ZNF652

gene
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Also known as KIAA0924

Summary

ZNF652 (zinc finger protein 652, HGNC:29147) is a protein-coding gene on chromosome 17q21.32, encoding Zinc finger protein 652 (Q9Y2D9). DNA-binding transcription repressor that acts together with CBFA2T2 to repress expression of target genes, such as TCF12.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 22834 — RefSeq curated summary.

At a glance

  • GWAS associations: 60
  • Clinical variants (ClinVar): 87 total
  • MANE Select transcript: NM_001145365

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29147
Approved symbolZNF652
Namezinc finger protein 652
Location17q21.32
Locus typegene with protein product
StatusApproved
AliasesKIAA0924
Ensembl geneENSG00000198740
Ensembl biotypeprotein_coding
OMIM613907
Entrez22834

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 14 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000362063, ENST00000430262, ENST00000508237, ENST00000513488, ENST00000899840, ENST00000899841, ENST00000899842, ENST00000899843, ENST00000899844, ENST00000923162, ENST00000923163, ENST00000949717, ENST00000949718, ENST00000949719, ENST00000949720, ENST00000949721

RefSeq mRNA: 2 — MANE Select: NM_001145365 NM_001145365, NM_014897

CCDS: CCDS32677

Canonical transcript exons

ENST00000430262 — 6 exons

ExonStartEnd
ENSE000007362664931269849312845
ENSE000011372484931682649317983
ENSE000016003734936190949362250
ENSE000016236204931131249311456
ENSE000017700804931192749312042
ENSE000017923544928920649298924

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 96.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.2833 / max 238.1247, expressed in 1758 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1668009.91921650
1668015.39311507
1667990.8314527
1667970.118036
1667980.02165

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
medial globus pallidusUBERON:000247796.10gold quality
globus pallidusUBERON:000187595.35gold quality
inferior vagus X ganglionUBERON:000536394.29gold quality
nippleUBERON:000203094.09gold quality
cardia of stomachUBERON:000116292.70gold quality
olfactory segment of nasal mucosaUBERON:000538692.32gold quality
subthalamic nucleusUBERON:000190692.11gold quality
C1 segment of cervical spinal cordUBERON:000646991.96gold quality
pylorusUBERON:000116691.87gold quality
skin of hipUBERON:000155491.76gold quality
ventral tegmental areaUBERON:000269191.73gold quality
upper leg skinUBERON:000426291.73gold quality
superior vestibular nucleusUBERON:000722791.66gold quality
spinal cordUBERON:000224091.27gold quality
adult organismUBERON:000702391.21gold quality
superior surface of tongueUBERON:000737191.04gold quality
muscle layer of sigmoid colonUBERON:003580590.73gold quality
penisUBERON:000098990.60gold quality
saphenous veinUBERON:000731890.58gold quality
cranial nerve IIUBERON:000094190.25gold quality
renal medullaUBERON:000036290.24gold quality
pigmented layer of retinaUBERON:000178290.20gold quality
mucosa of paranasal sinusUBERON:000503089.95gold quality
medulla oblongataUBERON:000189689.91gold quality
ponsUBERON:000098889.86gold quality
fundus of stomachUBERON:000116089.71gold quality
lateral globus pallidusUBERON:000247689.56gold quality
skin of legUBERON:000151189.51gold quality
parotid glandUBERON:000183189.38gold quality
seminal vesicleUBERON:000099889.33gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-MTAB-6379no562.74
E-MTAB-6142no60.93
E-ANND-3no8.10

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
TCF12

JASPAR motifs

MotifNameFamily
MA1657.1ZNF652More than 3 adjacent zinc fingers
MA1657.2ZNF652More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:23332764

Upstream regulators (CollecTRI, top): CBFA2T3

miRNA regulators (miRDB)

413 targeting ZNF652, 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-5692A100.0074.406850
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-1277-5P100.0073.955056
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4510100.0066.602050
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4768-5P100.0069.492861

Literature-anchored findings (GeneRIF, showing 7)

  • CBFA2T3 interacts with ZNF652 to repress HEB expression, and in addition CBFA2T3 interacts with the HEB protein to inhibit its activator function. (PMID:18456661)
  • High levels of expression of both the androgen receptor and ZNF652 in clinically organ-defined prostate cancer are associated with a statistically increased risk of relapse (PMID:20204290)
  • variation in FGF5 and ZNF652 gene upstream regions with altered susceptibility to hypertension in Han Chinese (PMID:20542020)
  • De novo motif scanning of the ZNF652 binding sites identified a novel ZNF652 recognition motif that closely resembles the previously characterised in vitro binding site, being a 10 nucleotide core of that 13 nucleotide sequence. (PMID:21678463)
  • Genetic association studies identify a novel variant in ZNF652 gene suggesting its role in prostate cancer. (PMID:25335771)
  • Circular RNA circVRK1 suppresses the proliferation, migration and invasion of osteosarcoma cells by regulating zinc finger protein ZNF652 expression via microRNA miR-337-3p. (PMID:34424826)
  • ZNF652-Induced circRHOT1 Promotes SMAD5 Expression to Modulate Tumorigenic Properties and Nature Killer Cell-Mediated Toxicity in Bladder Cancer via Targeting miR-3666. (PMID:34926705)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioznf652ENSDARG00000062302
mus_musculusZfp652ENSMUSG00000075595
rattus_norvegicusZfp652ENSRNOG00000017001
drosophila_melanogasterdwgFBGN0000520
drosophila_melanogasterCG6654FBGN0038301
caenorhabditis_elegansWBGENE00003933

Paralogs (6): ZNF324 (ENSG00000083812), ZBTB47 (ENSG00000114853), GTF3A (ENSG00000122034), ZUP1 (ENSG00000153975), ZNF513 (ENSG00000163795), ZNF324B (ENSG00000249471)

Protein

Protein identifiers

Zinc finger protein 652Q9Y2D9 (reviewed: Q9Y2D9)

All UniProt accessions (2): Q9Y2D9, D6RF85

UniProt curated annotations — full annotation on UniProt →

Function. DNA-binding transcription repressor that acts together with CBFA2T2 to repress expression of target genes, such as TCF12. Specifically binds the DNA consensus sequence 5’-CGAAAGGGTTAAT-3'.

Subunit / interactions. Interacts with CBFA2T3. Interacts with TCF12; inhibiting TCF12 transcription factor activity. Interacts with Zincore complex components QRICH1 and SEPHS1; probably stabilizing ZNF652 at DNA-binding sites across the genome.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed with higher expression in breast, prostate, vulva and pancreas.

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

RefSeq proteins (2): NP_001138837, NP_055712 (=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096

UniProt features (24 total): zinc finger region 9, compositionally biased region 6, modified residue 5, region of interest 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2D9-F156.600.00

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): 57, 100, 103, 197, 204

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 228 (showing top): WANG_RECURRENT_LIVER_CANCER_UP, PATIL_LIVER_CANCER, HUTTMANN_B_CLL_POOR_SURVIVAL_DN, SMID_BREAST_CANCER_LUMINAL_B_UP, TCCAGAG_MIR518C, CCAGGGG_MIR331, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, AGCATTA_MIR155, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, LAIHO_COLORECTAL_CANCER_SERRATED_DN, CAGCTTT_MIR320, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GCACTTT_MIR175P_MIR20A_MIR106A_MIR106B_MIR20B_MIR519D, MODULE_456

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
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
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

896 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF652CBFA2T3O75081758
ZNF652CABCOCO1Q8IVU9668
ZNF652GUCD1Q96NT3603
ZNF652PLCD3Q8N3E9576
ZNF652PLEKHA7Q6IQ23447
ZNF652ULK4Q96C45417
ZNF652OR4K15Q8NH41403
ZNF652SH2B3Q9UQQ2403
ZNF652NUDT11Q96G61380
ZNF652ATP2B1P20020374
ZNF652JAG1P78504373
ZNF652ULK3Q6PHR2370
ZNF652CDC7O00311368
ZNF652SATL1Q86VE3362
ZNF652MAD2L1Q13257360

IntAct

9 interactions, top by confidence:

ABTypeScore
CBFA2T3ZNF652psi-mi:“MI:0915”(physical association)0.510
ZNF652RUNX1T1psi-mi:“MI:0915”(physical association)0.400
ZNF652CBFA2T2psi-mi:“MI:0915”(physical association)0.400
ZNF652PDIA4psi-mi:“MI:0915”(physical association)0.400
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
AFG2BMMP24OSpsi-mi:“MI:0914”(association)0.350
ZNF652FOSpsi-mi:“MI:0915”(physical association)0.000

BioGRID (7): ZNF652 (Two-hybrid), ZNF652 (Affinity Capture-MS), ZNF652 (Affinity Capture-MS), ZNF652 (Proximity Label-MS), ZNF652 (Affinity Capture-MS), ZNF652 (Proximity Label-MS), ZNF652 (Affinity Capture-MS)

ESM2 similar proteins: A0JPB4, A1L1J6, A4IFJ6, D3ZUU2, E9Q8T2, G5E8B9, O08954, O15060, O42409, O43623, O57415, O70237, O75626, O95625, P19382, P25932, P36197, P37275, P97469, Q20082, Q2EI20, Q3MHQ4, Q3UH06, Q4VBD9, Q5DU09, Q5R9W9, Q5SVQ8, Q5T0B9, Q5ZLR2, Q60542, Q60636, Q62947, Q64318, Q6DCW1, Q6GNP2, Q6INV8, Q6NRM0, Q7TS63, Q7ZVR6, Q80X44

Diamond homologs: A1L1J6, Q5DU09, Q6GNP2, Q6INV8, Q8BI66, Q8TF50, Q9UFB7, Q9Y2D9, A0JC51, A2ANX9, A6QR00, A7Y7X5, D3ZUU2, O60315, O95863, P28166, P36197, P39956, Q02026, Q02027, Q02085, Q03833, Q22678, Q29RK0, Q4R8S8, Q4VBD9, Q504L7, Q569E7, Q5R4P8, Q5TEC3, Q60542, Q62947, Q642B2, Q64318, Q6GL52, Q6ZN55, Q8BY46, Q99LH4, Q99M85, Q9BWW7

SIGNOR signaling

2 interactions.

AEffectBMechanism
CBFA2T3“down-regulates activity”ZNF652binding
CBFA2T3/ZNF651“down-regulates quantity by repression”ZNF652“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1715 predictions. Top by Δscore:

VariantEffectΔscore
17:49298922:CTC:Cacceptor_gain1.0000
17:49298925:C:CCacceptor_gain1.0000
17:49311308:TTAC:Tdonor_loss1.0000
17:49311309:TA:Tdonor_loss1.0000
17:49311310:A:ACdonor_gain1.0000
17:49311310:A:ATdonor_loss1.0000
17:49311311:C:CCdonor_gain1.0000
17:49311452:CAGTT:Cacceptor_gain1.0000
17:49312691:AACTT:Adonor_loss1.0000
17:49312692:ACTTA:Adonor_loss1.0000
17:49312693:CTTA:Cdonor_loss1.0000
17:49312694:TTACC:Tdonor_loss1.0000
17:49312695:TA:Tdonor_loss1.0000
17:49312696:A:ACdonor_gain1.0000
17:49312696:A:Tdonor_loss1.0000
17:49312696:AC:Adonor_gain1.0000
17:49312697:C:CAdonor_gain1.0000
17:49312697:C:Gdonor_loss1.0000
17:49312697:CC:Cdonor_gain1.0000
17:49312697:CCA:Cdonor_gain1.0000
17:49312697:CCAA:Cdonor_gain1.0000
17:49312841:ACACA:Aacceptor_gain1.0000
17:49312842:CACA:Cacceptor_gain1.0000
17:49312842:CACAC:Cacceptor_gain1.0000
17:49312843:ACA:Aacceptor_gain1.0000
17:49312844:CA:Cacceptor_gain1.0000
17:49312844:CAC:Cacceptor_gain1.0000
17:49312846:C:CCacceptor_gain1.0000
17:49312846:CTGA:Cacceptor_loss1.0000
17:49312852:A:Tacceptor_gain1.0000

AlphaMissense

4080 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:49298775:G:CH487D1.000
17:49298783:A:GL484P1.000
17:49298794:G:CF480L1.000
17:49298794:G:TF480L1.000
17:49298796:A:GF480L1.000
17:49298800:G:CF478L1.000
17:49298800:G:TF478L1.000
17:49298801:A:GF478S1.000
17:49298802:A:GF478L1.000
17:49298813:C:TC474Y1.000
17:49298814:A:GC474R1.000
17:49298822:C:TC471Y1.000
17:49298823:A:GC471R1.000
17:49298845:G:CH463Q1.000
17:49298845:G:TH463Q1.000
17:49298846:T:CH463R1.000
17:49298847:G:AH463Y1.000
17:49298847:G:CH463D1.000
17:49298847:G:TH463N1.000
17:49298851:T:AR461S1.000
17:49298851:T:GR461S1.000
17:49298855:C:GR460P1.000
17:49298857:G:CH459Q1.000
17:49298857:G:TH459Q1.000
17:49298858:T:CH459R1.000
17:49298859:G:CH459D1.000
17:49298859:G:TH459N1.000
17:49298860:T:AR458S1.000
17:49298860:T:GR458S1.000
17:49298884:G:CF450L1.000

dbSNP variants (sampled 300 via entrez): RS1000019830 (17:49292630 G>A), RS1000045933 (17:49303145 G>T), RS1000074174 (17:49336648 A>C,G), RS1000089625 (17:49294149 T>C), RS1000112474 (17:49293673 A>C,G), RS1000143947 (17:49362162 GGCGGGGCGGGCAGC>G,GGCGGGGCGGGCAGCGCGGGGCGGGCAGC), RS1000165408 (17:49360610 TCGA>T), RS1000197974 (17:49296869 A>G), RS1000231376 (17:49336747 C>T), RS1000270668 (17:49334835 C>A,G,T), RS1000333132 (17:49305491 G>C), RS1000344944 (17:49342686 C>T), RS1000386980 (17:49342958 T>C,G), RS1000429100 (17:49348661 A>G,T), RS1000478496 (17:49328487 G>A,C)

Disease associations

OMIM: gene MIM:613907 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

60 associations (top):

StudyTraitp-value
GCST000394_6Diastolic blood pressure5.000000e-09
GCST000817_138Height4.000000e-08
GCST001078_1Prostate cancer3.000000e-13
GCST001236_27Blood pressure2.000000e-07
GCST001612_13Sex hormone-binding globulin levels4.000000e-14
GCST001612_30Sex hormone-binding globulin levels2.000000e-10
GCST001942_17Prostate cancer2.000000e-09
GCST004600_146Eosinophil percentage of white cells5.000000e-13
GCST004606_24Eosinophil count1.000000e-13
GCST004617_124Eosinophil percentage of granulocytes1.000000e-11
GCST004623_86Neutrophil percentage of granulocytes9.000000e-10
GCST004777_55Diastolic blood pressure1.000000e-08
GCST005038_100Allergic disease (asthma, hay fever or eczema)1.000000e-15
GCST005195_141Coronary artery disease2.000000e-15
GCST005196_220Coronary artery disease3.000000e-16
GCST005212_35Asthma7.000000e-09
GCST005275_26Cancer7.000000e-07
GCST005728_1Egg allergy (maternal genetic effects)4.000000e-07
GCST006020_37Diastolic blood pressure3.000000e-07
GCST006166_22Diastolic blood pressure x alcohol consumption interaction (2df test)1.000000e-18
GCST006166_41Diastolic blood pressure x alcohol consumption interaction (2df test)3.000000e-17
GCST006167_17Mean arterial pressure x alcohol consumption interaction (2df test)6.000000e-10
GCST006169_14Diastolic blood pressure x alcohol consumption (light vs heavy) interaction (2df test)2.000000e-09
GCST006169_27Diastolic blood pressure x alcohol consumption (light vs heavy) interaction (2df test)1.000000e-10
GCST006172_11Mean arterial pressure x alcohol consumption (light vs heavy) interaction (2df test)5.000000e-09
GCST006258_55Diastolic blood pressure1.000000e-12
GCST006259_15Systolic blood pressure7.000000e-08
GCST006412_99Intraocular pressure8.000000e-08
GCST006434_49Systolic blood pressure x alcohol consumption interaction (2df test)3.000000e-11
GCST006862_3Asthma3.000000e-09

EFO canonical traits (17, from GWAS)

EFO IDTrait name
EFO:0006336diastolic blood pressure
EFO:0006340mean arterial pressure
EFO:0004696sex hormone-binding globulin measurement
EFO:0007991eosinophil percentage of leukocytes
EFO:0004842eosinophil count
EFO:0007996eosinophil percentage of granulocytes
EFO:0007994neutrophil percentage of granulocytes
EFO:0005939parental genotype effect measurement
EFO:0007018egg allergy measurement
EFO:0004329alcohol drinking
EFO:0006335systolic blood pressure
EFO:0004695intraocular pressure measurement
EFO:0004341body fat distribution
EFO:1002011adult onset asthma
EFO:0004530triglyceride measurement
EFO:0004346neuroimaging measurement
EFO:0010701mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs16948048ZNF6520.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression6
Benzo(a)pyreneaffects expression, decreases expression, decreases methylation4
Formaldehydedecreases expression2
Phenylmercuric Acetatedecreases expression, affects cotreatment2
Quercetindecreases expression, decreases phosphorylation2
Tetrachlorodibenzodioxindecreases expression2
Cyclosporinedecreases expression, increases expression2
Aflatoxin B1affects expression, decreases expression2
Cadmium Chlorideincreases expression, decreases expression, increases abundance2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
bisphenol Faffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
2-butenaldecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
ochratoxin Adecreases expression1
benzo(e)pyreneincreases methylation1
beta-methylcholineaffects expression1
pentanaldecreases expression1
gadodiamideincreases expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Saffects cotreatment, decreases expression1
jinfukangdecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): atopic eczema, cancer