pathway1
response to hormone1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
cis-regulatory region sequence-specific DNA binding1
transcription cis-regulatory region binding1
regulation of DNA-templated transcription1
transcription regulator activity1
transcription coregulator activity1
transition metal ion binding1
nuclear receptor binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

806 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF366CTBP1Q13363775
ZNF366TMEM171Q8WVE6537
ZNF366OR5M8Q8NGP6474
ZNF366UBOX5O94941458
ZNF366ZNF654Q8IZM8456
ZNF366LZTS3O60299448
ZNF366NRIP1P48552441
ZNF366TMEM174Q8WUU8430
ZNF366THNSL2Q86YJ6428
ZNF366DDRGK1Q96HY6426
ZNF366BTBD9Q96Q07426
ZNF366DCLK3Q9C098415
ZNF366TADA3O75528400
ZNF366HLXQ14774393
ZNF366SMYD1Q8NB12393

IntAct

127 interactions, top by confidence:

ABTypeScore
ZNF366CEP70psi-mi:“MI:0915”(physical association)0.830
CEP70ZNF366psi-mi:“MI:0915”(physical association)0.830
PSMA3ZNF366psi-mi:“MI:0915”(physical association)0.740
ESR1ZNF366psi-mi:“MI:0915”(physical association)0.630
ZNF366ESR1psi-mi:“MI:0915”(physical association)0.630
ESR1ZNF366psi-mi:“MI:0407”(direct interaction)0.630
CTBP1ZNF366psi-mi:“MI:0407”(direct interaction)0.630
CTBP1ZNF366psi-mi:“MI:0915”(physical association)0.630
ZNF366CTBP1psi-mi:“MI:0915”(physical association)0.630
ZNF366ESR1psi-mi:“MI:0407”(direct interaction)0.630
TARDBPZNF366psi-mi:“MI:0915”(physical association)0.610
ZNF366CARD10psi-mi:“MI:0915”(physical association)0.560
ZNF366AKAP8Lpsi-mi:“MI:0915”(physical association)0.560
ZNF366A2Mpsi-mi:“MI:0915”(physical association)0.560
ZNF366APBB2psi-mi:“MI:0915”(physical association)0.560

BioGRID (9): ZNF366 (Two-hybrid), ZNF366 (Two-hybrid), PSMA3 (Two-hybrid), ZNF366 (Two-hybrid), ZNF366 (Two-hybrid), ZNF366 (Two-hybrid), ZNF366 (Two-hybrid), KLHL15 (Affinity Capture-MS), UBE3A (Affinity Capture-MS)

ESM2 similar proteins: A0JPB4, A0PJY2, A1YPR0, A2A935, A4IFJ6, B0K011, B7ZRM8, B7ZRU9, O13089, O15090, O57415, O75626, P14404, P41182, P41183, P86413, Q03112, Q03267, Q05516, Q08DS3, Q0VDQ9, Q13422, Q15911, Q5XJQ7, Q60636, Q61329, Q62255, Q66JF8, Q6DBW0, Q6NS86, Q86UP3, Q86V15, Q8C208, Q8I7Z8, Q8K083, Q8N895, Q8TAX0, Q8VCZ7, Q8VDL9, Q90277

Diamond homologs: Q3U288, Q6NS86, Q8N1W2, Q8N895

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance131
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1306 predictions. Top by Δscore:

VariantEffectΔscore
5:72447239:TTACC:Tdonor_loss1.0000
5:72447240:TACCT:Tdonor_loss1.0000
5:72447241:ACCTT:Adonor_loss1.0000
5:72447242:CCTT:Cdonor_loss1.0000
5:72447413:CAAAG:Cacceptor_gain1.0000
5:72447416:AG:Aacceptor_gain1.0000
5:72447417:GC:Gacceptor_loss1.0000
5:72447418:C:CAacceptor_loss1.0000
5:72444291:CCTG:Cacceptor_loss0.9900
5:72444292:C:CCacceptor_gain0.9900
5:72444292:CTGCA:Cacceptor_loss0.9900
5:72444293:T:Cacceptor_loss0.9900
5:72447414:AAAG:Aacceptor_gain0.9900
5:72447415:AAG:Aacceptor_gain0.9900
5:72447418:C:CCacceptor_gain0.9900
5:72447421:T:Cacceptor_gain0.9900
5:72447421:T:TCacceptor_gain0.9900
5:72448034:C:CTacceptor_gain0.9900
5:72448035:A:Tacceptor_gain0.9900
5:72448038:C:CTacceptor_gain0.9900
5:72456399:CCCA:Cdonor_loss0.9900
5:72456400:CCA:Cdonor_loss0.9900
5:72456401:CAC:Cdonor_loss0.9900
5:72456402:A:Cdonor_loss0.9900
5:72456421:T:TAdonor_gain0.9900
5:72456421:TC:Tdonor_gain0.9900
5:72456592:CACC:Cacceptor_gain0.9900
5:72456594:CC:Cacceptor_gain0.9900
5:72456595:CC:Cacceptor_gain0.9900
5:72456595:CCTG:Cacceptor_loss0.9900

AlphaMissense

4975 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:72447289:G:CH551Q1.000
5:72447289:G:TH551Q1.000
5:72447291:G:CH551D1.000
5:72447299:A:GL548P1.000
5:72447301:G:CN547K1.000
5:72447301:G:TN547K1.000
5:72447305:C:TG546E1.000
5:72447306:C:GG546R1.000
5:72447306:C:TG546R1.000
5:72447311:A:GL544P1.000
5:72447316:G:CF542L1.000
5:72447316:G:TF542L1.000
5:72447317:A:GF542S1.000
5:72447318:A:GF542L1.000
5:72447328:G:CC538W1.000
5:72447330:A:GC538R1.000
5:72447337:G:CC535W1.000
5:72447339:A:GC535R1.000
5:72447343:G:CF533L1.000
5:72447343:G:TF533L1.000
5:72447345:A:GF533L1.000
5:72447361:G:CH527Q1.000
5:72447361:G:TH527Q1.000
5:72447363:G:CH527D1.000
5:72447365:A:GL526P1.000
5:72447373:G:CH523Q1.000
5:72447373:G:TH523Q1.000
5:72447374:T:CH523R1.000
5:72447375:G:CH523D1.000
5:72447375:G:TH523N1.000

dbSNP variants (sampled 300 via entrez): RS1000032618 (5:72502034 A>C,G), RS1000051475 (5:72459258 C>G), RS1000084919 (5:72466143 T>A), RS1000118851 (5:72503384 T>C), RS1000173744 (5:72462946 T>A), RS1000180850 (5:72504348 C>G), RS1000256759 (5:72465021 G>A), RS1000279346 (5:72492005 G>A), RS1000468800 (5:72442141 C>T), RS1000507729 (5:72461910 C>A,T), RS1000518171 (5:72457669 T>C), RS1000623866 (5:72461480 T>C), RS1000671216 (5:72508804 T>G), RS1000751351 (5:72490064 G>A), RS1000785411 (5:72509077 C>A,G,T)

Disease associations

OMIM: gene MIM:610159 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

23 associations (top):

StudyTraitp-value
GCST000101_10Hip geometry6.000000e-07
GCST003654_8Bone mineral density (Ward’s triangle area)2.000000e-06
GCST004625_13Monocyte count4.000000e-10
GCST005580_261Intraocular pressure2.000000e-10
GCST005580_84Intraocular pressure3.000000e-11
GCST006291_97Spherical equivalent or myopia (age of diagnosis)7.000000e-09
GCST006979_105Heel bone mineral density5.000000e-10
GCST007843_8Rheumatoid arthritis3.000000e-10
GCST007995_22Asthma (childhood onset)5.000000e-08
GCST008508_1Stress sensitivity (neuroticism score x major depressive disorder status interaction)3.000000e-06
GCST010002_30Refractive error1.000000e-12
GCST010243_1Apolipoprotein B levels4.000000e-15
GCST010245_109LDL cholesterol levels1.000000e-13
GCST90002389_205Lymphocyte percentage of white cells5.000000e-17
GCST90002389_206Lymphocyte percentage of white cells9.000000e-14
GCST90002393_151Monocyte count8.000000e-14
GCST90002393_152Monocyte count5.000000e-09
GCST90002398_468Neutrophil count1.000000e-24
GCST90002398_469Neutrophil count9.000000e-12
GCST90002399_393Neutrophil percentage of white cells2.000000e-21
GCST90002407_459White blood cell count4.000000e-28
GCST90013406_140Liver enzyme levels (alkaline phosphatase)3.000000e-14
GCST90020029_1263Waist circumference adjusted for body mass index6.000000e-09

EFO canonical traits (14, from GWAS)

EFO IDTrait name
EFO:0004685hip geometry
EFO:0007785femoral neck bone mineral density
EFO:0005091monocyte count
EFO:0004695intraocular pressure measurement
EFO:0004847age at onset
EFO:0009270heel bone mineral density
EFO:0007660neuroticism measurement
EFO:0004615apolipoprotein B measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0007993lymphocyte percentage of leukocytes
EFO:0004833neutrophil count
EFO:0007990neutrophil percentage of leukocytes
EFO:0004533alkaline phosphatase measurement
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

ChemicalActions (top 5)PubMed papers
GW 1929increases reaction, affects binding, increases activity1
bisphenol Sincreases methylation1
Troglitazoneincreases activity, increases reaction, affects binding1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation1
Estradioldecreases reaction, increases activity1
Progesteronedecreases reaction, increases activity1
Promegestonedecreases reaction, increases activity1
Tobacco Smoke Pollutionincreases expression1
Tretinoinaffects binding, increases activity, increases reaction1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_XW38HEK293 eGFP-ZNF366Transformed cell lineFemale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): refractive error