ZNF462 Gene (Protein Coding)

Zinc Finger Protein 462

GC09P106860
GIFtS:
41
The protein encoded by this gene belongs to C2H2-type zinc finger family of proteins. It contains multiple C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016] See more...

Aliases for ZNF462 Gene

Aliases for ZNF462 Gene

  • Zinc Finger Protein 462 2 3 4 5
  • Zinc Finger PBX1-Interacting Protein 3 4
  • KIAA1803 2 4
  • Zfp462 2 3
  • ZFPIP 3 4
  • DKFZP762N2316 2
  • ZNF462 5
  • WSKA 3

External Ids for ZNF462 Gene

Previous GeneCards Identifiers for ZNF462 Gene

  • GC09P105069
  • GC09P106704
  • GC09P108665
  • GC09P109626
  • GC09P079228

Summaries for ZNF462 Gene

Entrez Gene Summary for ZNF462 Gene

  • The protein encoded by this gene belongs to C2H2-type zinc finger family of proteins. It contains multiple C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

GeneCards Summary for ZNF462 Gene

ZNF462 (Zinc Finger Protein 462) is a Protein Coding gene. Diseases associated with ZNF462 include Weiss-Kruszka Syndrome and Metopic Ridging-Ptosis-Facial Dysmorphism Syndrome. Among its related pathways are Mesodermal Commitment Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is ZNF521.

UniProtKB/Swiss-Prot Summary for ZNF462 Gene

  • Zinc finger nuclear factor involved in transcription by regulating chromatin structure and organization (PubMed:20219459, PubMed:21570965). Involved in the pluripotency and differentiation of embryonic stem cells by regulating SOX2, POU5F1/OCT4, and NANOG (PubMed:21570965). By binding PBX1, prevents the heterodimerization of PBX1 and HOXA9 and their binding to DNA (By similarity). Regulates neuronal development and neural cell differentiation (PubMed:21570965).

Additional gene information for ZNF462 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZNF462 Gene

Genomics for ZNF462 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ZNF462 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH09J106859 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 262.7 +2.8 2807 7.3 ZSCAN16 ZBTB10 FEZF1 ETS1 CTCF ZIC2 ZNF513 SIN3A ZNF639 TRIM22 ZNF462 HSALNG0073492 HSALNG0073493 LOC105376204 RAD23B
GH09J106858 Enhancer 0.3 Ensembl 261.7 -1.7 -1653 0.2 FOS ZNF462 LOC105376204 RNA5SP292 RF00001-345
GH09J106876 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 28.3 +22.1 22067 10.8 FEZF1 MAFK CTCF REST ZNF189 TAF1 ZBTB21 RCOR1 BHLHE40 ZNF561 HSALNG0073494 ZNF462 LOC105376204 HSALNG0073495 RAD23B
GH09J106888 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 23.6 +31.4 31432 6.4 DEK ZNF217 CEBPB SIN3A EP300 CTBP1 RFX5 YY1 JUND SMARCE1 ZNF462 HSALNG0073494 LOC105376204 HSALNG0073495 RAD23B
GH09J106914 Enhancer 1.7 UCNEbase Ensembl ENCODE CraniofacialAtlas dbSUPER 16 +58.9 58934 9 NR2C1 CEBPB ZNF623 EP300 RXRA ZNF433 CTBP1 FOXA2 YY1 SMARCA5 ZNF462 HSALNG0073495 HSALNG0073494 LOC105376204 RAD23B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZNF462 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZNF462

Top Transcription factor binding sites by QIAGEN in the ZNF462 gene promoter:
  • FOXJ2
  • FOXJ2 (long isoform)
  • GATA-1
  • GATA-3
  • p300
  • POU2F1
  • POU2F1a
  • Roaz
  • SRF
  • SRF (504 AA)

Genomic Locations for ZNF462 Gene

Latest Assembly
chr9:106,860,154-107,013,634
(GRCh38/hg38)
Size:
153,481 bases
Orientation:
Plus strand

Previous Assembly
chr9:109,625,447-109,775,915
(GRCh37/hg19 by Entrez Gene)
Size:
150,469 bases
Orientation:
Plus strand

chr9:109,625,378-109,775,915
(GRCh37/hg19 by Ensembl)
Size:
150,538 bases
Orientation:
Plus strand

Genomic View for ZNF462 Gene

Genes around ZNF462 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF462 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF462 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ZNF462 Gene

Proteins for ZNF462 Gene

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  • Protein details for ZNF462 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96JM2-ZN462_HUMAN
    Recommended name:
    Zinc finger protein 462
    Protein Accession:
    Q96JM2
    Secondary Accessions:
    • Q5T0T4
    • Q8N408

    Protein attributes for ZNF462 Gene

    Size:
    2506 amino acids
    Molecular mass:
    284688 Da
    Quaternary structure:
    • Interacts with PBX1; this interaction prevents PBX1-HOXA9 heterodimer from forming and binding to DNA.
    SequenceCaution:
    • Sequence=AAH36884.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ZNF462 Gene

    Alternative splice isoforms for ZNF462 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ZNF462 Gene

Protein Expression for ZNF462 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for ZNF462 Gene

  • O-GlcNAcylated with O-GlcNAc-6-phosphate.
  • Glycosylation at Ser292 and Ser309
  • Modification sites at PhosphoSitePlus

Other Protein References for ZNF462 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZNF462 Gene

Domains & Families for ZNF462 Gene

Gene Families for ZNF462 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZNF462 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ZNF462 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger protein 462 (Q5T0T2_HUMAN)
  • Zinc finger protein 462 (Q5T0T3_HUMAN)
  • Zinc finger protein 462 (ZN462_HUMAN)
genes like me logo Genes that share domains with ZNF462: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ZNF462 Gene

Function for ZNF462 Gene

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  6. Cell Lines for research

Molecular function for ZNF462 Gene

UniProtKB/Swiss-Prot Function:
Zinc finger nuclear factor involved in transcription by regulating chromatin structure and organization (PubMed:20219459, PubMed:21570965). Involved in the pluripotency and differentiation of embryonic stem cells by regulating SOX2, POU5F1/OCT4, and NANOG (PubMed:21570965). By binding PBX1, prevents the heterodimerization of PBX1 and HOXA9 and their binding to DNA (By similarity). Regulates neuronal development and neural cell differentiation (PubMed:21570965).

Phenotypes From GWAS Catalog for ZNF462 Gene

Gene Ontology (GO) - Molecular Function for ZNF462 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 27705803
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNF462: view
genes like me logo Genes that share phenotypes with ZNF462: view

Human Phenotype Ontology for ZNF462 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

miRNA for ZNF462 Gene

miRTarBase miRNAs that target ZNF462

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZNF462

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for ZNF462 Gene

Localization for ZNF462 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF462 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZNF462 gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNF462 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with ZNF462: view

Pathways & Interactions for ZNF462 Gene

PathCards logo

SuperPathways for ZNF462 Gene

genes like me logo Genes that share pathways with ZNF462: view

Pathways by source for ZNF462 Gene

2 BioSystems pathways for ZNF462 Gene

Gene Ontology (GO) - Biological Process for ZNF462 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0010468 regulation of gene expression IBA 21873635
GO:0043392 negative regulation of DNA binding IEA --
GO:0045944 positive regulation of transcription by RNA polymerase II IBA 21873635
genes like me logo Genes that share ontologies with ZNF462: view

No data available for SIGNOR curated interactions for ZNF462 Gene

Drugs & Compounds for ZNF462 Gene

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No Compound Related Data Available

Transcripts for ZNF462 Gene

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mRNA/cDNA for ZNF462 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZNF462

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF462 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^
SP1: - - -
SP2: - - - -
SP3: - - -
SP4:
SP5: - - - - - -
SP6:
SP7: -
SP8:
SP9: - - - -

ExUns: 18
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for ZNF462 Gene

GeneLoc Exon Structure for
ZNF462

Expression for ZNF462 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZNF462 Gene

mRNA expression in normal human tissues for ZNF462 Gene
mRNA expression by BioGPS for ZNF462 GenemRNA expression by GTEx for ZNF462 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZNF462 Gene

This gene is overexpressed in Cervix (56.2) and Bone (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ZNF462 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZNF462

SOURCE GeneReport for Unigene cluster for ZNF462 Gene:

Hs.370379

Evidence on tissue expression from TISSUES for ZNF462 Gene

  • Nervous system(4.4)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with ZNF462: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNF462 Gene

Orthologs for ZNF462 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZNF462 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia ZNF462 30 31
  • 99.71 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia ZNF462 30 31
  • 92.08 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia ZNF462 30 31
  • 90.6 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Zfp462 30 17 31
  • 90.09 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Zfp462 30
  • 89.54 (n)
Oppossum
(Monodelphis domestica)
 Mammalia ZNF462 31
  • 87 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia ZNF462 31
  • 85 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves ZNF462 30 31
  • 78.94 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 81 (a)
 OneToMany
-- 31
  • 81 (a)
 OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia znf462 30
  • 67.51 (n)
Zebrafish
(Danio rerio)
 Actinopterygii znf462 30
  • 60.75 (n)
ZNF462 31
  • 52 (a)
 OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.7801 30
Fruit Fly
(Drosophila melanogaster)
 Insecta hb 31
  • 17 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea hbl-1 31
  • 15 (a)
 OneToMany
Species where no ortholog for ZNF462 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ZNF462 Gene

ENSEMBL:
Gene Tree for ZNF462 (if available)
TreeFam:
Gene Tree for ZNF462 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZNF462: view image

Paralogs for ZNF462 Gene

Paralogs for ZNF462 Gene

(8) SIMAP similar genes for ZNF462 Gene using alignment to 5 proteins:

  • ZN462_HUMAN
  • F5H0Z0_HUMAN
  • H0Y6H9_HUMAN
  • H3BLX4_HUMAN
  • U3KQU3_HUMAN
genes like me logo Genes that share paralogs with ZNF462: view

Variants for ZNF462 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZNF462 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
929764 Likely Pathogenic: Premature ovarian failure 106,927,427(+) C/G
NM_021224.6(ZNF462):c.3515C>G (p.Pro1172Arg) 		MISSENSE_VARIANT,INTRON
976789 Pathogenic: Weiss-kruszka syndrome 106,932,499(+) GGACAA/G
NM_021224.6(ZNF462):c.6068_6072del (p.Asp2023fs) 		FRAMESHIFT
977141 Likely Pathogenic: Metopic ridging-ptosis-facial dysmorphism syndrome 106,972,206(+) AC/A
NM_021224.6(ZNF462):c.6631del (p.Arg2211fs) 		FRAMESHIFT
977407 Uncertain Significance: Seizures 106,927,999(+) C/T
NM_021224.6(ZNF462):c.4087C>T (p.Pro1363Ser) 		MISSENSE_VARIANT,INTRON
985184 Pathogenic: Inborn genetic diseases 106,935,596(+) AAC/A
NM_021224.6(ZNF462):c.6214_6215del (p.His2072fs) 		FRAMESHIFT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ZNF462 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ZNF462 Gene

Variant ID Type Subtype PubMed ID
esv2669661 CNV deletion 23128226
esv2673055 CNV deletion 23128226
esv2738890 CNV deletion 23290073
esv29808 CNV loss 19812545
esv3545265 CNV deletion 23714750
esv3621391 CNV loss 21293372
esv3621392 CNV loss 21293372
nsv474945 CNV novel sequence insertion 20440878
nsv831680 CNV loss 17160897
nsv950923 CNV deletion 24416366
nsv968743 CNV duplication 23825009

Variation tolerance for ZNF462 Gene

Residual Variation Intolerance Score: 0.608% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.98; 87.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNF462 Gene

Human Gene Mutation Database (HGMD)
ZNF462
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZNF462

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF462 Gene

Disorders for ZNF462 Gene

MalaCards: The human disease database

(10) MalaCards diseases for ZNF462 Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
weiss-kruszka syndrome
  • wska
metopic ridging-ptosis-facial dysmorphism syndrome
autosomal dominant non-syndromic intellectual disability
  • autosomal dominant mental retardation
craniosynostosis
  • premature closure of cranial sutures
craniosynostosis 1
  • crs1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

ZN462_HUMAN
  • Weiss-Kruszka syndrome (WSKA) [MIM:618619]: An autosomal dominant, multiple congenital anomaly syndrome with variable expressivity and complete penetrance. Patients manifest developmental delay, hypotonia, feeding difficulties, craniofacial abnormalities including ptosis, abnormal head shape, downslanting palpebral fissures, metopic ridging, and craniosynostosis. Variable congenital heart defects can be observed in some patients. A few patients show agenesis of the corpus callosum on brain imaging. {ECO:0000269 PubMed:28513610, ECO:0000269 PubMed:29427787, ECO:0000269 PubMed:31361404}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for ZNF462

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with ZNF462: view

No data available for Genatlas for ZNF462 Gene

Publications for ZNF462 Gene

  1. Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay. (PMID: 28513610) Weiss K … Kruszka P (European journal of human genetics : EJHG 2017) 3 4 74
  2. Phenotype delineation of ZNF462 related syndrome. (PMID: 31361404) Kruszka P … Muenke M (American journal of medical genetics. Part A 2019) 3 4
  3. ZNF462 and KLF12 are disrupted by a de novo translocation in a patient with syndromic intellectual disability and autism spectrum disorder. (PMID: 29427787) Cosemans N … Peeters H (European journal of medical genetics 2018) 3 4
  4. Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data. (PMID: 22826440) Hahne H … Kuster B (Molecular & cellular proteomics : MCP 2012) 3 4
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41

ExternalLinks

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