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    ZNF410 zinc finger protein 410 [ Homo sapiens (human) ]

    Gene ID: 57862, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZNF410provided by HGNC
    Official Full Name
    zinc finger protein 410provided by HGNC
    Primary source
    HGNC:HGNC:20144
    See related
    Ensembl:ENSG00000119725 MIM:619427; AllianceGenome:HGNC:20144
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    APA1; APA-1
    Summary
    Enables DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of gene expression and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 23.4), bone marrow (RPKM 18.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF410 in Genome Data Viewer
    Location:
    14q24.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (73886859..73932521)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (68094511..68140172)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (74353562..74399224)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2274 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:74302771-74302949 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:74305149-74305318 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:74318268-74318670 Neighboring gene prostaglandin reductase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8722 Neighboring gene FAM161 centrosomal protein B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74416687-74417687 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:74418757-74419055 Neighboring gene coenzyme Q6, monooxygenase Neighboring gene ectonucleoside triphosphate diphosphohydrolase 5 (inactive) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74459045-74459546 Neighboring gene ribosomal protein L41 pseudogene 4

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZNF410 represses fetal globin by singular control of CHD4.
      Title: ZNF410 represses fetal globin by singular control of CHD4.
    2. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression.
      Title: ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression.
    3. The HG-stimulated proliferative capacity was abolished upon decreasing O-GlcNAcylation, which could be reversed gradually by the simultaneous overexpression of APA1 and GJC1. Therefore, GJC1 could be a potential target for preventing liver cancer in patients with diabetes.
      Title: High glucose stimulates proliferative capacity of liver cancer cells possibly via O-GlcNAcylation-dependent transcriptional regulation of GJC1.
    4. No association was found between Apa1 genotypes and osteoporosis
      Title: [Apa1 VDR polymorphism and osteoporosis risk in postmenopausal Mexican women].
    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. VDR polymorphism genotypes and haplotypes did not directly alter recurrence risk, but the reduction in risk associated with high dairy product intake was confined to individuals with ApaI aA/AA genotype.
      Title: Dairy products, polymorphisms in the vitamin D receptor gene and colorectal adenoma recurrence.
    7. APA1 has a role in inducing extracellular matrix remodeling genes
      Title: Induction of extracellular matrix-remodeling genes by the senescence-associated protein APA-1.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    Potential readthrough

    Included gene: PTGR2

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    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 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 410
    Names
    another partner for ARF 1
    clones 23667 and 23775 zinc finger protein
    zinc finger protein APA-1

    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.

    mRNA and Protein(s)

    1. NM_001242924.2 → NP_001229853.1  zinc finger protein 410 isoform a

      See identical proteins and their annotated locations for NP_001229853.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a)
      Source sequence(s)
      AA652386, AC005480, AC005520, AK293350
      Consensus CDS
      CCDS55929.1
      UniProtKB/TrEMBL
      B2RCP6, Q53FM1
      Related
      ENSP00000407130.3, ENST00000442160.7
      Conserved Domains (4) summary
      sd00017
      Location:298 → 320
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:271 → 290
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:342 → 367
      zf-H2C2_2; Zinc-finger double domain
      pfam15909
      Location:268 → 351
      zf-C2H2_8; C2H2-type zinc ribbon

    2. NM_001242926.2 → NP_001229855.1  zinc finger protein 410 isoform c

      See identical proteins and their annotated locations for NP_001229855.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in both the 5' and central coding regions, and it also lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (c) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AA652386, AC005480, BC050683
      Consensus CDS
      CCDS55930.1
      UniProtKB/TrEMBL
      B2RCP6, Q53FM1
      Related
      ENSP00000323293.6, ENST00000324593.10
      Conserved Domains (3) summary
      COG5048
      Location:148 → 367
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:281 → 303
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:254 → 273
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. NM_001242927.2 → NP_001229856.1  zinc finger protein 410 isoform d

      See identical proteins and their annotated locations for NP_001229856.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons in the 5' coding region, and it also lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AA652386, AC005480, AK299138
      Consensus CDS
      CCDS55931.1
      UniProtKB/TrEMBL
      B4DPE9
      Related
      ENSP00000442228.1, ENST00000540593.5
      Conserved Domains (4) summary
      sd00017
      Location:208 → 230
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:181 → 200
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:252 → 277
      zf-H2C2_2; Zinc-finger double domain
      pfam15909
      Location:178 → 261
      zf-C2H2_8; C2H2-type zinc ribbon

    4. NM_001242928.2 → NP_001229857.1  zinc finger protein 410 isoform e

      See identical proteins and their annotated locations for NP_001229857.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in its 5' UTR and 5' coding region, uses an alternate downstream start codon, and includes alternate exon structure in the 3' coding region, compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.
      Source sequence(s)
      AA652386, AC005480, BC000330, DC379519
      Conserved Domains (4) summary
      sd00017
      Location:85 → 107
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:58 → 77
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:129 → 154
      zf-H2C2_2; Zinc-finger double domain
      pfam13900
      Location:276 → 310
      GVQW; Putative domain of unknown function

    5. NM_021188.3 → NP_067011.1  zinc finger protein 410 isoform b

      See identical proteins and their annotated locations for NP_067011.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, and it also lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AA652386, AC005480, AK223261
      Consensus CDS
      CCDS9821.1
      UniProtKB/Swiss-Prot
      B4DDV5, B4DR78, O00153, Q86VK4, Q9BQ19
      UniProtKB/TrEMBL
      B2RCP6, Q53FM1
      Related
      ENSP00000451763.2, ENST00000555044.6
      Conserved Domains (4) summary
      sd00017
      Location:281 → 303
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:254 → 273
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:325 → 350
      zf-H2C2_2; Zinc-finger double domain
      pfam15909
      Location:251 → 334
      zf-C2H2_8; C2H2-type zinc ribbon

    RNA

    1. NR_040251.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an alternate exon and uses an alternate splice site in the 5' region, and also lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA652386, AC005480, AK298520
      Related
      ENST00000398139.7

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      73886859..73932521
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      68094511..68140172
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VK4.2 GenPept UniProtKB/Swiss-Prot:Q86VK4

    Gene LinkOut

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

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