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

Gene ID: 57862, updated on 5-Mar-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 sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 23.4), bone marrow (RPKM 18.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q24.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (73886859..73932521)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (68094511..68140172)
105.20220307 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
  • 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. [Apa1 VDR polymorphism and osteoporosis risk in postmenopausal Mexican women]. Castelán-Martínez OD, et al. Gac Med Mex, 2015 Jul-Aug. PMID 26290023
  2. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression. Lan X, et al. Mol Cell, 2021 Jan 21. PMID 33301730, Free PMC Article
  3. High glucose stimulates proliferative capacity of liver cancer cells possibly via O-GlcNAcylation-dependent transcriptional regulation of GJC1. Chen Y, et al. J Cell Physiol, 2018 Jan. PMID 30078215
  4. Dairy products, polymorphisms in the vitamin D receptor gene and colorectal adenoma recurrence. Hubner RA, et al. Int J Cancer, 2008 Aug 1. PMID 18470879
  5. Induction of extracellular matrix-remodeling genes by the senescence-associated protein APA-1. Benanti JA, et al. Mol Cell Biol, 2002 Nov. PMID 12370286, Free PMC Article

See all (23) citations in PubMed

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)

Genotypes

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_2023_10

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

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