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ZNF408 zinc finger protein 408 [ Homo sapiens (human) ]

Gene ID: 79797, updated on 7-Apr-2024

Summary

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Official Symbol
ZNF408provided by HGNC
Official Full Name
zinc finger protein 408provided by HGNC
Primary source
HGNC:HGNC:20041
See related
Ensembl:ENSG00000175213 MIM:616454; AllianceGenome:HGNC:20041
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
EVR6; RP72
Summary
The protein encoded by this gene contains ten tandem zinc fingers and an N-terminal SET domain, so it is likely a DNA binding protein that interacts with other proteins. In adults, the encoded protein is expressed most highly in retina. Consequently, defects in this gene have been associated with familial exudative vitreoretinopathy (FEVR) and retinitis pigmentosa (RP). [provided by RefSeq, Dec 2016]
Expression
Ubiquitous expression in bone marrow (RPKM 5.1), ovary (RPKM 3.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11p11.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (46701031..46705912)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46857047..46861916)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (46722581..46727462)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 32 Neighboring gene harbinger transposase derived 1 Neighboring gene autophagy related 13 Neighboring gene Rho GTPase activating protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:46715957-46716456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4684 Neighboring gene coagulation factor II, thrombin Neighboring gene cytoskeleton associated protein 5 Neighboring gene microRNA 5582

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. An FEVR-associated mutation in ZNF408 alters the expression of genes involved in the development of vasculature. Karjosukarso DW, et al. Hum Mol Genet, 2018 Oct 15. PMID 29982478
  2. Exome sequencing confirms ZNF408 mutations as a cause of familial retinitis pigmentosa. Habibi I, et al. Ophthalmic Genet, 2017 Sep-Oct. PMID 28095122
  3. Whole-Exome Sequencing Identifies Novel Variants that Co-segregates with Autosomal Recessive Retinal Degeneration in a Pakistani Pedigree. Biswas P, et al. Adv Exp Med Biol, 2018. PMID 29721947
  4. Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations. Avila-Fernandez A, et al. Hum Mol Genet, 2015 Jul 15. PMID 25882705
  5. Mutation spectrum of the FZD-4, TSPAN12 AND ZNF408 genes in Indian FEVR patients. Musada GR, et al. BMC Ophthalmol, 2016 Jun 17. PMID 27316669, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic and clinical characteristics of ZNF408-related familial exudative vitreoretinopathy.
    Title: Genetic and clinical characteristics of ZNF408-related familial exudative vitreoretinopathy.
  2. p.H455Y ZNF408 has reduced DNA-binding ability, as compared to the wild-type protein. The fact that the p.H455Y mutation disrupts the expression of genes important for the development of vasculature sheds further light on the molecular mechanisms underlying ZNF408-associated familial exudative vitreoretinopathy.
    Title: An FEVR-associated mutation in ZNF408 alters the expression of genes involved in the development of vasculature.
  3. In a Pakistani family with retinal degeneration, whole-exome sequencing identified 2 homozygous missense variants: c.1304G>A; p.Arg435Gln in ZNF408 (NM_024741) and c.902G>A; p.Gly301Asp in C1QTNF4 (NM_031909). Both segregated with the retinal phenotype in this family and were absent in ethnically matched control chromosomes.
    Title: Whole-Exome Sequencing Identifies Novel Variants that Co-segregates with Autosomal Recessive Retinal Degeneration in a Pakistani Pedigree.
  4. This is the first study to report a group of patients with digenic familial exudative vitreoretinopathy (FEVR). In most affected eyes, the stage was more severe than stage 3. We speculate that the phenotype of FEVR is more severe in patients with digenic rather than monogenic variants of FEVR-related genes.
    Title: The characteristics of digenic familial exudative vitreoretinopathy.
  5. In conclusion, we report a novel mutation in ZNF408 causing autosomal recessive retinitis pigmentosa with vitreal alterations in three members of a Tunisian family, which further accentuates the role of this new gene in the susceptibility to retinitis pigmentosa.
    Title: Exome sequencing confirms ZNF408 mutations as a cause of familial retinitis pigmentosa.
  6. Several novel mutations (missense, non-stop and insertion) were detected in the coding regions of FZD4, TSPAN12 and ZNF408 genes among the unrelated vitreoretinopathy probands.
    Title: Mutation spectrum of the FZD-4, TSPAN12 AND ZNF408 genes in Indian FEVR patients.
  7. ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing autosomal recessive rtinitis pigmentosa.
    Title: Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations.
  8. Data indicate ZNF408 missense variant (p.Ser126Asn) in 132 familial exudative vitreoretinopathy (FEVR) individuals in a Japanese family.
    Title: ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature.
Submit: New GeneRIF Correction

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
Exudative vitreoretinopathy 6
MedGen: C4225316 OMIM: 616468 GeneReviews: Not available
Compare labs
Retinitis pigmentosa 72
MedGen: C4225315 OMIM: 616469 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
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

  • FLJ12827

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger protein 408
Names
PR domain zinc finger protein 17

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_052967.1 RefSeqGene

    Range
    5265..10146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001184751.2 → NP_001171680.1  zinc finger protein 408 isoform 2

    See identical proteins and their annotated locations for NP_001171680.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC115088, AK022889, AK302180, AW246726, BC015708
    UniProtKB/TrEMBL
    B4DXY4
    Conserved Domains (3) summary
    COG5048
    Location:300 → 508
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:403 → 423
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:474 → 499
    zf-H2C2_2; Zinc-finger double domain

  2. NM_024741.3 → NP_079017.1  zinc finger protein 408 isoform 1

    See identical proteins and their annotated locations for NP_079017.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK022889, AW246726, BC015708
    Consensus CDS
    CCDS7923.1
    UniProtKB/Swiss-Prot
    Q9H9D4
    Related
    ENSP00000309606.2, ENST00000311764.3
    Conserved Domains (3) summary
    COG5048
    Location:308 → 516
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:411 → 431
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:482 → 507
    zf-H2C2_2; Zinc-finger double domain

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    46701031..46705912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    46857047..46861916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H9D4.1 GenPept UniProtKB/Swiss-Prot:Q9H9D4

Gene LinkOut

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