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    ZNF407 zinc finger protein 407 [ Homo sapiens (human) ]

    Gene ID: 55628, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZNF407provided by HGNC
    Official Full Name
    zinc finger protein 407provided by HGNC
    Primary source
    HGNC:HGNC:19904
    See related
    Ensembl:ENSG00000215421 MIM:615894; AllianceGenome:HGNC:19904
    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
    SIMHA
    Summary
    This gene encodes a zinc finger protein whose exact function is not known. It may be involved in transcriptional regulation. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
    Expression
    Ubiquitous expression in testis (RPKM 1.7), ovary (RPKM 1.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF407 in Genome Data Viewer
    Location:
    18q22.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (74597870..75065671)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (74825251..75295135)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (72265106..72777627)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904324 Neighboring gene carnosine dipeptidase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13501 Neighboring gene ZNF407 antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:72345358-72346557 Neighboring gene VISTA enhancer hs378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13503 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:72517901-72519100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:72531111-72531933 Neighboring gene VISTA enhancer hs824 Neighboring gene uncharacterized LOC124904323 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:72632804-72633403 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:72633404-72634002 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:72640049-72640868 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:72641053-72642252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:72706703-72707204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:72707205-72707704 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:72734840-72735036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:72765356-72765856 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:72782275-72783474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:72784554-72785054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:72785055-72785555 Neighboring gene uncharacterized LOC124904325 Neighboring gene uncharacterized LOC124904326 Neighboring gene uncharacterized LOC105376874

    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. Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism. Zahra Q, et al. J Hum Genet, 2020 Dec. PMID 32737394
    2. Balanced translocation t(3;18)(p13;q22.3) and points mutation in the ZNF407 gene detected in patients with both moderate non-syndromic intellectual disability and autism. Ren CM, et al. Biochim Biophys Acta, 2013 Mar. PMID 23195952
    3. PI3K/AKT-mediated upregulation of WDR5 promotes colorectal cancer metastasis by directly targeting ZNF407. Tan X, et al. Cell Death Dis, 2017 Mar 16. PMID 28300833, Free PMC Article
    4. Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families. Kapoor M, et al. Drug Alcohol Depend, 2014 Sep 1. PMID 24962325, Free PMC Article
    5. Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping. McDonough CW, et al. Hum Genet, 2009 Dec. PMID 19690890, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism.
      Title: Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism.
    2. WDR5 shows a direct binding to the ZNF407 promoter.
      Title: PI3K/AKT-mediated upregulation of WDR5 promotes colorectal cancer metastasis by directly targeting ZNF407.
    3. Data indicate that mutations in the ZNF407 gene contribute to the pathogenesis of a group of intellectual disability (ID) patients with autism.
      Title: Balanced translocation t(3;18)(p13;q22.3) and points mutation in the ZNF407 gene detected in patients with both moderate non-syndromic intellectual disability and autism.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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
    Short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies
    MedGen: C5561998 OMIM: 619557 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-07-11)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-07-11)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women.
    EBI GWAS Catalog
    Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.
    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

    • FLJ13839, FLJ20307, KIAA1703

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 407

    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_013216.2 RefSeqGene

      Range
      5002..472803
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001146189.1 → NP_001139661.1  zinc finger protein 407 isoform 2

      See identical proteins and their annotated locations for NP_001139661.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is missing the 3' terminal exon, and contains an alternate segment at the 3' end compared to variant 1. This results in a shorter isoform (2) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AB051490, AC138660, AK000314, AK056288, DB096147
      Consensus CDS
      CCDS58634.1
      UniProtKB/Swiss-Prot
      Q9C0G0
      Related
      ENSP00000463270.1, ENST00000577538.5
      Conserved Domains (3) summary
      sd00017
      Location:1630 → 1650
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1642 → 1669
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001146190.1 → NP_001139662.1  zinc finger protein 407 isoform 3

      See identical proteins and their annotated locations for NP_001139662.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) is missing several exons from the 3' end, and contains an alternate exon at the 3' end compared to variant 1. This results in a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AB051490, AC138660, AK000314, AK000317, AK056288, DB096147
      Consensus CDS
      CCDS54191.1
      UniProtKB/Swiss-Prot
      Q9C0G0
      Related
      ENSP00000310359.5, ENST00000309902.10
      Conserved Domains (3) summary
      sd00017
      Location:1539 → 1561
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1557 → 1578
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001384475.1 → NP_001371404.1  zinc finger protein 407 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC015819, AC023380, AC091589, AC100783, AC138660, FP565322
      Consensus CDS
      CCDS45885.1
      UniProtKB/Swiss-Prot
      B5MD54, Q96MY0, Q9C0G0, Q9H8A1, Q9NXD4, Q9NXD7
      Conserved Domains (4) summary
      sd00017
      Location:1630 → 1650
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1642 → 1669
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:1714 → 1738
      zf-H2C2_5; C2H2-type zinc-finger domain

    4. NM_017757.3 → NP_060227.2  zinc finger protein 407 isoform 1

      See identical proteins and their annotated locations for NP_060227.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC015819, AC023380, AC091589, AC100783, AC138660, FP565322
      Consensus CDS
      CCDS45885.1
      UniProtKB/Swiss-Prot
      B5MD54, Q96MY0, Q9C0G0, Q9H8A1, Q9NXD4, Q9NXD7
      Related
      ENSP00000299687.4, ENST00000299687.10
      Conserved Domains (4) summary
      sd00017
      Location:1630 → 1650
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1642 → 1669
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:1714 → 1738
      zf-H2C2_5; C2H2-type zinc-finger domain

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      74597870..75065671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017025838.3 → XP_016881327.1  zinc finger protein 407 isoform X1

    2. XM_011526069.4 → XP_011524371.1  zinc finger protein 407 isoform X2

      Conserved Domains (3) summary
      sd00017
      Location:1539 → 1561
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1557 → 1578
      zf-H2C2_2; Zinc-finger double domain

    3. XM_011526070.3 → XP_011524372.1  zinc finger protein 407 isoform X3

      See identical proteins and their annotated locations for XP_011524372.1

      UniProtKB/Swiss-Prot
      Q9C0G0
      Related
      ENSP00000462348.1, ENST00000582337.5
      Conserved Domains (3) summary
      sd00017
      Location:1539 → 1561
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1557 → 1578
      zf-H2C2_2; Zinc-finger double domain

    4. XM_006722500.5 → XP_006722563.1  zinc finger protein 407 isoform X4

      Conserved Domains (3) summary
      sd00017
      Location:1539 → 1561
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00020
      Location:1416 → 1445
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:1557 → 1578
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      74825251..75295135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318801.1 → XP_054174776.1  zinc finger protein 407 isoform X1

    2. XM_054318802.1 → XP_054174777.1  zinc finger protein 407 isoform X2

    3. XM_054318803.1 → XP_054174778.1  zinc finger protein 407 isoform X3

    4. XM_054318804.1 → XP_054174779.1  zinc finger protein 407 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C0G0.2 GenPept UniProtKB/Swiss-Prot:Q9C0G0

    Gene LinkOut

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

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