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Aliases for ZNF397 Gene

Aliases for ZNF397 Gene

  • Zinc Finger Protein 397 2 3 5
  • Zinc Finger Protein 47 2 3 4
  • Zinc Finger And SCAN Domain-Containing Protein 15 3 4
  • ZSCAN15 3 4
  • ZNF47 3 4

External Ids for ZNF397 Gene

Previous HGNC Symbols for ZNF397 Gene

  • ZNF47

Previous GeneCards Identifiers for ZNF397 Gene

  • GC18P032855
  • GC18P032640
  • GC18P031072
  • GC18P031073
  • GC18P031074
  • GC18P032820
  • GC18P029679

Summaries for ZNF397 Gene

Entrez Gene Summary for ZNF397 Gene

  • This gene encodes a protein with a N-terminal SCAN domain, and the longer isoform contains nine C2H2-type zinc finger repeats in the C-terminal domain. The protein localizes to centromeres during interphase and early prophase, and different isoforms can repress or activate transcription in transfection studies. Multiple transcript variants encoding different isoforms have been found for this gene. Additional variants have been described, but their biological validity has not been determined. [provided by RefSeq, Oct 2009]

GeneCards Summary for ZNF397 Gene

ZNF397 (Zinc Finger Protein 397) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. An important paralog of this gene is ZKSCAN8.

UniProtKB/Swiss-Prot for ZNF397 Gene

  • Isoform 3 acts as a DNA-dependent transcriptional repressor.

Additional gene information for ZNF397 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNF397 Gene

Genomics for ZNF397 Gene

GeneHancer (GH) Regulatory Elements for ZNF397 Gene

Promoters and enhancers for ZNF397 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18I035239 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.5 508 2.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF397 ENSG00000268573 ZNF396 ZNF24 PIR50065
GH18I035495 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 81 +256.3 256327 3.1 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 INO80C ENSG00000267140 ENSG00000268573 ZNF397 ZSCAN30 ELP2 RPRD1A C18orf21 ZNF271P ZNF396
GH18I035289 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 31.3 +49.6 49576 2.3 MLX ZFP64 DMAP1 YY1 E2F8 ZNF143 SP3 ZNF610 NBN NR2C1 ENSG00000268573 ZSCAN30 ZNF271P ZNF397 C18orf21 ZNF24 GC18M035301 PIR53427
GH18I036127 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 24.3 +889.8 889816 5.2 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ELP2 SLC39A6 ENSG00000268573 ZNF397 KIAA1328 LOC101927809 MOCOS LOC791126 PIR50550
GH18I035967 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.8 +730.1 730140 5.8 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B C18orf21 LOC105372066 ENSG00000278986 ENSG00000268573 ZNF397 ELP2 RPRD1A GC18M035972 GC18P035965
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZNF397 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZNF397 gene promoter:

Genomic Locations for ZNF397 Gene

Genomic Locations for ZNF397 Gene
26,416 bases
Plus strand

Genomic View for ZNF397 Gene

Genes around ZNF397 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF397 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF397 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNF397 Gene

Proteins for ZNF397 Gene

  • Protein details for ZNF397 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein 397
    Protein Accession:
    Secondary Accessions:
    • Q9BRM2

    Protein attributes for ZNF397 Gene

    534 amino acids
    Molecular mass:
    61139 Da
    Quaternary structure:
    • Isoforms 1 and 3 can both homo- and hetero-associate. Homo-association of isoform 1 is dependent on the presence of the SCAN domain.

    Alternative splice isoforms for ZNF397 Gene


neXtProt entry for ZNF397 Gene

Post-translational modifications for ZNF397 Gene

No data available for DME Specific Peptides for ZNF397 Gene

Domains & Families for ZNF397 Gene

Gene Families for ZNF397 Gene

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

Suggested Antigen Peptide Sequences for ZNF397 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with ZNF397: view

Function for ZNF397 Gene

Molecular function for ZNF397 Gene

UniProtKB/Swiss-Prot Function:
Isoform 3 acts as a DNA-dependent transcriptional repressor.

Phenotypes From GWAS Catalog for ZNF397 Gene

Gene Ontology (GO) - Molecular Function for ZNF397 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNF397: view
genes like me logo Genes that share phenotypes with ZNF397: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZNF397 Gene

Localization for ZNF397 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF397 Gene

Isoform 1: Nucleus.
Isoform 3: Nucleus. Cytoplasm.

Subcellular locations from

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 ZNF397 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Microtubules (2)
  • Nucleoli (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNF397 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with ZNF397: view

Pathways & Interactions for ZNF397 Gene

SuperPathways for ZNF397 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZNF397 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with ZNF397: view

No data available for Pathways by source and SIGNOR curated interactions for ZNF397 Gene

Drugs & Compounds for ZNF397 Gene

No Compound Related Data Available

Transcripts for ZNF397 Gene

Unigene Clusters for ZNF397 Gene

Zinc finger protein 397:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF397 Gene

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

Relevant External Links for ZNF397 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZNF397 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZNF397 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZNF397 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (52.2) and Blymphocyte (16.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZNF397 Gene

Protein tissue co-expression partners for ZNF397 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZNF397 Gene:


SOURCE GeneReport for Unigene cluster for ZNF397 Gene:


mRNA Expression by UniProt/SwissProt for ZNF397 Gene:

Tissue specificity: Expressed strongly in testis, moderately in skeletal muscle, pancreas and prostate, and weakly in heart, placenta, liver, kidney, spleen, thymus and small intestine.

Evidence on tissue expression from TISSUES for ZNF397 Gene

  • Nervous system(2)
genes like me logo Genes that share expression patterns with ZNF397: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNF397 Gene

Orthologs for ZNF397 Gene

This gene was present in the common ancestor of mammals.

Orthologs for ZNF397 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZNF397 33 34
  • 99.75 (n)
(Canis familiaris)
Mammalia ZNF397 33 34
  • 90.83 (n)
(Mus musculus)
Mammalia Zfp397 33 16 34
  • 87.07 (n)
(Bos Taurus)
Mammalia ZNF397 33
  • 86.87 (n)
(Rattus norvegicus)
Mammalia Zfp397 33
  • 86.19 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 38 (a)
-- 34
  • 37 (a)
Species where no ortholog for ZNF397 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for ZNF397 Gene

Gene Tree for ZNF397 (if available)
Gene Tree for ZNF397 (if available)

Paralogs for ZNF397 Gene

(490) SIMAP similar genes for ZNF397 Gene using alignment to 5 proteins: Pseudogenes for ZNF397 Gene

genes like me logo Genes that share paralogs with ZNF397: view

Variants for ZNF397 Gene

Sequence variations from dbSNP and Humsavar for ZNF397 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs1000012686 -- 35,245,560(+) T/C coding_sequence_variant, intron_variant, synonymous_variant
rs1000014415 -- 35,251,456(+) AAAGA/A 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000247201 -- 35,242,403(+) T/C 5_prime_UTR_variant
rs1000662403 -- 35,241,278(+) C/T intron_variant
rs1000663655 -- 35,255,443(+) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZNF397 Gene

Variant ID Type Subtype PubMed ID
esv3642197 CNV gain 21293372
esv3390534 CNV insertion 20981092
esv3305949 CNV mobile element insertion 20981092

Variation tolerance for ZNF397 Gene

Gene Damage Index Score: 0.56; 12.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNF397 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF397 Gene

Disorders for ZNF397 Gene

Additional Disease Information for ZNF397

No disorders were found for ZNF397 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZNF397 Gene

Publications for ZNF397 Gene

  1. Identification and characterization of two novel human SCAN domain-containing zinc finger genes ZNF396 and ZNF397. (PMID: 12801647) Wu Y … Zhao S (Gene 2003) 3 4 22 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for ZNF397 Gene

Sources for ZNF397 Gene

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