ZNF589

gene
On this page

Also known as SZF1

Summary

ZNF589 (zinc finger protein 589, HGNC:16747) is a protein-coding gene on chromosome 3p21.31, encoding Zinc finger protein 589 (Q86UQ0). May play a role in hematopoietic stem/progenitor cell differentiation.

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleoplasm.

Source: NCBI Gene 51385 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC)
  • GWAS associations: 7
  • Clinical variants (ClinVar): 54 total
  • MANE Select transcript: NM_016089

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16747
Approved symbolZNF589
Namezinc finger protein 589
Location3p21.31
Locus typegene with protein product
StatusApproved
AliasesSZF1
Ensembl geneENSG00000164048
Ensembl biotypeprotein_coding
OMIM616702
Entrez51385

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000354698, ENST00000412564, ENST00000427617, ENST00000440261, ENST00000448461, ENST00000454212, ENST00000457782, ENST00000929429

RefSeq mRNA: 1 — MANE Select: NM_016089 NM_016089

CCDS: CCDS43085

Canonical transcript exons

ENST00000354698 — 4 exons

ExonStartEnd
ENSE000014243094826791548270990
ENSE000016587294824762548247677
ENSE000035928084826081348260939
ENSE000038441294824110448241214

Expression profiles

Bgee: expression breadth ubiquitous, 219 present calls, max score 96.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.4584 / max 185.4348, expressed in 1695 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
365708.38931433
365693.10131184
365710.9678457

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233696.35gold quality
spleenUBERON:000210687.95gold quality
granulocyteCL:000009487.39gold quality
cortical plateUBERON:000534387.15gold quality
right lobe of thyroid glandUBERON:000111987.07gold quality
lower esophagus mucosaUBERON:003583486.80gold quality
cerebellar hemisphereUBERON:000224586.77gold quality
ganglionic eminenceUBERON:000402386.64gold quality
cerebellar cortexUBERON:000212986.57gold quality
right hemisphere of cerebellumUBERON:001489086.44gold quality
left lobe of thyroid glandUBERON:000112086.25gold quality
thyroid glandUBERON:000204685.32gold quality
ventricular zoneUBERON:000305385.20gold quality
monocyteCL:000057685.12gold quality
mononuclear cellCL:000084285.09gold quality
cerebellumUBERON:000203784.86gold quality
leukocyteCL:000073884.84gold quality
prostate glandUBERON:000236784.13gold quality
small intestine Peyer’s patchUBERON:000345483.92gold quality
right ovaryUBERON:000211883.74gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.61gold quality
left ovaryUBERON:000211983.22gold quality
right lungUBERON:000216783.10gold quality
right adrenal gland cortexUBERON:003582783.05gold quality
right adrenal glandUBERON:000123382.86gold quality
left uterine tubeUBERON:000130382.34gold quality
mucosa of stomachUBERON:000119982.18gold quality
lymph nodeUBERON:000002981.91gold quality
skin of legUBERON:000151181.90gold quality
left adrenal glandUBERON:000123481.77gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.65

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

84 targeting ZNF589, 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-6867-5P100.0082.213464
HSA-MIR-574-5P100.0066.01989
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-186-5P99.9970.833707
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-627-3P99.9071.423316
HSA-MIR-449399.9066.48977
HSA-MIR-797899.8666.90856
HSA-MIR-629-3P99.8567.991875
HSA-MIR-76599.8468.242442
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-197699.7465.481127
HSA-MIR-182599.7268.111089
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-320299.6667.702737
HSA-MIR-450299.6566.991021
HSA-MIR-561-3P99.6470.903647
HSA-MIR-29899.6367.561916
HSA-MIR-397599.6265.97697
HSA-MIR-612699.6268.09996
HSA-MIR-6733-3P99.5467.801281
HSA-MIR-199A-5P99.5169.711107

Literature-anchored findings (GeneRIF, showing 2)

  • The stem cell zinc finger 1 (SZF1)/ZNF589 protein has a human-specific evolutionary nucleotide DNA change and acts as a regulator of cell viability in the hematopoietic system (PMID:26738774)
  • A heterochromatin inducing protein differentially recognizes self versus foreign genomes. (PMID:33730092)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
drosophila_melanogasterCG2712FBGN0024975
drosophila_melanogasterPhsFBGN0036522
drosophila_melanogasterCG3281FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 589Q86UQ0 (reviewed: Q86UQ0)

Alternative names: Stem cell zinc finger protein 1

All UniProt accessions (5): B4DQF9, C9J1J1, C9JGA6, Q86UQ0, F8VZ09

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in hematopoietic stem/progenitor cell differentiation. May play a role as a DNA binding-dependent transcriptional repressor.

Subunit / interactions. Interacts with TRIM28.

Subcellular location. Nucleus.

Tissue specificity. Isoform 2 is widely expressed. Isoform 3 is only expressed in CD34(+) cells.

Domain organisation. The KRAB domain mediates interaction with TRIM28.

Miscellaneous. Probable target of nonsense-mediated mRNA decay. The proposed CDS is dubious. Probable target of nonsense-mediated mRNA decay. The proposed CDS is dubious. Isoform produced through aberrant splice sites.

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

Isoforms (3)

UniProt IDNamesCanonical?
Q86UQ0-11yes
Q86UQ0-22, SZF1-2
Q86UQ0-33, SZF1-1

RefSeq proteins (1): NP_057173* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR048414PDRM9-like_Znf-C2H2Domain

Pfam: PF00096, PF01352, PF21225

UniProt features (14 total): zinc finger region 4, splice variant 3, sequence variant 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UQ0-F154.470.06

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 (1): 190

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 88 (showing top): LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, BENPORATH_ES_1, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WANG_CISPLATIN_RESPONSE_AND_XPC_UP, LU_EZH2_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ZWANG_DOWN_BY_2ND_EGF_PULSE, chr3p21, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, E2F5_TARGET_GENES, KAT5_TARGET_GENES, ZBTB18_TARGET_GENES

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), DNA binding (GO:0003677), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

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

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription cis-regulatory region binding1
negative regulation of transcription by RNA polymerase II1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
transition metal ion binding1
nucleic acid binding1
DNA binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

394 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF589MAN1A1P33908432
ZNF589DNAJC13O75165406
ZNF589CLVS1Q8IUQ0394
ZNF589N4BP2L1Q5TBK1392
ZNF589C1orf167Q5SNV9369
ZNF589TMEM92Q6UXU6358
ZNF589CCT8P50990352
ZNF589ZNF618Q5T7W0348
ZNF589FOXI2Q6ZQN5348
ZNF589C7orf25Q9BPX7348
ZNF589ERC1Q8IUD2337
ZNF589VPS13CQ709C8315
ZNF589CDC42BPAQ5VT25314
ZNF589TIGD4Q8IY51314
ZNF589PTK7Q13308313

IntAct

6 interactions, top by confidence:

ABTypeScore
RBPJNOTCH1psi-mi:“MI:0914”(association)0.910
POLR2EPOLR3Apsi-mi:“MI:0914”(association)0.870
TRIM28ZNF316psi-mi:“MI:0914”(association)0.530
CBX1EXOC5psi-mi:“MI:0914”(association)0.350
MFAP4PEX1psi-mi:“MI:0914”(association)0.350

BioGRID (25): ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-RNA), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-RNA), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS), ZNF589 (Affinity Capture-MS)

ESM2 similar proteins: A0JPK3, A1YFX5, A2RQG7, A7KBS4, F4JUI3, G3X9G7, O49498, P03131, P04605, P04614, P05909, P0C1K0, P11332, P12453, P18098, P24109, P35965, P98182, Q09424, Q0VCB0, Q19203, Q2YDJ5, Q3UZB0, Q567C6, Q5BI31, Q5EXX3, Q5M948, Q62396, Q6AXY9, Q6PB60, Q6PI77, Q71HP2, Q74124, Q7JUR5, Q7Z142, Q7Z2Y5, Q80YD3, Q86UQ0, Q8C0P7, Q8C6P8

Diamond homologs: A0A163UT06, A2AGX3, A6QPM3, B1AUS7, E9Q3T6, O60224, O75626, P0C6Y7, P52736, Q13029, Q16384, Q16385, Q3UZD5, Q5R5M1, Q60636, Q63755, Q6P2A1, Q6PGE4, Q7RTT6, Q80V63, Q86UQ0, Q8BZ97, Q8TD17, Q96EQ9, Q99909, Q9GZV8, Q9NQV5, Q9NQV7, Q9NQV8, Q9NQW5, Q9NQX0, Q9QZP2, Q9UDV7, Q9UKN5, Q9ULD5, A2VDP4, A3KN32, A3KN36, A6NM28, A6QLU5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign3
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1437 predictions. Top by Δscore:

VariantEffectΔscore
3:48247676:TGGTG:Tdonor_loss1.0000
3:48247678:G:Adonor_loss1.0000
3:48247679:T:Gdonor_loss1.0000
3:48260938:GG:Gdonor_gain1.0000
3:48260939:GG:Gdonor_gain1.0000
3:48260940:G:GAdonor_loss1.0000
3:48260940:G:GGdonor_gain1.0000
3:48260941:T:Adonor_loss1.0000
3:48295070:CTCA:Cdonor_loss1.0000
3:48295071:TCA:Tdonor_loss1.0000
3:48295073:A:ACdonor_gain1.0000
3:48295073:A:Tdonor_loss1.0000
3:48295073:AC:Adonor_gain1.0000
3:48295074:C:CAdonor_loss1.0000
3:48295074:C:CCdonor_gain1.0000
3:48295074:CC:Cdonor_gain1.0000
3:48295074:CCCGA:Cdonor_gain1.0000
3:48295231:GCCCG:Gacceptor_gain1.0000
3:48295232:CCCG:Cacceptor_gain1.0000
3:48295232:CCCGC:Cacceptor_gain1.0000
3:48295233:CCG:Cacceptor_gain1.0000
3:48295233:CCGC:Cacceptor_gain1.0000
3:48295234:CG:Cacceptor_gain1.0000
3:48295234:CGC:Cacceptor_gain1.0000
3:48295236:C:CCacceptor_gain1.0000
3:48295236:CT:Cacceptor_loss1.0000
3:48295238:G:Cacceptor_gain1.0000
3:48295238:G:GCacceptor_gain1.0000
3:48295243:C:CTacceptor_gain1.0000
3:48295244:A:Tacceptor_gain1.0000

AlphaMissense

2381 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:48268544:T:CF285L0.999
3:48268546:T:AF285L0.999
3:48268546:T:GF285L0.999
3:48268460:T:CF257L0.998
3:48268462:T:AF257L0.998
3:48268462:T:GF257L0.998
3:48268628:T:CF313L0.998
3:48268630:T:AF313L0.998
3:48268630:T:GF313L0.998
3:48268712:T:CF341L0.998
3:48268714:T:AF341L0.998
3:48268714:T:GF341L0.998
3:48268545:T:CF285S0.996
3:48268629:T:CF313S0.995
3:48268713:T:CF341S0.995
3:48268573:C:AH294Q0.994
3:48268573:C:GH294Q0.994
3:48268461:T:CF257S0.993
3:48268487:C:GH266D0.993
3:48268571:C:GH294D0.993
3:48268731:T:CL347P0.993
3:48268741:C:AH350Q0.993
3:48268741:C:GH350Q0.993
3:48268489:C:AH266Q0.992
3:48268489:C:GH266Q0.992
3:48268491:A:CQ267P0.992
3:48268655:C:GH322D0.992
3:48268657:T:AH322Q0.992
3:48268657:T:GH322Q0.992
3:48268659:A:CQ323P0.992

dbSNP variants (sampled 300 via entrez): RS1000096079 (3:48263703 G>T), RS1000116200 (3:48258818 G>A,C), RS1000166995 (3:48252624 T>TC), RS1000252678 (3:48258266 C>T), RS1000321688 (3:48260490 C>T), RS1000373611 (3:48245618 G>A), RS1000419319 (3:48268163 A>G,T), RS1000437948 (3:48252005 C>T), RS1000454968 (3:48260379 A>G), RS1000536478 (3:48265027 G>A,T), RS1000588375 (3:48259931 A>T), RS1000682493 (3:48253716 A>C), RS1000707299 (3:48246909 C>T), RS1000746465 (3:48252353 G>A), RS1000945818 (3:48247125 C>T)

Disease associations

OMIM: gene MIM:616702 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
complex neurodevelopmental disorderLimitedAutosomal recessive

Mondo (1): complex neurodevelopmental disorder (MONDO:0100038)

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST006231_20Mean arterial pressure1.000000e-06
GCST006941_60Irritable mood1.000000e-09
GCST010698_80Subcortical volume (min-P)3.000000e-24
GCST010699_110Brain morphology (min-P)4.000000e-08
GCST010701_52Cortical surface area (MOSTest)1.000000e-16
GCST010702_36Subcortical volume (MOSTest)1.000000e-10
GCST010703_262Brain morphology (MOSTest)2.000000e-13

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0006340mean arterial pressure
EFO:0009594irritability measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
entinostatincreases expression, affects cotreatment2
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, affects expression2
Cisplatinaffects cotreatment, increases expression, decreases expression2
Ozoneaffects cotreatment, decreases expression, increases abundance, affects expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
FR900359increases phosphorylation1
methylmercuric chloridedecreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
geraniolincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arsenitedecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
azoxystrobindecreases expression1
deguelindecreases expression1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamidedecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment, increases expression1
dorsomorphindecreases expression, affects cotreatment, increases expression1
bisphenol Saffects cotreatment, decreases expression1
jinfukangincreases expression, affects cotreatment1
Vorinostatincreases expression1
Leflunomidedecreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Air Pollutants, Occupationalaffects expression, increases abundance, increases expression1
Antimycin Adecreases expression1
Vehicle Emissionsincreases abundance, increases expression1
Benzo(a)pyrenedecreases expression1
Curcumindecreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Doxorubicinaffects expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_HA05K562 eGFP-ZNF589Cancer cell lineFemale
CVCL_TZ40HAP1 ZNF589 (-) 1Cancer cell lineMale
CVCL_TZ41HAP1 ZNF589 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT06310681Not specifiedCOMPLETEDPilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049Not specifiedNOT_YET_RECRUITINGCognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder