ZNF408 Gene (Protein Coding)

Zinc Finger Protein 408

GC11P046700
GIFtS:
38
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). [provid... See more...

Aliases for ZNF408 Gene

Aliases for ZNF408 Gene

  • Zinc Finger Protein 408 2 3 4 5
  • PR Domain Zinc Finger Protein 17 3 4
  • FLJ12827 2
  • ZNF408 5
  • PRDM17 4
  • PFM14 4
  • EVR6 3
  • RP72 3

External Ids for ZNF408 Gene

Previous GeneCards Identifiers for ZNF408 Gene

  • GC11P047600
  • GC11P046753
  • GC11P046686
  • GC11P046678
  • GC11P046428
  • GC11P046722

Summaries for ZNF408 Gene

Entrez Gene Summary for ZNF408 Gene

  • 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]

GeneCards Summary for ZNF408 Gene

ZNF408 (Zinc Finger Protein 408) is a Protein Coding gene. Diseases associated with ZNF408 include Exudative Vitreoretinopathy 6 and Retinitis Pigmentosa 72. Gene Ontology (GO) annotations related to this gene include identical protein binding. An important paralog of this gene is ZKSCAN7.

UniProtKB/Swiss-Prot Summary for ZNF408 Gene

Additional gene information for ZNF408 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZNF408 Gene

Genomics for ZNF408 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ZNF408 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZNF408 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZNF408

Top Transcription factor binding sites by QIAGEN in the ZNF408 gene promoter:
  • AREB6
  • ATF-2
  • c-Jun
  • CREB
  • deltaCREB
  • Lmo2
  • Nkx2-5

Genomic Locations for ZNF408 Gene

Latest Assembly
chr11:46,701,030-46,705,912
(GRCh38/hg38)
Size:
4,883 bases
Orientation:
Plus strand

Previous Assembly
chr11:46,722,581-46,727,462
(GRCh37/hg19 by Entrez Gene)
Size:
4,882 bases
Orientation:
Plus strand

chr11:46,722,368-46,727,462
(GRCh37/hg19 by Ensembl)
Size:
5,095 bases
Orientation:
Plus strand

Genomic View for ZNF408 Gene

Genes around ZNF408 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF408 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF408 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ZNF408 Gene

Proteins for ZNF408 Gene

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  • Protein details for ZNF408 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9D4-ZN408_HUMAN
    Recommended name:
    Zinc finger protein 408
    Protein Accession:
    Q9H9D4

    Protein attributes for ZNF408 Gene

    Size:
    720 amino acids
    Molecular mass:
    78439 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZNF408 Gene

Protein Expression for ZNF408 Gene

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

Post-translational modifications for ZNF408 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZNF408 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZNF408 Gene

Domains & Families for ZNF408 Gene

Gene Families for ZNF408 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZNF408 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ZNF408 Gene

GenScript: Design optimal peptide antigens:
  • PR domain zinc finger protein 17 (ZN408_HUMAN)
genes like me logo Genes that share domains with ZNF408: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ZNF408 Gene

Function for ZNF408 Gene

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  6. Cell Lines for research

Molecular function for ZNF408 Gene

UniProtKB/Swiss-Prot Function:
May be involved in transcriptional regulation.

Phenotypes From GWAS Catalog for ZNF408 Gene

Gene Ontology (GO) - Molecular Function for ZNF408 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IBA 21873635
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 14667819
GO:0042802 identical protein binding IPI 15231747
genes like me logo Genes that share ontologies with ZNF408: view
genes like me logo Genes that share phenotypes with ZNF408: view

Human Phenotype Ontology for ZNF408 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ZNF408 Gene

MGI Knock Outs for ZNF408:
  • Zfp408 Zfp408<tm1b(EUCOMM)Wtsi>

Animal Models for research

miRNA for ZNF408 Gene

miRTarBase miRNAs that target ZNF408

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZNF408

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ZNF408 Gene

Localization for ZNF408 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF408 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 ZNF408 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centriolar satellite (2)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNF408 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus IEA,IDA 23716654
genes like me logo Genes that share ontologies with ZNF408: view

Pathways & Interactions for ZNF408 Gene

PathCards logo

SuperPathways for ZNF408 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZNF408 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
genes like me logo Genes that share ontologies with ZNF408: view

No data available for Pathways by source and SIGNOR curated interactions for ZNF408 Gene

Drugs & Compounds for ZNF408 Gene

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No Compound Related Data Available

Transcripts for ZNF408 Gene

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mRNA/cDNA for ZNF408 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
5 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 ZNF408

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF408 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5
SP1: - - - -
SP2: - - -
SP3: - - -
SP4: - -
SP5: -

Relevant External Links for ZNF408 Gene

GeneLoc Exon Structure for
ZNF408

Expression for ZNF408 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZNF408 Gene

mRNA expression in normal human tissues for ZNF408 Gene
mRNA expression by GTEx for ZNF408 GenemRNA expression by BioGPS for ZNF408 Gene

Protein differential expression in normal tissues from HIPED for ZNF408 Gene

This gene is overexpressed in Adipocyte (59.1) and Lymph node (9.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZNF408 Gene



Protein tissue co-expression partners for ZNF408 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZNF408

SOURCE GeneReport for Unigene cluster for ZNF408 Gene:

Hs.656931

mRNA Expression by UniProt/SwissProt for ZNF408 Gene:

Q9H9D4-ZN408_HUMAN
Tissue specificity: Highest expression is observed in adult retina; abundantly expressed in the fetal eye (PubMed:23716654). In the retina, it is detected in the outer nuclear layer, especially cone and rod photoreceptor cells, ganglion cell layer and both outer and inner plexiform layers (at protein level) (PubMed:25882705). Expressed in retinal blood vessels (at protein level) (PubMed:25882705).

Evidence on tissue expression from TISSUES for ZNF408 Gene

  • Nervous system(4.3)
  • Lung(4.2)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNF408 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
  • penis
  • testicle
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with ZNF408: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ZNF408 Gene

Orthologs for ZNF408 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZNF408 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia ZNF408 30 31
  • 99.26 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia ZNF408 30 31
  • 85.21 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia ZNF408 30 31
  • 82.16 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Zfp408 30 17 31
  • 76.99 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia LOC100362202 30
  • 76.16 (n)
Oppossum
(Monodelphis domestica)
 Mammalia ZNF408 31
  • 47 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia ZNF408 31
  • 57 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia znf408 30
  • 56.28 (n)
Zebrafish
(Danio rerio)
 Actinopterygii LOC793421 30
  • 50.65 (n)
ZNF408 31
  • 35 (a)
 OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.7747 30
Species where no ortholog for ZNF408 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)
  • Chicken (Gallus gallus)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for ZNF408 Gene

ENSEMBL:
Gene Tree for ZNF408 (if available)
TreeFam:
Gene Tree for ZNF408 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZNF408: view image

Paralogs for ZNF408 Gene

Paralogs for ZNF408 Gene

(46) SIMAP similar genes for ZNF408 Gene using alignment to 1 proteins:

  • ZN408_HUMAN
genes like me logo Genes that share paralogs with ZNF408: view

Variants for ZNF408 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZNF408 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
835031 Uncertain Significance: not provided 46,701,067(+) T/C
NM_024741.3(ZNF408):c.20T>C (p.Leu7Pro) 		MISSENSE_VARIANT,FIVE_PRIME_UTR
836954 Uncertain Significance: not provided 46,704,443(+) A/G
NM_024741.3(ZNF408):c.743A>G (p.Asp248Gly) 		MISSENSE
838525 Uncertain Significance: not provided 46,705,234(+) C/T
NM_024741.3(ZNF408):c.1534C>T (p.Arg512Cys) 		MISSENSE
841370 Uncertain Significance: not provided 46,705,007(+) C/T
NM_024741.3(ZNF408):c.1307C>T (p.Pro436Leu) 		MISSENSE
844030 Uncertain Significance: not provided 46,705,247(+) G/A
NM_024741.3(ZNF408):c.1547G>A (p.Arg516Gln) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ZNF408 Gene

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

Variation tolerance for ZNF408 Gene

Residual Variation Intolerance Score: 11.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.00; 87.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNF408 Gene

Human Gene Mutation Database (HGMD)
ZNF408
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZNF408

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for ZNF408 Gene

Disorders for ZNF408 Gene

MalaCards: The human disease database

(15) MalaCards diseases for ZNF408 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

ZN408_HUMAN
  • Vitreoretinopathy, exudative 6 (EVR6) [MIM:616468]: A form of exudative vitreoretinopathy, a disorder of the retinal vasculature characterized by an abrupt cessation of growth of peripheral capillaries, leading to an avascular peripheral retina. This may lead to compensatory retinal neovascularization, which is thought to be induced by hypoxia from the initial avascular insult. New vessels are prone to leakage and rupture causing exudates and bleeding, followed by scarring, retinal detachment and blindness. Clinical features can be highly variable, even within the same family. Patients with mild forms of the disease are asymptomatic, and their only disease related abnormality is an arc of avascular retina in the extreme temporal periphery. {ECO:0000269 PubMed:23716654}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Retinitis pigmentosa 72 (RP72) [MIM:616469]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:25882705}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for ZNF408

Genetic Association Database
(GAD)
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 ZNF408: view

No data available for Genatlas for ZNF408 Gene

Publications for ZNF408 Gene

  1. Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations. (PMID: 25882705) Avila-Fernandez A … Ayuso C (Human molecular genetics 2015) 3 4 74
  2. ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature. (PMID: 23716654) Collin RW … Cremers FP (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4 74
  3. An FEVR-associated mutation in ZNF408 alters the expression of genes involved in the development of vasculature. (PMID: 29982478) Karjosukarso DW … Collin RWJ (Human molecular genetics 2018) 3 74
  4. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. (PMID: 19801982) Rivadeneira F … Genetic Factors for Osteoporosis (GEFOS) Consortium (Nature genetics 2009) 3 41
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

ExternalLinks

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