ZNF609

gene
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Also known as KIAA0295

Summary

ZNF609 (zinc finger protein 609, HGNC:29003) is a protein-coding gene on chromosome 15q22.1, encoding Zinc finger protein 609 (O15014). Transcription factor, which activates RAG1, and possibly RAG2, transcription.

Predicted to enable promoter-specific chromatin binding activity. Involved in regulation of myoblast proliferation. Located in nucleoplasm.

Source: NCBI Gene 23060 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 232 total
  • MANE Select transcript: NM_015042

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29003
Approved symbolZNF609
Namezinc finger protein 609
Location15q22.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0295
Ensembl geneENSG00000180357
Ensembl biotypeprotein_coding
OMIM617474
Entrez23060

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000326648, ENST00000416172, ENST00000558680, ENST00000559364, ENST00000925215, ENST00000925216

RefSeq mRNA: 1 — MANE Select: NM_015042 NM_015042

CCDS: CCDS32270

Canonical transcript exons

ENST00000326648 — 10 exons

ExonStartEnd
ENSE000012492886468064664680862
ENSE000012492936468018564680360
ENSE000012493016467811664678482
ENSE000012493086468130964681387
ENSE000012493116467391664676256
ENSE000014842996468169264686068
ENSE000014843086449929364500166
ENSE000034592296462282764623052
ENSE000036652636467034664670433
ENSE000039329926446057864460838

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 93.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.8839 / max 197.0913, expressed in 1767 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1471768.38771746
1471771.6801976
1471780.8161445

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305393.54gold quality
colonic epitheliumUBERON:000039792.60gold quality
ganglionic eminenceUBERON:000402391.38gold quality
cortical plateUBERON:000534390.64gold quality
calcaneal tendonUBERON:000370187.85gold quality
tendonUBERON:000004386.83gold quality
medial globus pallidusUBERON:000247786.46gold quality
buccal mucosa cellCL:000233685.80gold quality
adrenal tissueUBERON:001830385.57gold quality
left ovaryUBERON:000211984.86gold quality
tendon of biceps brachiiUBERON:000818884.71gold quality
stromal cell of endometriumCL:000225584.23gold quality
globus pallidusUBERON:000187584.19gold quality
right ovaryUBERON:000211884.18gold quality
embryoUBERON:000092283.56gold quality
secondary oocyteCL:000065583.26gold quality
lower esophagus muscularis layerUBERON:003583383.00gold quality
lower esophagusUBERON:001347382.99gold quality
islet of LangerhansUBERON:000000682.69gold quality
mucosa of stomachUBERON:000119982.69gold quality
ovaryUBERON:000099282.65gold quality
pancreatic ductal cellCL:000207982.60silver quality
inferior olivary complexUBERON:000212782.54gold quality
sural nerveUBERON:001548882.53gold quality
body of uterusUBERON:000985382.45gold quality
esophagogastric junction muscularis propriaUBERON:003584182.10gold quality
right uterine tubeUBERON:000130281.94gold quality
smooth muscle tissueUBERON:000113581.78gold quality
leukocyteCL:000073881.77gold quality
monocyteCL:000057681.69gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.62
E-CURD-112no2.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

383 targeting ZNF609, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4476100.0068.182030
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3163100.0077.238605
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-6873-3P100.0071.422626
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692A100.0074.406850
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-607799.9968.042299
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-56899.9869.862084
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939

Literature-anchored findings (GeneRIF, showing 9)

  • these findings illustrated that cir-ZNF609 took part in the onset of HSCR through the crosstalk with AKT3 by competing for shared miR-150-5p. (PMID:27903978)
  • Circular RNA circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, resulting in a protein that controls myoblast proliferation. (PMID:28344082)
  • our current study reveals the role of the circ-ZNF609/miR-138-5p/FOXP4 regulatory network in renal carcinoma and provides a new perspective for the pathogenesis of renal carcinoma. (PMID:30478938)
  • CircRNA ZNF609 promotes growth and metastasis of nasopharyngeal carcinoma by competing with microRNA-150-5p. (PMID:31002133)
  • Circ-ZNF609 promotes carcinogenesis of gastric cancer cells by inhibiting miRNA-145-5p expression. (PMID:31773689)
  • CircRNA ZNF609 promotes angiogenesis in nasopharyngeal carcinoma by regulating miR-145/STMN1 axis. (PMID:33943007)
  • YY1 and eIF4A3 are mediators of the cell proliferation, migration and invasion in cholangiocarcinoma promoted by circ-ZNF609 by targeting miR-432-5p to regulate LRRC1. (PMID:34898474)
  • A protein encoded by circular ZNF609 RNA induces acute kidney injury by activating the AKT/mTOR-autophagy pathway. (PMID:36110046)
  • CircZNF609 inhibits miR-150-5p to promote high glucose-induced damage to retinal microvascular endothelial cells. (PMID:38679361)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioznf609aENSDARG00000103388
danio_rerioznf609bENSDARG00000104530
mus_musculusZfp609ENSMUSG00000040524
rattus_norvegicusZfp609ENSRNOG00000015977
drosophila_melanogastersbbFBGN0285917

Paralogs (1): ZNF608 (ENSG00000168916)

Protein

Protein identifiers

Zinc finger protein 609O15014 (reviewed: O15014)

All UniProt accessions (2): O15014, E7ERY8

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor, which activates RAG1, and possibly RAG2, transcription. Through the regulation of RAG1/2 expression, may regulate thymocyte maturation. Along with NIPBL and the multiprotein complex Integrator, promotes cortical neuron migration during brain development by regulating the transcription of crucial genes in this process. Preferentially binds promoters containing paused RNA polymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1 and GABBR2 genes, among others. Involved in the regulation of myoblast proliferation during myogenesis.

Subunit / interactions. Interacts (via N-terminus) with NIPBL. Interacts with INTS13; promoting association with the integrator complex.

Subcellular location. Nucleus Nucleus.

Tissue specificity. Isoform 1: Expressed in myoblasts and myotubes. Isoform 2: Expressed in myoblasts and myotubes, with a preference in undifferentiated myoblasts.

Induction. Isoform 1: Up-regulated during neuronal differentiation in retinoic acid-treated SH-SY5Y cells. Isoform 2: Down-regulated during myogenesis.

Miscellaneous. Produced by a back-splicing reaction which joins the 5’-splice site of the first coding exon with the 3’-splice site of the upstream intron resulting in a circular RNA, called circ-ZNF609. The translation starts with the same initiator methionine as that of the linear transcript encoding isoform 1. The stop codon is created upon circularization.

Isoforms (2)

UniProt IDNamesCanonical?
O15014-11yes
O15014-22

RefSeq proteins (1): NP_055857* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR040010ZN608/ZN609Family

UniProt features (63 total): modified residue 22, compositionally biased region 19, region of interest 8, cross-link 5, splice variant 2, mutagenesis site 2, strand 2, chain 1, zinc finger region 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8PK5X-RAY DIFFRACTION2.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15014-F145.990.04

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 (27): 358, 361, 379, 381, 413, 433, 446, 452, 467, 470, 533, 576, 578, 743, 746, 758, 804, 823, 842, 846 …

Mutagenesis-validated functional residues (2):

PositionPhenotype
36abolished interaction with ints13 component of the integrator complex.
37abolished interaction with ints13 component of the integrator complex.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 216 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_NEUROGENESIS, CACCAGC_MIR138, CTATGCA_MIR153, GTGCCTT_MIR506, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GTGTTGA_MIR505, GOBP_REGULATION_OF_NEURON_MIGRATION, GOBP_NEURON_MIGRATION, GOBP_POSITIVE_REGULATION_OF_NEURON_MIGRATION, CCCAGAG_MIR326, AGTCAGC_MIR345, CCAGGGG_MIR331, CTTTGTA_MIR524

GO Biological Process (5): regulation of transcription by RNA polymerase II (GO:0006357), muscle organ development (GO:0007517), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of myoblast proliferation (GO:2000291), positive regulation of neuron migration (GO:2001224)

GO Molecular Function (4): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), promoter-specific chromatin binding (GO:1990841), 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
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II2
regulation of DNA-templated transcription1
animal organ development1
muscle structure development1
positive regulation of DNA-templated transcription1
regulation of cell population proliferation1
myoblast proliferation1
neuron migration1
positive regulation of cell migration1
regulation of neuron migration1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
transition metal ion binding1
chromatin binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

1100 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF609SHPRHQ149N8732
ZNF609EIF4G2P78344701
ZNF609MBNL3Q9NUK0599
ZNF609MBNL2Q5VZF2592
ZNF609ANKRD52Q8NB46573
ZNF609HIPK3Q9H422565
ZNF609MBNL1Q9NR56564
ZNF609FOXP4Q8IVH2538
ZNF609YTHDF3Q7Z739527
ZNF609QKIQ96PU8512
ZNF609FBXW7Q969H0506
ZNF609FUSP35637488
ZNF609PABPN1Q86U42476
ZNF609ITCHQ96J02466
ZNF609AKT3Q9Y243437

IntAct

142 interactions, top by confidence:

ABTypeScore
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
NFICNFIBpsi-mi:“MI:2364”(proximity)0.690
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
RFPL4BRFPL4Apsi-mi:“MI:0914”(association)0.640
PIGTZNF609psi-mi:“MI:0914”(association)0.530
SBSPONZNF609psi-mi:“MI:0914”(association)0.530
BAG2HGSpsi-mi:“MI:0914”(association)0.530
FLCNZNF609psi-mi:“MI:0914”(association)0.530
CLEC11AVWA8psi-mi:“MI:0914”(association)0.530
PIPTBKBP1psi-mi:“MI:0914”(association)0.530
EXOC5ZNF609psi-mi:“MI:0914”(association)0.510
EN1NFIBpsi-mi:“MI:2364”(proximity)0.470
Dynll1psi-mi:“MI:0915”(physical association)0.400
MagohTRAPPC13psi-mi:“MI:0914”(association)0.350
PRKCITRAPPC13psi-mi:“MI:0914”(association)0.350
ATL3SNX14psi-mi:“MI:0914”(association)0.350
HDAC1TRAK1psi-mi:“MI:0914”(association)0.350
INTS14DKFZP586J0619psi-mi:“MI:0914”(association)0.350
USP7STILpsi-mi:“MI:0914”(association)0.350
AUTS2ZNF609psi-mi:“MI:0914”(association)0.350
THSD4KRBA1psi-mi:“MI:0914”(association)0.350
FLCNAGAP1psi-mi:“MI:0914”(association)0.350

BioGRID (173): ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Proximity Label-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IBL7, A2A891, A3RK74, A4L7N3, B5DE09, E1BPQ1, G3V7R4, O15014, O43524, P11420, P15806, P15881, P15884, P15923, P21677, P30985, P51514, P70365, P98180, Q01978, Q12778, Q14135, Q15596, Q15788, Q4PJW2, Q53TQ3, Q60420, Q60722, Q61026, Q61286, Q62655, Q66IY8, Q66JJ0, Q6DIH5, Q6EUW2, Q6NZT6, Q6PCG7, Q7T2G1, Q7ZXS3, Q80V24

Diamond homologs: O15014, Q56A10, Q8BZ47, Q9ULD9, Q9UTH8, P32432, Q5RDF5, Q80ZQ5, Q86VZ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 165 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
RNA Polymerase III Transcription Termination524.1×4e-04
Deactivation of the beta-catenin transactivating complex818.1×6e-06
RNA Polymerase III Abortive And Retractive Initiation513.5×4e-03
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)79.9×1e-03

GO biological processes:

GO termPartnersFoldFDR
neuron fate specification523.9×2e-04
cell fate commitment612.1×9e-04
positive regulation of miRNA transcription611.9×9e-04
cartilage development610.3×1e-03
inner ear morphogenesis510.2×4e-03
anatomical structure morphogenesis109.5×2e-05
retina development in camera-type eye58.7×8e-03
somatic stem cell population maintenance58.4×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance210
Likely benign4
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2843 predictions. Top by Δscore:

VariantEffectΔscore
15:64526535:G:GTdonor_gain1.0000
15:64622824:C:Gacceptor_gain1.0000
15:64622825:A:AGacceptor_gain1.0000
15:64622825:AGAT:Aacceptor_gain1.0000
15:64622826:G:GAacceptor_gain1.0000
15:64622826:GAT:Gacceptor_gain1.0000
15:64622826:GATG:Gacceptor_gain1.0000
15:64623048:AGATG:Adonor_gain1.0000
15:64623049:GATG:Gdonor_gain1.0000
15:64623049:GATGG:Gdonor_gain1.0000
15:64623050:ATG:Adonor_gain1.0000
15:64623051:TG:Tdonor_gain1.0000
15:64623052:GG:Gdonor_gain1.0000
15:64623053:G:GAdonor_loss1.0000
15:64623053:G:GGdonor_gain1.0000
15:64623054:T:Adonor_loss1.0000
15:64640812:G:GTdonor_gain1.0000
15:64670430:CAAG:Cdonor_loss1.0000
15:64670431:AAGG:Adonor_loss1.0000
15:64670432:AGGTA:Adonor_loss1.0000
15:64670433:GGTA:Gdonor_loss1.0000
15:64670434:GT:Gdonor_loss1.0000
15:64670435:T:Adonor_loss1.0000
15:64673909:T:TAacceptor_gain1.0000
15:64673911:CCAA:Cacceptor_loss1.0000
15:64673912:CAAG:Cacceptor_loss1.0000
15:64673913:A:AGacceptor_gain1.0000
15:64673913:AAG:Aacceptor_gain1.0000
15:64673914:A:Cacceptor_loss1.0000
15:64673914:A:Gacceptor_gain1.0000

AlphaMissense

9230 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:64499498:T:AW27R1.000
15:64499498:T:CW27R1.000
15:64499499:G:CW27S1.000
15:64499500:G:CW27C1.000
15:64499500:G:TW27C1.000
15:64499505:T:AI29N1.000
15:64499507:G:AG30R1.000
15:64499507:G:CG30R1.000
15:64499508:G:AG30E1.000
15:64499513:G:AG32R1.000
15:64499513:G:CG32R1.000
15:64499513:G:TG32W1.000
15:64499514:G:AG32E1.000
15:64499514:G:TG32V1.000
15:64499520:T:AL34H1.000
15:64499520:T:CL34P1.000
15:64499523:T:AI35N1.000
15:64499523:T:CI35T1.000
15:64499523:T:GI35S1.000
15:64499526:T:AI36N1.000
15:64499526:T:CI36T1.000
15:64499526:T:GI36S1.000
15:64499528:G:CD37H1.000
15:64499529:A:CD37A1.000
15:64499529:A:GD37G1.000
15:64499529:A:TD37V1.000
15:64499530:C:AD37E1.000
15:64499530:C:GD37E1.000
15:64499532:T:AL38Q1.000
15:64499532:T:CL38P1.000

dbSNP variants (sampled 300 via entrez): RS1000001346 (15:64642522 A>G), RS1000021495 (15:64622143 T>C), RS1000028472 (15:64665686 G>C), RS1000037287 (15:64685897 C>G), RS1000052779 (15:64573661 C>G), RS1000055093 (15:64535264 G>A), RS1000073415 (15:64545351 A>G), RS1000087406 (15:64481809 A>C), RS1000087831 (15:64528119 T>G), RS1000088012 (15:64592577 A>G), RS1000090437 (15:64685208 T>C), RS1000101056 (15:64629324 G>A,T), RS1000152775 (15:64580666 C>T), RS1000167797 (15:64667008 T>C), RS1000169671 (15:64672828 G>A)

Disease associations

OMIM: gene MIM:617474 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST005232_36Neuroticism3.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007660neuroticism measurement

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
Benzo(a)pyrenedecreases expression, affects methylation3
Cisplatindecreases response to substance, decreases expression2
Aflatoxin B1decreases expression, increases methylation2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
butyraldehydedecreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideincreases abundance, decreases expression1
benzo(e)pyrenedecreases methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2decreases methylation1
coumarinincreases phosphorylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
perfluorohexanesulfonic aciddecreases expression1
abrineincreases expression1
Leflunomideincreases expression1
Arsenicaffects methylation1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Leaddecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2LVAbcam HeLa ZNF609 KOCancer 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.