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ZNF480 zinc finger protein 480 [ Homo sapiens (human) ]

Gene ID: 147657, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF480provided by HGNC
Official Full Name
zinc finger protein 480provided by HGNC
Primary source
HGNC:HGNC:23305
See related
Ensembl:ENSG00000198464 MIM:613910; AllianceGenome:HGNC:23305
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
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 3.1), lymph node (RPKM 2.7) and 25 other tissues See more
Orthologs
all
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Genomic context

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See ZNF480 in Genome Data Viewer
Location:
19q13.41
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (52297169..52325922)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (55384358..55413117)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (52800422..52829175)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904763 Neighboring gene Sharpr-MPRA regulatory region 2064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15043 Neighboring gene zinc finger protein 766 Neighboring gene microRNA 643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:52841280-52841780 Neighboring gene zinc finger protein 610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15048 Neighboring gene zinc finger protein 880 Neighboring gene ZNF528 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:52900414-52901613

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. A novel KRAB zinc-finger protein, ZNF480, expresses in human heart and activates transcriptional activities of AP-1 and SRE. Yi Z, et al. Biochem Biophys Res Commun, 2004 Jul 23. PMID 15219843
  2. Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease. Jouan L, et al. Behav Brain Funct, 2013 Feb 20. PMID 23425335, Free PMC Article
  3. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. König R, et al. Cell, 2008 Oct 3. PMID 18854154, Free PMC Article
  4. A Y2H-seq approach defines the human protein methyltransferase interactome. Weimann M, et al. Nat Methods, 2013 Apr. PMID 23455924
  5. Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. Kouranti I, et al. Int J Mol Sci, 2022 May 5. PMID 35563538, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This supports the notion that de novo mutations in ZNF480 are extremely rare in schizophrenia
    Title: Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease.
  2. 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.
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

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of zinc finger protein 480 (ZNF480) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • MGC32104

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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 480

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_001297624.2 → NP_001284553.1  zinc finger protein 480 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
    Source sequence(s)
    AC010320, AK303271, AL832560, DA501214
    Consensus CDS
    CCDS77346.1
    UniProtKB/TrEMBL
    F8WEZ9
    Related
    ENSP00000334164.6, ENST00000334564.11
    Conserved Domains (6) summary
    smart00349
    Location:27 → 67
    KRAB; krueppel associated box
    COG5048
    Location:115 → 458
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:302 → 322
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:356 → 378
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:27 → 66
    KRAB; KRAB box
    pfam13465
    Location:454 → 479
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001297625.2 → NP_001284554.1  zinc finger protein 480 isoform 3

    See identical proteins and their annotated locations for NP_001284554.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC010320, AK096442, AL832560, DA501214
    Consensus CDS
    CCDS74437.1
    UniProtKB/Swiss-Prot
    Q8WV37
    Related
    ENSP00000335670.6, ENST00000335090.6
    Conserved Domains (4) summary
    COG5048
    Location:81 → 424
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268 → 288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:322 → 344
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:420 → 445
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001412109.1 → NP_001399038.1  zinc finger protein 480 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) represents an alternate allele of this gene in several human genome assemblies including T2T-CHM13v2.0. It includes a 'TG' deletion (rs3217319) compared to GRCh38, resulting in the use of a downstream start codon. The encoded protein (isoform 4) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    CP068259

  4. NM_144684.4 → NP_653285.2  zinc finger protein 480 isoform 1

    See identical proteins and their annotated locations for NP_653285.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein.
    Source sequence(s)
    AC010320, AK096442, AK303271, AL832560, AY512662, DA501214
    Consensus CDS
    CCDS12850.2
    UniProtKB/Swiss-Prot
    Q5JPG9, Q6P0Q4, Q8N1M5, Q8WV37
    Related
    ENSP00000471754.1, ENST00000595962.6
    Conserved Domains (6) summary
    smart00349
    Location:27 → 87
    KRAB; krueppel associated box
    COG5048
    Location:158 → 501
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:345 → 365
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:399 → 421
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:27 → 66
    KRAB; KRAB box
    pfam13465
    Location:497 → 522
    zf-H2C2_2; Zinc-finger double 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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    52297169..52325922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    55384358..55413117
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WV37.2 GenPept UniProtKB/Swiss-Prot:Q8WV37

Gene LinkOut

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