ZNF444

gene
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Also known as ZSCAN17FLJ11137EZF2

Summary

ZNF444 (zinc finger protein 444, HGNC:16052) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 444 (Q8N0Y2). Transcriptional regulator.

This gene encodes a zinc finger protein which activates transcription of a scavenger receptor gene involved in the degradation of acetylated low density lipoprotein (Ac-LDL) (PMID: 11978792). This gene is located in a cluster of zinc finger genes on chromosome 19 at q13.4. A pseudogene of this gene is located on chromosome 15. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 55311 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 56 total
  • MANE Select transcript: NM_018337

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16052
Approved symbolZNF444
Namezinc finger protein 444
Location19q13.43
Locus typegene with protein product
StatusApproved
AliasesZSCAN17, FLJ11137, EZF2
Ensembl geneENSG00000167685
Ensembl biotypeprotein_coding
OMIM607874
Entrez55311

Gene structure

Transcript identifiers

Ensembl transcripts: 47 — 43 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000337080, ENST00000586123, ENST00000587195, ENST00000587236, ENST00000587467, ENST00000587664, ENST00000588203, ENST00000588358, ENST00000591564, ENST00000592171, ENST00000592949, ENST00000593100, ENST00000875358, ENST00000875359, ENST00000875360, ENST00000875361, ENST00000875362, ENST00000875363, ENST00000875364, ENST00000875365, ENST00000875366, ENST00000875367, ENST00000875368, ENST00000875369, ENST00000875370, ENST00000875371, ENST00000875372, ENST00000875373, ENST00000875374, ENST00000875375, ENST00000875376, ENST00000875377, ENST00000924374, ENST00000924375, ENST00000924376, ENST00000924377, ENST00000924378, ENST00000924379, ENST00000924380, ENST00000924381, ENST00000924382, ENST00000924383, ENST00000924384, ENST00000969530, ENST00000969531, ENST00000969532, ENST00000969533

RefSeq mRNA: 2 — MANE Select: NM_018337 NM_001253792, NM_018337

CCDS: CCDS12939, CCDS59426

Canonical transcript exons

ENST00000337080 — 5 exons

ExonStartEnd
ENSE000013426845615962456160893
ENSE000014229035614624756146420
ENSE000014236825614128756141357
ENSE000034989855615849456158602
ENSE000036192135614689056147208

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 95.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.3255 / max 66.4794, expressed in 1729 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1776995.55811638
1777021.3987759
1776981.1809788
1777000.9478656
1777010.2399120

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
type B pancreatic cellCL:000016995.19gold quality
olfactory bulbUBERON:000226494.88gold quality
vena cavaUBERON:000408794.57gold quality
right uterine tubeUBERON:000130294.03gold quality
right lobe of liverUBERON:000111493.99gold quality
cerebellar vermisUBERON:000472093.88gold quality
body of pancreasUBERON:000115093.17gold quality
diaphragmUBERON:000110392.17silver quality
cervix squamous epitheliumUBERON:000692292.11gold quality
cingulate cortexUBERON:000302792.08gold quality
anterior cingulate cortexUBERON:000983592.06gold quality
pancreatic ductal cellCL:000207991.92silver quality
fundus of stomachUBERON:000116091.89gold quality
putamenUBERON:000187491.81gold quality
nucleus accumbensUBERON:000188291.77gold quality
amygdalaUBERON:000187691.69gold quality
body of stomachUBERON:000116191.65gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.50gold quality
pituitary glandUBERON:000000791.42gold quality
right frontal lobeUBERON:000281091.40gold quality
adenohypophysisUBERON:000219691.33gold quality
lower esophagus muscularis layerUBERON:003583391.31gold quality
lower esophagusUBERON:001347391.29gold quality
tongue squamous epitheliumUBERON:000691991.25gold quality
esophagogastric junction muscularis propriaUBERON:003584191.03gold quality
muscle layer of sigmoid colonUBERON:003580591.01gold quality
caudate nucleusUBERON:000187390.86gold quality
dorsal motor nucleus of vagus nerveUBERON:000287090.84gold quality
right lobe of thyroid glandUBERON:000111990.55gold quality
Brodmann (1909) area 9UBERON:001354090.52gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.42

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
SCARF1Activation

miRNA regulators (miRDB)

61 targeting ZNF444, 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-12118100.0065.881270
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
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-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4692100.0067.322066
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-76599.8468.242442
HSA-MIR-132199.8465.301811
HSA-MIR-473999.8465.251832
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-556-3P99.7468.751203
HSA-MIR-430699.7270.503630
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-6751-5P99.5664.991145
HSA-MIR-486-3P99.5166.821901

Literature-anchored findings (GeneRIF, showing 2)

  • regulates the human gene encoding the scavenger receptor expressed by endothelial cells (PMID:11978792)
  • t(19;22)(q13;q12) Translocation leading to the novel fusion gene EWSR1-ZNF444 is associated with soft tissue myoepithelial carcinoma. (PMID:19760602)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_rerioplagxENSDARG00000036855
danio_rerioovol1aENSDARG00000076472
danio_rerioplagl2ENSDARG00000076657
danio_rerioovol1bENSDARG00000078256
mus_musculusZfp444ENSMUSG00000044876
rattus_norvegicusZfp444ENSRNOG00000015517
drosophila_melanogasterhbFBGN0001180
drosophila_melanogasterCG12391FBGN0033581
caenorhabditis_elegansWBGENE00001824
caenorhabditis_elegansWBGENE00003033
caenorhabditis_elegansWBGENE00012385

Paralogs (29): ZNF446 (ENSG00000083838), REST (ENSG00000084093), ZNF174 (ENSG00000103343), OVOL3 (ENSG00000105261), PLAGL1 (ENSG00000118495), ZSCAN18 (ENSG00000121413), ZNF576 (ENSG00000124444), OVOL2 (ENSG00000125850), PLAGL2 (ENSG00000126003), ZSCAN5A (ENSG00000131848), ZSCAN29 (ENSG00000140265), ZSCAN32 (ENSG00000140987), ZSCAN1 (ENSG00000152467), ZNF18 (ENSG00000154957), ZKSCAN2 (ENSG00000155592), ZNF496 (ENSG00000162714), ZNF202 (ENSG00000166261), ZNF641 (ENSG00000167528), SCAND1 (ENSG00000171222), ZNF274 (ENSG00000171606), ZNF131 (ENSG00000172262), OVOL1 (ENSG00000172818), ZNF518A (ENSG00000177853), ZNF518B (ENSG00000178163), PLAG1 (ENSG00000181690), ZSCAN5B (ENSG00000197213), ZNF770 (ENSG00000198146), PEG3 (ENSG00000198300), ZSCAN5C (ENSG00000204532)

Protein

Protein identifiers

Zinc finger protein 444Q8N0Y2 (reviewed: Q8N0Y2)

Alternative names: Endothelial zinc finger protein 2, Zinc finger and SCAN domain-containing protein 17

All UniProt accessions (7): Q8N0Y2, K7EJ91, K7EJH4, K7EK55, K7ELZ3, K7EMV5, K7ESL2

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional regulator. Binds to the 5’-flanking critical region of the SCARF1 promoter.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N0Y2-11yes
Q8N0Y2-22

RefSeq proteins (2): NP_001240721, NP_060807* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF02023

UniProt features (20 total): modified residue 4, zinc finger region 4, compositionally biased region 3, region of interest 3, cross-link 2, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N0Y2-F169.090.03

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): 1, 18, 104, 235, 8, 190

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 109 (showing top): CACCAGC_MIR138, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, MODULE_205, BLALOCK_ALZHEIMERS_DISEASE_UP, MODULE_206, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, SANSOM_APC_MYC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, GOCC_NUCLEOLUS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING, GCM_RAB10

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

860 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF444SCARF1Q14162789
ZNF444EWSR1Q01844772
ZNF444PBX1P40424625
ZNF444CLEC7AQ9BXN2586
ZNF444PBX3P40426542
ZNF444SCARB2Q14108502
ZNF444CD36P16671502
ZNF444SCARB1Q8WTV0475
ZNF444NR4A3Q92570461
ZNF444POU5F1P31359450
ZNF444FUSP35637439
ZNF444SMARCB1Q12824373
ZNF444TLR2O60603351
ZNF444TEKQ02763337
ZNF444DUX4L2P0CJ85327

IntAct

38 interactions, top by confidence:

ABTypeScore
PPP2CBCEP43psi-mi:“MI:0914”(association)0.730
P4HA3FAM171A2psi-mi:“MI:0914”(association)0.640
GPR156PLD2psi-mi:“MI:0914”(association)0.640
CHCHD10CLPXpsi-mi:“MI:0914”(association)0.640
VWCEZNF316psi-mi:“MI:0914”(association)0.530
ZSCAN32ZNF197psi-mi:“MI:0914”(association)0.530
ZNF397ZNF197psi-mi:“MI:0914”(association)0.530
PNLIPLAMC1psi-mi:“MI:0914”(association)0.530
ZNF263AHCYL1psi-mi:“MI:0914”(association)0.530
CCDC6LZTS3psi-mi:“MI:0914”(association)0.530
ZNF444SRPK1psi-mi:“MI:0217”(phosphorylation reaction)0.440
AP3B1psi-mi:“MI:0914”(association)0.350
HTRA4PSMD12psi-mi:“MI:0914”(association)0.350
BMI1MEIS3P1psi-mi:“MI:0914”(association)0.350
FBLN5ZNF320psi-mi:“MI:0914”(association)0.350
NOTCH2ZNF320psi-mi:“MI:0914”(association)0.350
LTBP2ZNF320psi-mi:“MI:0914”(association)0.350
LRP3TMEM131Lpsi-mi:“MI:0914”(association)0.350
SHISA3ZNF316psi-mi:“MI:0914”(association)0.350
EFEMP1ZNF316psi-mi:“MI:0914”(association)0.350
ZNF174FAM171A2psi-mi:“MI:0914”(association)0.350
PRM2IPO5psi-mi:“MI:0914”(association)0.350
PTX3POLRMTpsi-mi:“MI:0914”(association)0.350
ZNF232ZNF197psi-mi:“MI:0914”(association)0.350
MZF1ZNF213psi-mi:“MI:0914”(association)0.350
TNFRSF19PLD2psi-mi:“MI:0914”(association)0.350
ZNF263PPP1R12Apsi-mi:“MI:0914”(association)0.350
ZNF444AHCYL1psi-mi:“MI:0914”(association)0.350
RNH1DUSP11psi-mi:“MI:0914”(association)0.350
BCL10VAPBpsi-mi:“MI:0914”(association)0.350

BioGRID (159): ZNF444 (Affinity Capture-MS), ZNF444 (Affinity Capture-MS), ZNF444 (Affinity Capture-MS), ZNF444 (Affinity Capture-MS), CCDC6 (Affinity Capture-MS), STRN4 (Affinity Capture-MS), KLHL15 (Affinity Capture-MS), MIA3 (Affinity Capture-MS), RBM22 (Affinity Capture-MS), YBEY (Affinity Capture-MS), STRN3 (Affinity Capture-MS), ZKSCAN8 (Affinity Capture-MS), ZNF174 (Affinity Capture-MS), ZNF446 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS)

ESM2 similar proteins: A2T7E6, A4D1S0, A6NGW2, B2RU40, C9JH25, C9JTQ0, D4A9R4, F2YMG0, O15533, O43593, O70146, O94761, P03971, P03972, P0CW18, P0DPE3, P27106, P49000, P79295, Q15569, Q17RM4, Q1JPB9, Q28616, Q3UM83, Q4TUC0, Q5M844, Q5R732, Q5TJE4, Q63572, Q6NZ36, Q6PZD2, Q6ZS72, Q6ZV89, Q7RTU9, Q866Y3, Q86YV9, Q8CAI1, Q8N0Y2, Q8N4L8, Q8N729

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance51
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1320 predictions. Top by Δscore:

VariantEffectΔscore
19:56155854:C:Gdonor_gain1.0000
19:56158542:G:GTdonor_gain1.0000
19:56146888:A:AGacceptor_gain0.9900
19:56146889:G:GGacceptor_gain0.9900
19:56146889:GGC:Gacceptor_gain0.9900
19:56147143:GCC:Gdonor_gain0.9900
19:56147207:GG:Gdonor_gain0.9900
19:56147208:GG:Gdonor_gain0.9900
19:56158488:TTTCA:Tacceptor_loss0.9900
19:56158490:TCAG:Tacceptor_loss0.9900
19:56158491:CAGG:Cacceptor_loss0.9900
19:56158492:A:AGacceptor_gain0.9900
19:56158492:A:Cacceptor_loss0.9900
19:56158492:AG:Aacceptor_gain0.9900
19:56158492:AGG:Aacceptor_gain0.9900
19:56158493:G:GGacceptor_gain0.9900
19:56158493:GG:Gacceptor_gain0.9900
19:56158493:GGG:Gacceptor_gain0.9900
19:56158571:TGGA:Tdonor_gain0.9900
19:56158578:G:GTdonor_gain0.9900
19:56158600:TAGG:Tdonor_loss0.9900
19:56158602:GGT:Gdonor_loss0.9900
19:56158603:G:GAdonor_loss0.9900
19:56158604:T:Adonor_loss0.9900
19:56159622:AGCAG:Aacceptor_gain0.9900
19:56159623:GCA:Gacceptor_gain0.9900
19:56159623:GCAGG:Gacceptor_gain0.9900
19:56159624:CAG:Cacceptor_loss0.9900
19:56159625:A:ACacceptor_loss0.9900
19:56159625:A:AGacceptor_gain0.9900

AlphaMissense

2082 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:56159863:T:CF216L1.000
19:56159865:T:AF216L1.000
19:56159865:T:GF216L1.000
19:56159992:T:CF259L1.000
19:56159994:C:AF259L1.000
19:56159994:C:GF259L1.000
19:56160076:T:CF287L1.000
19:56160078:C:AF287L1.000
19:56160078:C:GF287L1.000
19:56159864:T:CF216S0.999
19:56160019:C:AH268N0.999
19:56160019:C:GH268D0.999
19:56160021:C:AH268Q0.999
19:56160021:C:GH268Q0.999
19:56160033:C:AH272Q0.999
19:56160033:C:GH272Q0.999
19:56160077:T:CF287S0.999
19:56160103:C:AH296N0.999
19:56160103:C:GH296D0.999
19:56147114:T:CF68S0.998
19:56159806:C:AH197N0.998
19:56159806:C:GH197D0.998
19:56159863:T:AF216I0.998
19:56159890:C:AH225N0.998
19:56159890:C:GH225D0.998
19:56159993:T:CF259S0.998
19:56160011:T:CL265P0.998
19:56160031:C:GH272D0.998
19:56160049:T:CF278L0.998
19:56160051:T:AF278L0.998

dbSNP variants (sampled 300 via entrez): RS1000017491 (19:56133828 T>A,G), RS1000018935 (19:56160708 TG>T), RS1000155870 (19:56160488 C>G,T), RS1000170673 (19:56131716 T>C), RS1000228577 (19:56152622 G>A), RS1000307036 (19:56159380 C>T), RS1000317050 (19:56156689 C>T), RS1000356894 (19:56141651 A>G), RS1000435056 (19:56159218 T>C), RS1000455297 (19:56142751 G>A), RS1000483096 (19:56154927 G>A,T), RS1000533586 (19:56137873 G>A), RS1000669242 (19:56147266 C>T), RS1000712044 (19:56153271 AGTTT>A), RS1001019325 (19:56132359 T>C)

Disease associations

OMIM: gene MIM:607874 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003253_2Microalbuminuria5.000000e-06
GCST005991_73Platelet count2.000000e-17

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004309platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression2
Acetaminophendecreases expression2
Valproic Aciddecreases expression, decreases methylation2
Cadmium Chlorideincreases expression2
FR900359increases phosphorylation1
di-n-butylphosphoric acidaffects expression1
ICG 001decreases expression1
abrineincreases expression1
eprenetapoptaffects expression, affects reaction1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Arsenicaffects methylation1
Benzo(a)pyrenedecreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Estradioldecreases expression1
Plant Extractsdecreases expression, affects cotreatment1
Smokedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Urethanedecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1

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.