ZNF395

gene
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Also known as PRF-1HDBP2PBFDKFZp434K1210

Summary

ZNF395 (zinc finger protein 395, HGNC:18737) is a protein-coding gene on chromosome 8p21.1, encoding Zinc finger protein 395 (Q9H8N7). Plays a role in papillomavirus genes transcription.

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol and nuclear speck.

Source: NCBI Gene 55893 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 82 total
  • Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
  • MANE Select transcript: NM_018660

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18737
Approved symbolZNF395
Namezinc finger protein 395
Location8p21.1
Locus typegene with protein product
StatusApproved
AliasesPRF-1, HDBP2, PBF, DKFZp434K1210
Ensembl geneENSG00000186918
Ensembl biotypeprotein_coding
OMIM609494
Entrez55893

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 36 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000344423, ENST00000517372, ENST00000517459, ENST00000519730, ENST00000520290, ENST00000520535, ENST00000521185, ENST00000521912, ENST00000522795, ENST00000523095, ENST00000523202, ENST00000887379, ENST00000887380, ENST00000887381, ENST00000887382, ENST00000887383, ENST00000887384, ENST00000887385, ENST00000887386, ENST00000887387, ENST00000887388, ENST00000887389, ENST00000887390, ENST00000887391, ENST00000887392, ENST00000887393, ENST00000887394, ENST00000887395, ENST00000887396, ENST00000887397, ENST00000887398, ENST00000914548, ENST00000942495, ENST00000942496, ENST00000942497, ENST00000942498, ENST00000942499, ENST00000942500

RefSeq mRNA: 1 — MANE Select: NM_018660 NM_018660

CCDS: CCDS6067

Canonical transcript exons

ENST00000344423 — 10 exons

ExonStartEnd
ENSE000014147882834559028348830
ENSE000014209322838639328386460
ENSE000035050292835667028356779
ENSE000035165372835257328352673
ENSE000035435682835317328353408
ENSE000036186112835149528351807
ENSE000036410162835959228359824
ENSE000036533682835006428350156
ENSE000036764922836088528361182
ENSE000036837752834912528349228

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 96.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9241 / max 128.3385, expressed in 1619 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
925274.55931424
925311.58321034
925290.2951136
925260.2729136
925280.197567
925320.01616

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
nippleUBERON:000203096.02gold quality
parietal pleuraUBERON:000240095.15gold quality
tendon of biceps brachiiUBERON:000818895.10gold quality
secondary oocyteCL:000065594.78gold quality
tongue squamous epitheliumUBERON:000691994.77gold quality
germinal epithelium of ovaryUBERON:000130494.63gold quality
left ovaryUBERON:000211994.48gold quality
mucosa of stomachUBERON:000119994.26gold quality
pericardiumUBERON:000240794.25gold quality
cartilage tissueUBERON:000241894.06gold quality
ovaryUBERON:000099294.05gold quality
tonsilUBERON:000237294.01gold quality
esophagus squamous epitheliumUBERON:000692093.99gold quality
tibiaUBERON:000097993.96gold quality
right ovaryUBERON:000211893.90gold quality
palpebral conjunctivaUBERON:000181293.82gold quality
tibial arteryUBERON:000761093.81gold quality
popliteal arteryUBERON:000225093.80gold quality
parotid glandUBERON:000183193.78gold quality
upper leg skinUBERON:000426293.71gold quality
body of pancreasUBERON:000115093.62gold quality
saphenous veinUBERON:000731893.62gold quality
cervix squamous epitheliumUBERON:000692293.58gold quality
squamous epitheliumUBERON:000691493.52gold quality
epithelium of esophagusUBERON:000197693.36gold quality
ventricular zoneUBERON:000305393.27gold quality
sural nerveUBERON:001548893.25gold quality
esophagus mucosaUBERON:000246993.18gold quality
skin of legUBERON:000151193.10gold quality
zone of skinUBERON:000001493.05gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

8 targets.

TargetRegulation
HTT
IFIT1
PRF1
SAP30
SLC16A2
SLC5A5
SUPT7L
TP53

JASPAR motifs

MotifNameFamily
MA2566.1ZNF395More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:14625278

miRNA regulators (miRDB)

179 targeting ZNF395, 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-3163100.0077.238605
HSA-MIR-9-5P100.0072.282361
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-5692A100.0074.406850
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4692100.0067.322066
HSA-MIR-607799.9968.042299
HSA-MIR-451499.9967.101870
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548N99.9871.944170
HSA-MIR-314899.9775.066478
HSA-MIR-365899.9673.874379
HSA-MIR-426799.9666.532368
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502

Literature-anchored findings (GeneRIF, showing 12)

  • HDBP1 and HDBP2 are novel transcription factors shuttling between nucleus and cytoplasm and bind to the specific GCCGGCG, which is an essential cis-element for HD gene expression in neuronal cells (PMID:14625278)
  • PBF is an osteosarcoma-associated antigen recognized by autologous cytotoxic T-lymphocyte clone in the context of HLA-B*5502. (PMID:15289353)
  • PBF is a new cellular factor mediating the effects of PI3K/Akt signaling and 14-3-3 on cell growth (PMID:17531190)
  • PBF binds to SAP30 and represses transcription via recruitment of the HDAC1 co-repressor complex (PMID:17897615)
  • colocalization of PBF and Scythe/BAT3 in the nucleus might be an important factor for survival of osteosarcoma cells. (PMID:19018758)
  • ZNF395 coordinate the transcriptional regulatory pathway with PPARG2, which may be necessary for the genesis of adipocytes. (PMID:23142027)
  • Studies indicate that ZNF395 was strongly expressed in adipocytes, and suggest a role for ZNF395 as a modulator of adipogenesis. (PMID:23760207)
  • IkBalpha kinase (IKK)-signaling is necessary to allow ZNF395 to activate transcription and simultaneously enhances its proteolytic degradation. (PMID:24086395)
  • miR-525-3p promotes liver cancer cell migration and invasion by directly targeting ZNF395. (PMID:24599008)
  • The transcriptional activation of CXCL10 and CXCL11 by ZNF395 was abolished after inhibition of IKK by BMS-345541, which increased the stability of ZNF395. ZNF395 encodes at least two motifs that mediate the enhanced degradation of ZNF395 in response to IKK activation. Thus, IKK is required for ZNF395-mediated activation of transcription and enhances its turn-over to keep the activity of ZNF395 low. (PMID:28316371)
  • epigenomic profiling of clear cell renal cell carcinoma (ccRCC) establishes a compendium of somatically altered cis-regulatory elements, uncovering new potential targets including ZNF395. Loss of VHL, a ccRCC signature event, causes pervasive enhancer malfunction, with binding of enhancer-centric HIF2a and recruitment of histone acetyltransferase p300 at preexisting lineage-specific promoter-enhancer complexes (PMID:28893800)
  • Downregulation of ZNF395 Drives Progression of Pancreatic Ductal Adenocarcinoma through Enhancement of Growth Potential. (PMID:33794543)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioznf395bENSDARG00000024195
danio_rerioznf395aENSDARG00000060113
mus_musculusZfp395ENSMUSG00000034522
rattus_norvegicusZfp395ENSRNOG00000014191
drosophila_melanogasterGlut4EFFBGN0267336

Paralogs (2): SLC2A4RG (ENSG00000125520), ZNF704 (ENSG00000164684)

Protein

Protein identifiers

Zinc finger protein 395Q9H8N7 (reviewed: Q9H8N7)

Alternative names: HD-regulating factor 2, Huntington disease gene regulatory region-binding protein 2, Papillomavirus regulatory factor 1, Papillomavirus-binding factor

All UniProt accessions (7): Q9H8N7, A0A0C4DGD9, E5RFV4, E5RG59, E5RGF1, E5RH90, H0YAN1

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in papillomavirus genes transcription.

Subunit / interactions. Interacts with repression-mediating E2 binding site P2 of human papillomavirus type 8 (HPV8).

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Widely expressed.

RefSeq proteins (1): NP_061130* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR031940ZNF395/ZNF704_NDomain
IPR052253CR1/CR2-DNA-binding_regulatorFamily

Pfam: PF15997

UniProt features (20 total): compositionally biased region 5, mutagenesis site 4, modified residue 3, region of interest 3, sequence conflict 2, chain 1, zinc finger region 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H8N7-F159.530.18

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 (3): 248, 376, 449

Mutagenesis-validated functional residues (4):

PositionPhenotype
109no change in subcellular location; when associated with a-113.
113no change in subcellular location; when associated with a-109.
169no shuttle from the nucleus to the cytoplasm; when associated with a-172.
172no shuttle from the nucleus to the cytoplasm; when associated with a-169.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 239 (showing top): TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MITSIADES_RESPONSE_TO_APLIDIN_DN, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP, MODULE_205, chr8p21, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, RIGGI_EWING_SARCOMA_PROGENITOR_DN, MODULE_301, AIYAR_COBRA1_TARGETS_DN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, HOOI_ST7_TARGETS_DN, P300_01

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), cis-regulatory region sequence-specific DNA binding (GO:0000987), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
regulation of DNA-templated transcription2
transcription by RNA polymerase II2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
transcription cis-regulatory region binding2
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
regulation of transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
cis-regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
nucleic acid binding1
transcription regulator activity1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

1766 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF395DYNC1I1O14576547
ZNF395GTF3AQ92664541
ZNF395MINK1Q8N4C8517
ZNF395LCP1P13796497
ZNF395TUBB2AQ13885484
ZNF395PTOV1Q86YD1473
ZNF395GAPDHP00354459
ZNF395ZNF638Q14966446
ZNF395ZNF773Q6PK81437
ZNF395TUBBP05218437
ZNF395PLS3P13797436
ZNF395S100A6P06703433
ZNF395RESTQ13127428
ZNF395ZNF671Q8TAW3426
ZNF395PMLP29590425

IntAct

19 interactions, top by confidence:

ABTypeScore
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
ZNF395YWHAGpsi-mi:“MI:0914”(association)0.530
YWHABZNF395psi-mi:“MI:0914”(association)0.530
YWHAQPLEKHG3psi-mi:“MI:0914”(association)0.480
ZNF395H3-4psi-mi:“MI:0915”(physical association)0.400
ZNF395H2AC4psi-mi:“MI:0915”(physical association)0.400
ZNF395Nfkbiapsi-mi:“MI:0915”(physical association)0.400
ZNF395Ikbkbpsi-mi:“MI:0915”(physical association)0.400
WASLZNF395psi-mi:“MI:0915”(physical association)0.370
YWHABPLEKHG3psi-mi:“MI:0914”(association)0.350
YWHAEDEPDC5psi-mi:“MI:0914”(association)0.350
YWHAGBRAFpsi-mi:“MI:0914”(association)0.350
YWHABFOXO6psi-mi:“MI:0914”(association)0.350
YWHAQFOXO6psi-mi:“MI:0914”(association)0.350
CREB3L2PLEKHG3psi-mi:“MI:0914”(association)0.350

BioGRID (31): ZNF395 (Affinity Capture-MS), ZNF395 (Affinity Capture-MS), ZNF395 (Affinity Capture-MS), ZNF395 (Affinity Capture-Western), ZNF395 (Affinity Capture-Western), ZNF395 (Affinity Capture-MS), ZNF395 (Proximity Label-MS), ZNF395 (Proximity Label-MS), ZNF395 (Affinity Capture-MS), ZNF395 (Proximity Label-MS), ZNF395 (Proximity Label-MS), BTRC (Affinity Capture-MS), ZNF395 (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), YWHAH (Affinity Capture-MS)

ESM2 similar proteins: A0JNG6, A2AKB4, A7YWL5, B0BN13, O35181, O43734, O70142, O70240, O88286, O88566, P0DPB3, P0DPB4, P56975, P70298, P86174, P97303, Q00IB7, Q1LY51, Q2M3C6, Q2T9L4, Q3TY60, Q498S6, Q4V7B1, Q568Z1, Q5HZN9, Q5JTD0, Q5SYB0, Q5U5E5, Q5VT97, Q69ZB8, Q6PG95, Q6UXB0, Q6ZU67, Q76N89, Q80YE4, Q86XD5, Q8BWU3, Q8BZB3, Q8CD60, Q8N365

Diamond homologs: Q1LY51, Q6DFC8, Q6ZNC4, Q9ERQ3, Q9H8N7, Q9NR83

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 17 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
Activation of BAD and translocation to mitochondria6304.5×8e-13
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex6268.7×1e-12
SARS-CoV-1 targets host intracellular signalling and regulatory pathways6268.7×1e-12
Activation of BH3-only proteins6198.6×7e-12
RHO GTPases activate PKNs6126.9×9e-11
Intrinsic Pathway for Apoptosis6117.1×1e-10
SARS-CoV-1-host interactions670.3×3e-09
Apoptosis667.2×3e-09

GO biological processes:

GO termPartnersFoldFDR
protein targeting5122.1×5e-08
intracellular protein localization641.9×2e-07

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — NSCLC.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance68
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2016 predictions. Top by Δscore:

VariantEffectΔscore
8:28348826:CTTTC:Cacceptor_gain1.0000
8:28349227:ACC:Aacceptor_loss1.0000
8:28349234:C:CTacceptor_gain1.0000
8:28351739:T:TAdonor_gain1.0000
8:28351807:CCTG:Cacceptor_gain1.0000
8:28352570:TA:Tdonor_loss1.0000
8:28352571:A:Cdonor_loss1.0000
8:28352571:AC:Adonor_gain1.0000
8:28352571:ACC:Adonor_gain1.0000
8:28352572:CC:Cdonor_gain1.0000
8:28352572:CCC:Cdonor_gain1.0000
8:28352669:GAGTT:Gacceptor_gain1.0000
8:28352670:AGTT:Aacceptor_gain1.0000
8:28352671:GTT:Gacceptor_gain1.0000
8:28352672:TT:Tacceptor_gain1.0000
8:28352672:TTCTA:Tacceptor_loss1.0000
8:28352674:C:CAacceptor_loss1.0000
8:28352674:C:CCacceptor_gain1.0000
8:28356787:C:CTacceptor_gain1.0000
8:28359591:CCT:Cdonor_gain1.0000
8:28359820:TAAAC:Tacceptor_gain1.0000
8:28359821:AAAC:Aacceptor_gain1.0000
8:28359822:AAC:Aacceptor_gain1.0000
8:28359823:AC:Aacceptor_gain1.0000
8:28359824:CC:Cacceptor_gain1.0000
8:28359824:CCT:Cacceptor_loss1.0000
8:28359825:C:CAacceptor_loss1.0000
8:28359825:C:CCacceptor_gain1.0000
8:28360946:T:TAdonor_gain1.0000
8:28348827:TTTC:Tacceptor_gain0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000097506 (8:28381360 T>C), RS1000172920 (8:28359133 A>C), RS1000261658 (8:28347775 A>G), RS1000273344 (8:28365356 C>T), RS1000283474 (8:28352916 T>C), RS1000405495 (8:28381674 T>C), RS1000460609 (8:28383453 C>A), RS1000466018 (8:28377232 T>C), RS1000536592 (8:28385055 C>G), RS1000561976 (8:28376945 T>C), RS1000603211 (8:28383728 C>A), RS1000693725 (8:28350850 T>G), RS1000723310 (8:28365141 C>T), RS1000748903 (8:28371622 T>C), RS1000836005 (8:28359319 G>A,T)

Disease associations

OMIM: gene MIM:609494 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, decreases methylation, increases expression5
Benzo(a)pyrenedecreases expression, decreases methylation, increases expression4
bisphenol Aaffects expression, affects cotreatment, increases expression2
Estradiolaffects cotreatment, decreases expression, affects expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cyclosporinedecreases expression2
Aflatoxin B1decreases expression2
Particulate Matterincreases expression, decreases expression, increases abundance, affects cotreatment2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
methylmercuric chloridedecreases expression1
propionaldehydedecreases expression1
trichostatin Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
3,4,5,3’,4’-pentachlorobiphenylincreases expression1
ferrous chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
perfluorobutanesulfonic acidincreases expression1
bisphenol Sdecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantincreases methylation1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Carbamazepineaffects expression1
Coumestroldecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_HA02K562 eGFP-ZNF395Cancer cell lineFemale

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.