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

Gene ID: 84627, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88100931..88440753)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94449769..94508741)
105.20220307 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome. García de Oteyza G, et al. Cornea, 2023 Jul 1. PMID 37098112
  2. Corneal Perforation After Corneal Cross-Linking in Keratoconus Associated With Potentially Pathogenic ZNF469 Mutations. Zhang W, et al. Cornea, 2019 Aug. PMID 31107761, Free PMC Article
  3. Identification of a Novel ZNF469 Mutation in a Pakistani Family With Brittle Cornea Syndrome. Micheal S, et al. Cornea, 2019 Jun. PMID 30865045
  4. Rare, Potentially Pathogenic Variants in ZNF469 Are Not Enriched in Keratoconus in a Large Australian Cohort of European Descent. Lucas SEM, et al. Invest Ophthalmol Vis Sci, 2017 Dec 1. PMID 29228253
  5. Polymorphism rs13334190 in zinc finger protein 469 (ZNF469) is not a risk factor for keratoconus in a Saudi cohort. Kalantan H, et al. BMC Res Notes, 2017 Nov 29. PMID 29187250, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome.
    Title: New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Rare variants in ZNF469 do not contribute to keratoconus susceptibility and do not account for the association at rs9938149.
    Title: Rare, Potentially Pathogenic Variants in ZNF469 Are Not Enriched in Keratoconus in a Large Australian Cohort of European Descent.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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
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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)

Genotypes

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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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
    Related
    ENSP00000456500.2, ENST00000565624.3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

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

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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