ZNF229

gene
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Summary

ZNF229 (zinc finger protein 229, HGNC:13022) is a protein-coding gene on chromosome 19q13.31, encoding Zinc finger protein 229 (Q9UJW7). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 7772 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): schizophrenia (No Known Disease Relationship, GenCC)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 160 total
  • MANE Select transcript: NM_014518

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13022
Approved symbolZNF229
Namezinc finger protein 229
Location19q13.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000278318
Ensembl biotypeprotein_coding
OMIM620827
Entrez7772

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000591289, ENST00000592308, ENST00000613197, ENST00000614049, ENST00000620012, ENST00000911243, ENST00000911244

RefSeq mRNA: 2 — MANE Select: NM_014518 NM_001278510, NM_014518

CCDS: CCDS42574, CCDS62706

Canonical transcript exons

ENST00000614049 — 6 exons

ExonStartEnd
ENSE000028647494444830944448472
ENSE000034768534444751344447600
ENSE000037240014444281444443024
ENSE000037399054442625444430542
ENSE000037445964443222244432366
ENSE000037446674444256344442621

Expression profiles

Bgee: expression breadth ubiquitous, 168 present calls, max score 82.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0325 / max 132.9588, expressed in 1241 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1813934.03251241

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.97gold quality
adrenal tissueUBERON:001830380.32gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.98gold quality
cortical plateUBERON:000534379.68gold quality
ventricular zoneUBERON:000305379.35gold quality
ganglionic eminenceUBERON:000402378.16gold quality
islet of LangerhansUBERON:000000677.89gold quality
secondary oocyteCL:000065576.94gold quality
stromal cell of endometriumCL:000225574.96gold quality
pigmented layer of retinaUBERON:000178271.60gold quality
epithelial cell of pancreasCL:000008369.59gold quality
smooth muscle tissueUBERON:000113569.49gold quality
germinal epithelium of ovaryUBERON:000130469.35silver quality
left adrenal glandUBERON:000123468.63gold quality
left adrenal gland cortexUBERON:003582568.60gold quality
ovaryUBERON:000099268.12gold quality
pancreasUBERON:000126468.03gold quality
right adrenal gland cortexUBERON:003582768.02gold quality
left ovaryUBERON:000211967.92gold quality
adrenal glandUBERON:000236967.85gold quality
right adrenal glandUBERON:000123367.84gold quality
heart left ventricleUBERON:000208467.69gold quality
thyroid glandUBERON:000204667.68gold quality
left lobe of thyroid glandUBERON:000112067.66gold quality
gall bladderUBERON:000211067.51gold quality
cardiac ventricleUBERON:000208267.23gold quality
right lobe of thyroid glandUBERON:000111966.76gold quality
adrenal cortexUBERON:000123566.72gold quality
right ovaryUBERON:000211866.70gold quality
heartUBERON:000094866.42gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

81 targeting ZNF229, 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-7110-3P100.0073.182486
HSA-MIR-8485100.0077.574731
HSA-MIR-340-5P100.0072.504437
HSA-MIR-150-5P99.9966.691976
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-808799.9069.551351
HSA-MIR-153-5P99.8973.866317
HSA-MIR-568299.8972.561005
HSA-MIR-95-5P99.8972.173973
HSA-MIR-806799.8669.592260
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-394199.8670.542735
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-430799.8270.453374
HSA-MIR-202-5P99.7867.65991
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-132-3P99.7370.561424

Cross-species orthologs

0 orthologs

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), ZNF189 (ENSG00000136870), 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)

Protein

Protein identifiers

Zinc finger protein 229Q9UJW7 (reviewed: Q9UJW7)

All UniProt accessions (4): Q9UJW7, A0A087WVZ7, A0A087X068, K7EIU9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q9UJW7-11yes
Q9UJW7-22

RefSeq proteins (2): NP_001265439, NP_055333* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF01352

UniProt features (28 total): zinc finger region 18, sequence variant 5, chain 1, domain 1, region of interest 1, cross-link 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UJW7-F162.770.03

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 (1): 543

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 60 (showing top): GOZGIT_ESR1_TARGETS_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KRIEG_HYPOXIA_NOT_VIA_KDM3A, ZNF10_TARGET_GENES, MIR153_5P, MIR548AR_3P, MIR548F_3P, MIR548BC, MIR548AZ_3P, MIR548A_3P, MIR548E_3P, GSE11057_NAIVE_VS_MEMORY_CD4_TCELL_UP, MIR10393_5P, MIR4450, MIR4771

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (4): 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 DNA-templated transcription1
transcription by RNA polymerase II1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF229PDE3BQ13370524
ZNF229OR4F6Q8NGB9506
ZNF229PHYHD1Q5SRE7323
ZNF229TMEM64Q6YI46321
ZNF229DENND4AQ7Z401308
ZNF229OR1M1Q8NGA1294
ZNF229FKBP9O95302293
ZNF229ZNF395Q9H8N7274
ZNF229EBLN2Q6P2I7271
ZNF229OR10K1Q8NGX5270
ZNF229ZNF503Q96F45261
ZNF229TRIM69Q86WT6260
ZNF229FMO2Q99518253
ZNF229FMO4P31512253
ZNF229TFB2MQ9H5Q4248
ZNF229MAMLD1Q13495248

IntAct

9 interactions, top by confidence:

ABTypeScore
CABP5ZNF229psi-mi:“MI:0915”(physical association)0.560
TPM2ZNF229psi-mi:“MI:0915”(physical association)0.560
Mpsi-mi:“MI:0914”(association)0.350
NDEL1ZNF229psi-mi:“MI:0915”(physical association)0.000
CABP5ZNF229psi-mi:“MI:0915”(physical association)0.000
TPM2ZNF229psi-mi:“MI:0915”(physical association)0.000

BioGRID (5): ZNF229 (Synthetic Lethality), ZNF229 (Two-hybrid), ZNF229 (Two-hybrid), ZNF229 (Affinity Capture-MS), ZNF229 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance137
Likely benign16
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1570 predictions. Top by Δscore:

VariantEffectΔscore
19:44432239:CCCA:Cdonor_gain1.0000
19:44432242:A:ACdonor_gain1.0000
19:44432243:C:CCdonor_gain1.0000
19:44432255:T:Adonor_gain1.0000
19:44445081:A:ACdonor_gain1.0000
19:44445082:C:CCdonor_gain1.0000
19:44445084:T:TAdonor_gain1.0000
19:44447508:CTCA:Cdonor_loss1.0000
19:44447509:TCACC:Tdonor_loss1.0000
19:44447510:CACC:Cdonor_loss1.0000
19:44447511:A:ACdonor_gain1.0000
19:44447511:A:Tdonor_loss1.0000
19:44447512:C:CCdonor_gain1.0000
19:44447512:C:CGdonor_loss1.0000
19:44447601:C:CCacceptor_gain1.0000
19:44448294:ACACC:Adonor_gain1.0000
19:44448295:CACCC:Cdonor_gain1.0000
19:44431492:G:Adonor_gain0.9900
19:44432231:T:TAdonor_gain0.9900
19:44432251:AGGTT:Adonor_gain0.9900
19:44432266:T:Adonor_gain0.9900
19:44432272:A:ACdonor_gain0.9900
19:44432364:CTC:Cacceptor_gain0.9900
19:44432367:C:CGacceptor_loss0.9900
19:44434581:A:ACdonor_gain0.9900
19:44434584:A:ACdonor_gain0.9900
19:44434585:C:CCdonor_gain0.9900
19:44445088:T:Adonor_gain0.9900
19:44446830:T:TAdonor_gain0.9900
19:44447597:AAGCC:Aacceptor_loss0.9900

AlphaMissense

5508 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:44428450:A:CF777L0.998
19:44428450:A:TF777L0.998
19:44428452:A:GF777L0.998
19:44429539:G:CF414L0.998
19:44429539:G:TF414L0.998
19:44429541:A:GF414L0.998
19:44428702:G:CF693L0.997
19:44428702:G:TF693L0.997
19:44428704:A:GF693L0.997
19:44428786:A:CF665L0.997
19:44428786:A:TF665L0.997
19:44428788:A:GF665L0.997
19:44429038:G:CF581L0.997
19:44429038:G:TF581L0.997
19:44429040:A:GF581L0.997
19:44429623:A:CF386L0.997
19:44429623:A:TF386L0.997
19:44429625:A:GF386L0.997
19:44428618:G:CF721L0.996
19:44428618:G:TF721L0.996
19:44428620:A:GF721L0.996
19:44428870:G:CF637L0.996
19:44428870:G:TF637L0.996
19:44428872:A:GF637L0.996
19:44428954:G:CF609L0.996
19:44428954:G:TF609L0.996
19:44428956:A:GF609L0.996
19:44429122:A:CF553L0.996
19:44429122:A:TF553L0.996
19:44429124:A:GF553L0.996

dbSNP variants (sampled 300 via entrez): RS1000026244 (19:44427171 T>C), RS1000243940 (19:44450390 C>A,T), RS1000354503 (19:44444114 C>A,T), RS1000462616 (19:44437924 G>A), RS1000514520 (19:44438154 T>C), RS1000579822 (19:44449153 A>G), RS1000598469 (19:44450150 C>T), RS1000645684 (19:44436928 T>C), RS1000785708 (19:44448873 G>T), RS1000882736 (19:44437211 T>C), RS1000962016 (19:44430289 C>A), RS1001075164 (19:44431964 C>T), RS1001139940 (19:44425795 C>T), RS1001203539 (19:44427271 G>A), RS1001277375 (19:44434367 T>C)

Disease associations

OMIM: gene MIM:620827 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
schizophreniaNo Known Disease RelationshipUnknown

Mondo (1): schizophrenia (MONDO:0005090)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST005950_15Body mass index x sex x age interaction (4df test)2.000000e-10
GCST005951_56Body mass index1.000000e-06
GCST005952_8Body mass index (age>50)9.000000e-12
GCST005954_4Body mass index x age interaction2.000000e-07
GCST009391_1533Metabolite levels2.000000e-07

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0009771methionine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
Decitabineincreases expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Catechinaffects cotreatment, decreases expression1
Methotrexatedecreases expression1
Cyclosporineincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091PHASE4TERMINATEDClozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423PHASE4COMPLETEDEfficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436PHASE4COMPLETEDAtomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008PHASE4COMPLETEDAripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety
  • Associated diseases: schizophrenia
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): schizophrenia