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

Gene ID: 55628, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (74597870..75065671)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (74825251..75295135)
105.20220307 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: 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. 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 (19) 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)

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

  • 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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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_2023_10

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

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