ZNF189

gene
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Summary

ZNF189 (zinc finger protein 189, HGNC:12980) is a protein-coding gene on chromosome 9q31.1, encoding Zinc finger protein 189 (O75820). May be involved in transcriptional regulation.

Kruppel-like zinc finger proteins such as ZNF189 contain a conserved stretch of 7 amino acids that connects a variable number of DNA-binding zinc finger repeats of the cys(2)his(2) (C2H2) type (summarized by Odeberg et al., 1998 [PubMed 9653648]). Approximately 30% of human Kruppel-like zinc finger proteins contain an N-terminal Kruppel-associated box (KRAB) domain. The KRAB domain consists of approximately 75 amino acids that may be subdivided into an A box, which is present in every KRAB domain and is essential for transcriptional repression, and a B box, which is not always present.

Source: NCBI Gene 7743 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 46 total
  • MANE Select transcript: NM_003452

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12980
Approved symbolZNF189
Namezinc finger protein 189
Location9q31.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000136870
Ensembl biotypeprotein_coding
OMIM603132
Entrez7743

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000259395, ENST00000339664, ENST00000374861, ENST00000615466

RefSeq mRNA: 5 — MANE Select: NM_003452 NM_001278231, NM_001278232, NM_001278240, NM_003452, NM_197977

CCDS: CCDS65096, CCDS6754, CCDS6755, CCDS75867

Canonical transcript exons

ENST00000339664 — 3 exons

ExonStartEnd
ENSE00001733032101399884101400010
ENSE00003665756101398851101399189
ENSE00003919561101407929101410654

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 97.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2566 / max 200.9506, expressed in 1712 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
977537.25661712

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
corpus epididymisUBERON:000435997.73gold quality
cauda epididymisUBERON:000436095.95gold quality
caput epididymisUBERON:000435895.40gold quality
adrenal tissueUBERON:001830395.16gold quality
CA1 field of hippocampusUBERON:000388194.92gold quality
inferior vagus X ganglionUBERON:000536394.85gold quality
subthalamic nucleusUBERON:000190694.15gold quality
corpus callosumUBERON:000233694.11gold quality
Brodmann (1909) area 23UBERON:001355493.50gold quality
medulla oblongataUBERON:000189693.48gold quality
superior vestibular nucleusUBERON:000722793.06gold quality
middle temporal gyrusUBERON:000277192.79gold quality
germinal epithelium of ovaryUBERON:000130492.54gold quality
ventral tegmental areaUBERON:000269192.02gold quality
substantia nigra pars reticulataUBERON:000196691.75gold quality
cranial nerve IIUBERON:000094191.64gold quality
body of pancreasUBERON:000115091.52gold quality
ponsUBERON:000098891.49gold quality
spinal cordUBERON:000224091.37gold quality
C1 segment of cervical spinal cordUBERON:000646991.37gold quality
lateral globus pallidusUBERON:000247691.14gold quality
parietal lobeUBERON:000187291.04gold quality
inferior olivary complexUBERON:000212791.01gold quality
heart right ventricleUBERON:000208090.92gold quality
superficial temporal arteryUBERON:000161490.88gold quality
postcentral gyrusUBERON:000258190.76gold quality
mucosa of paranasal sinusUBERON:000503090.59gold quality
dorsal plus ventral thalamusUBERON:000189790.44gold quality
epithelium of nasopharynxUBERON:000195190.43gold quality
gall bladderUBERON:000211090.22gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.62

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
CDKN2A

JASPAR motifs

MotifNameFamily
MA1725.1ZNF189More than 3 adjacent zinc fingers
MA1725.2ZNF189More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

miRNA regulators (miRDB)

71 targeting ZNF189, 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-150-5P99.9966.691976
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-426799.9666.532368
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548AZ-3P99.8270.563549

Literature-anchored findings (GeneRIF, showing 1)

  • Maternal genes FLNB, HIC1 and ZNF189 were strongly associated with risk of clefting. (PMID:20634891)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp189ENSMUSG00000039634
rattus_norvegicusZfp189ENSRNOG00000006972

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 189O75820 (reviewed: O75820)

All UniProt accessions (2): A0A087X0K2, O75820

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

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

Isoforms (4)

UniProt IDNamesCanonical?
O75820-11yes
O75820-22
O75820-33, B2
O75820-44

RefSeq proteins (5): NP_001265160, NP_001265161, NP_001265169, NP_003443, NP_932094 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050826Krueppel_C2H2_ZnFingerFamily

Pfam: PF00096, PF01352

UniProt features (28 total): zinc finger region 16, cross-link 5, splice variant 3, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75820-F174.240.09

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 (5): 67, 88, 160, 434, 452

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 151 (showing top): RRAGTTGT_UNKNOWN, MODULE_493, TTGGGAG_MIR150, AACWWCAANK_UNKNOWN, GTGCCTT_MIR506, CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, TGGNNNNNNKCCAR_UNKNOWN, CAIRO_HEPATOBLASTOMA_UP, ACTWSNACTNY_UNKNOWN, TCCCRNNRTGC_UNKNOWN, STAT1_02, YKACATTT_UNKNOWN, THUM_SYSTOLIC_HEART_FAILURE_DN, MATSUDA_NATURAL_KILLER_DIFFERENTIATION

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of biosynthetic process (GO:0009891), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): 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), DNA binding (GO:0003677), metal ion binding (GO:0046872)

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

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 II2
transcription by RNA polymerase II2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
biosynthetic process1
regulation of biosynthetic process1
positive regulation of metabolic process1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
transition metal ion binding1
nucleic acid binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

548 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF189MRPL50Q8N5N7624
ZNF189TMEM186Q96B77432
ZNF189ZMAT5Q9UDW3432
ZNF189NUDCD1Q96RS6409
ZNF189HMG20AQ9NP66409
ZNF189RSRC2Q7L4I2377
ZNF189ALG9Q9H6U8368
ZNF189ZNF277Q9NRM2339
ZNF189PHF1O43189323
ZNF189TPD52P55327303
ZNF189FOXE1O00358296
ZNF189APPBP2Q92624295
ZNF189ROR2Q01974293
ZNF189STRADBQ9C0K7280
ZNF189ZMYM4Q5VZL5270

IntAct

41 interactions, top by confidence:

ABTypeScore
H1-1RRP8psi-mi:“MI:0914”(association)0.640
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
AURKAZNF189psi-mi:“MI:0915”(physical association)0.370
ZNF189AXIN2psi-mi:“MI:0915”(physical association)0.370
ZNF189BMPR1Apsi-mi:“MI:0915”(physical association)0.370
ZNF189BRAFpsi-mi:“MI:0915”(physical association)0.370
BUB1ZNF189psi-mi:“MI:0915”(physical association)0.370
ZNF189CTNNA1psi-mi:“MI:0915”(physical association)0.370
ZNF189DLC1psi-mi:“MI:0915”(physical association)0.370
ZNF189ERBB2psi-mi:“MI:0915”(physical association)0.370
KRASZNF189psi-mi:“MI:0915”(physical association)0.370
MCCZNF189psi-mi:“MI:0915”(physical association)0.370
PMS2ZNF189psi-mi:“MI:0915”(physical association)0.370
SMAD4ZNF189psi-mi:“MI:0915”(physical association)0.370
SRCZNF189psi-mi:“MI:0915”(physical association)0.370
ZNF189STK11psi-mi:“MI:0915”(physical association)0.370
rl3_rl3l_humanNKRFpsi-mi:“MI:0914”(association)0.350
NOP2ZNF320psi-mi:“MI:0914”(association)0.350
NOTCH2ZNF320psi-mi:“MI:0914”(association)0.350
RPL28GTPBP10psi-mi:“MI:0914”(association)0.350
APOBEC3CGTPBP10psi-mi:“MI:0914”(association)0.350
OASLZNF316psi-mi:“MI:0914”(association)0.350
GLI4ZNF316psi-mi:“MI:0914”(association)0.350
RPS6CCDC85Cpsi-mi:“MI:0914”(association)0.350
NOL12psi-mi:“MI:0914”(association)0.350
SURF6psi-mi:“MI:0914”(association)0.350
FGFBP1ZNF724psi-mi:“MI:0914”(association)0.350
ZNF2APOBEC3DEpsi-mi:“MI:0914”(association)0.350
RPL17psi-mi:“MI:0914”(association)0.350

BioGRID (64): ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-RNA), ZNF189 (Affinity Capture-MS), ZNF189 (Affinity Capture-RNA), ZNF189 (Two-hybrid)

ESM2 similar proteins: A0JNB1, A6QLU5, O75123, O75820, P10076, P10755, P16374, P17031, P17097, P17141, P51814, Q02975, Q08ER8, Q14588, Q14590, Q32KN0, Q3V080, Q4V8A8, Q5CZA5, Q5R4K8, Q5R5Q6, Q5R9S5, Q5RBX0, Q61751, Q6GQR8, Q6P560, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q7Z3V5, Q8BLB0, Q8N141, Q8N184, Q8N823, Q8N8J6, Q8N9F8, Q8TBZ5, Q8TF47, Q96ND8

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 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
Peptide chain elongation724.0×1e-06
Viral mRNA Translation724.0×1e-06
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA723.7×1e-06
Selenocysteine synthesis722.7×1e-06
Eukaryotic Translation Termination722.7×1e-06
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)722.3×1e-06
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA722.3×1e-06
Formation of a pool of free 40S subunits721.2×1e-06

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation725.9×3e-06
rRNA processing822.7×1e-06
translation714.4×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

609 predictions. Top by Δscore:

VariantEffectΔscore
9:101400009:GG:Gdonor_gain1.0000
9:101400010:GG:Gdonor_gain1.0000
9:101399186:GAAG:Gdonor_gain0.9900
9:101399188:AG:Adonor_gain0.9900
9:101399189:GG:Gdonor_gain0.9900
9:101399189:GGTA:Gdonor_loss0.9900
9:101399190:G:GGdonor_gain0.9900
9:101400008:TGGG:Tdonor_loss0.9900
9:101400011:G:Cdonor_loss0.9900
9:101400011:G:GGdonor_gain0.9900
9:101400012:T:TCdonor_loss0.9900
9:101407927:A:AGacceptor_gain0.9900
9:101407928:G:GGacceptor_gain0.9900
9:101407928:GAT:Gacceptor_gain0.9900
9:101399187:AAG:Adonor_gain0.9800
9:101399194:G:GGdonor_gain0.9800
9:101407924:TCCA:Tacceptor_loss0.9800
9:101407925:CCA:Cacceptor_loss0.9800
9:101407926:CA:Cacceptor_loss0.9800
9:101399882:AGG:Aacceptor_gain0.9700
9:101399883:GGG:Gacceptor_gain0.9700
9:101407927:AGAT:Aacceptor_gain0.9700
9:101407928:GATG:Gacceptor_gain0.9700
9:101407928:GATGT:Gacceptor_gain0.9700
9:101399508:T:TAacceptor_gain0.9600
9:101407919:A:AGacceptor_gain0.9600
9:101399193:A:AGdonor_gain0.9500
9:101399882:AG:Aacceptor_gain0.9500
9:101399883:GG:Gacceptor_gain0.9500
9:101399188:AGGT:Adonor_gain0.9400

AlphaMissense

4242 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:101408573:T:CF269L0.998
9:101408575:C:AF269L0.998
9:101408575:C:GF269L0.998
9:101408657:T:CF297L0.998
9:101408659:T:AF297L0.998
9:101408659:T:GF297L0.998
9:101408741:T:CF325L0.998
9:101408743:T:AF325L0.998
9:101408743:T:GF325L0.998
9:101408825:T:CF353L0.998
9:101408827:C:AF353L0.998
9:101408827:C:GF353L0.998
9:101408909:T:CF381L0.998
9:101408911:C:AF381L0.998
9:101408911:C:GF381L0.998
9:101408405:T:CF213L0.997
9:101408407:T:AF213L0.997
9:101408407:T:GF213L0.997
9:101408489:T:CF241L0.997
9:101408491:C:AF241L0.997
9:101408491:C:GF241L0.997
9:101408993:T:CF409L0.997
9:101408995:T:AF409L0.997
9:101408995:T:GF409L0.997
9:101409245:T:CF493L0.997
9:101409247:C:AF493L0.997
9:101409247:C:GF493L0.997
9:101408321:T:CF185L0.995
9:101408323:T:AF185L0.995
9:101408323:T:GF185L0.995

dbSNP variants (sampled 300 via entrez): RS1000028563 (9:101397664 T>A,C), RS1000189078 (9:101403253 A>G), RS1000289701 (9:101397402 T>C), RS1000489863 (9:101402796 A>C,G), RS1000658529 (9:101407450 AAC>A), RS1000710475 (9:101407732 A>G), RS1000829027 (9:101401414 T>A,C), RS1001181821 (9:101396904 T>C,G), RS1001588711 (9:101401571 C>G), RS1001973419 (9:101407512 C>T), RS1002195319 (9:101400381 G>C), RS1002333255 (9:101406260 G>A), RS1002383964 (9:101406602 G>A), RS1002582345 (9:101397530 G>T), RS1002600774 (9:101399262 C>A,G)

Disease associations

OMIM: gene MIM:603132 | 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

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression4
Valproic Acidaffects expression, decreases expression, decreases methylation4
Acetaminophendecreases expression, increases expression3
Cyclosporinedecreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4decreases expression1
bisphenol Faffects cotreatment, increases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
geraniolincreases expression1
beta-methylcholineaffects expression1
abrineincreases expression1
jinfukangdecreases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases abundance, increases expression1
Azacitidinedecreases expression1
Benzo(a)pyrenedecreases expression1
Cadmiumincreases expression, increases abundance1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Leadaffects expression1
Quercetindecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
1-Methyl-3-isobutylxanthineincreases expression, affects cotreatment1
Aflatoxin B1decreases expression1
Aflatoxin M1decreases expression1

Cellosaurus cell lines

3 cell lines: 2 cancer cell line, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_E2PQHAP1 ZNF189 (-) 1Cancer cell lineMale
CVCL_E2PRHAP1 ZNF189 (-) 2Cancer cell lineMale
CVCL_XW13HEK293 eGFP-ZNF189Transformed 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.