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    ZNF469 zinc finger protein 469 [ Homo sapiens (human) ]

    Gene ID: 84627, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZNF469provided by HGNC
    Official Full Name
    zinc finger protein 469provided by HGNC
    Primary source
    HGNC:HGNC:23216
    See related
    Ensembl:ENSG00000225614 MIM:612078; AllianceGenome:HGNC:23216
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BCS; BCS1; Zfp469
    Summary
    This gene encodes a zinc-finger protein. Low-percent homology to certain collagens suggests that it may function as a transcription factor or extra-nuclear regulator factor for the synthesis or organization of collagen fibers. Mutations in this gene cause brittle cornea syndrome. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 1.0), endometrium (RPKM 0.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF469 in Genome Data Viewer
    Location:
    16q24.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88100931..88440753)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94449769..94508741)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88449367..88507161)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11345 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:87984965-87985607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87990141-87991083 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88000587-88001090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88008279-88008799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88016725-88017317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88033523-88034377 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88034378-88035231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88039157-88039702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88039703-88040246 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:88042179-88042892 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:88042893-88043606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88046491-88047404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88047405-88048317 Neighboring gene BTG3 associated nuclear protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:88058223-88058469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88060746-88061316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88064237-88064738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88069223-88069723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88078499-88079000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88096566-88097334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88098057-88098732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88099409-88100084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11349 Neighboring gene uncharacterized LOC124903754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88123859-88124486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88126373-88127000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88146853-88147354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88147355-88147854 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:88150297-88151496 Neighboring gene uncharacterized LOC400553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88181294-88181921 Neighboring gene uncharacterized LOC105371401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88220489-88221296 Neighboring gene Sharpr-MPRA regulatory region 11460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88228172-88228704 Neighboring gene long intergenic non-protein coding RNA 2182 Neighboring gene Sharpr-MPRA regulatory region 6305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88275942-88276442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88292312-88293058 Neighboring gene uncharacterized LOC124900374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88294229-88295094 Neighboring gene uncharacterized LOC107984862 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:88298191-88299390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88305120-88305626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88308260-88309065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88337429-88337930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88338969-88339468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88342417-88342918 Neighboring gene Sharpr-MPRA regulatory region 14328 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:88366225-88367424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88383362-88384329 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88448183-88448726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88447094-88447638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88463994-88464796 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:88476410-88477609 Neighboring gene uncharacterized LOC112268182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88499412-88499912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88509531-88510396 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:88513905-88514141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7851 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11352 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:88526556-88527059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88528211-88529126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88544251-88545176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88545177-88546101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88546568-88547068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88547069-88547569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88550149-88550654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11353 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88549643-88550148 Neighboring gene uncharacterized LOC107984890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88574841-88575346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88576357-88576860 Neighboring gene microRNA 5189 Neighboring gene zinc finger protein, FOG family member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Brittle cornea without clinically-evident extraocular findings in an adult harboring a novel homozygous ZNF469 mutation. Khan AO, et al. Ophthalmic Genet, 2012 Dec. PMID 22486320
    2. Brittle cornea syndrome ZNF469 mutation carrier phenotype and segregation analysis of rare ZNF469 variants in familial keratoconus. Davidson AE, et al. Invest Ophthalmol Vis Sci, 2015 Jan 6. PMID 25564447
    3. Mutations in the zinc finger protein gene, ZNF469, contribute to the pathogenesis of keratoconus. Vincent AL, et al. Invest Ophthalmol Vis Sci, 2014 Aug 5. PMID 25097247
    4. Evidence against ZNF469 being causative for keratoconus in Polish patients. Karolak JA, et al. Acta Ophthalmol, 2016 May. PMID 26806788
    5. Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus. Lechner J, et al. Hum Mol Genet, 2014 Oct 15. PMID 24895405, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZNF469 is a profibrotic regulator of extracellular matrix in hepatic stellate cells.
      Title: ZNF469 is a profibrotic regulator of extracellular matrix in hepatic stellate cells.
    2. Genetic variants in the FOXO1 and ZNF469 genes are associated with keratoconus in Sweden: a case-control study.
      Title: Genetic variants in the FOXO1 and ZNF469 genes are associated with keratoconus in Sweden: a case-control study.
    3. New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome.
      Title: New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome.
    4. More than meets the eye: Expanding and reviewing the clinical and mutational spectrum of brittle cornea syndrome.
      Title: More than meets the eye: Expanding and reviewing the clinical and mutational spectrum of brittle cornea syndrome.
    5. CXL may be associated with the development of corneal perforation in particular at-risk individuals with keratoconus. Identifying clinical and genetic risk factors, including screening of ZNF469 and PRDM5, may be useful in the prevention of significant complications after CXL.
      Title: Corneal Perforation After Corneal Cross-Linking in Keratoconus Associated With Potentially Pathogenic ZNF469 Mutations.
    6. This is the first report of a ZNF469 homozygous mutation causing a Brittle cornea syndrome phenotype in a consanguineous Pakistani family.
      Title: Identification of a Novel ZNF469 Mutation in a Pakistani Family With Brittle Cornea Syndrome.
    7. Linc-ZNF469-3 promotes lung metastasis of TNBC through miR-574-5p-ZEB1 signaling axis.
      Title: A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer.
    8. genotype frequencies did not differ between the sporadic or familial keratoconus cases
      Title: Polymorphism rs13334190 in zinc finger protein 469 (ZNF469) is not a risk factor for keratoconus in a Saudi cohort.
    9. ZNF469 has a pathogenic role in Chinese patients with keratoconus.
      Title: Identification of seven novel ZNF469 mutations in keratoconus patients in a Han Chinese population.
    10. New detected ZNF 469 P873T and Q2188H heterozygote coding variants in isolated advance keratoconus patients may be associated with the disease pathogenesis.
      Title: Novel Zinc Finger Protein Gene 469 (ZNF469) Variants in Advanced Keratoconus.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Brittle cornea syndrome 1
    MedGen: C0268344 OMIM: 229200 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Common genetic variants near the Brittle Cornea Syndrome locus ZNF469 influence the blinding disease risk factor central corneal thickness.
    EBI GWAS Catalog
    Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
    EBI GWAS Catalog
    New loci associated with central cornea thickness include COL5A1, AKAP13 and AVGR8.
    EBI GWAS Catalog
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    EBI GWAS Catalog
    Population-based meta-analysis in Caucasians confirms association with COL5A1 and ZNF469 but not COL8A2 with central corneal thickness.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1858

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of extracellular matrix organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 469

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012236.2 RefSeqGene

      Range
      5001..18283
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001367624.2 → NP_001354553.1  zinc finger protein 469

      Status: REVIEWED

      Source sequence(s)
      AC132804, AC135049, KF456226
      Consensus CDS
      CCDS92205.1
      UniProtKB/Swiss-Prot
      H3BS19, Q96JG9
      UniProtKB/TrEMBL
      A0AAA9X9E9
      Related
      ENSP00000456500.2, ENST00000565624.3

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      88100931..88440753
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434810.1 → XP_047290766.1  zinc finger protein 469 isoform X1

      UniProtKB/Swiss-Prot
      H3BS19, Q96JG9
      UniProtKB/TrEMBL
      A0AAA9X9E9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      94449769..94508741
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314200.1 → XP_054170175.1  zinc finger protein 469 isoform X1

      UniProtKB/TrEMBL
      A0AAA9X9E9

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001127464.2: Suppressed sequence

      Description
      NM_001127464.2: This RefSeq has been removed because currently there is insufficient support for the transcript and protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JG9.4 GenPept UniProtKB/Swiss-Prot:Q96JG9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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