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    ZNF516 zinc finger protein 516 [ Homo sapiens (human) ]

    Gene ID: 9658, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZNF516provided by HGNC
    Official Full Name
    zinc finger protein 516provided by HGNC
    Primary source
    HGNC:HGNC:28990
    See related
    Ensembl:ENSG00000101493 MIM:615114; AllianceGenome:HGNC:28990
    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
    HsT287
    Summary
    Zinc-finger proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. This gene encodes a zinc-finger protein, and belongs to the krueppel C2H2-type zinc-finger protein family. It may be involved in transcriptional regulation. [provided by RefSeq, Sep 2012]
    Expression
    Broad expression in endometrium (RPKM 13.5), testis (RPKM 10.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF516 in Genome Data Viewer
    Location:
    18q23
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (76357682..76496419, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (76587498..76725258, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (74069637..74207198, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372210 Neighboring gene uncharacterized LOC105372209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:73974705-73975358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:73977965-73978464 Neighboring gene uncharacterized LOC105372211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74073833-74074334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74074335-74074834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74083239-74083841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74102627-74103144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74116826-74117662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74123937-74124497 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:74135201-74135702 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74158054-74158632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74158633-74159211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74159212-74159789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74160675-74161176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74161177-74161676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74169047-74169548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74169549-74170048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74171461-74172058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74172059-74172656 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:74188803-74190002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74191127-74191698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74191699-74192269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13510 Neighboring gene ZNF516 antisense RNA 1 Neighboring gene ZNF516 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 8201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74240354-74240994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74240995-74241633 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:74241634-74242273 Neighboring gene long intergenic non-protein coding RNA 908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:74323725-74324238 Neighboring gene long intergenic non-protein coding RNA 683 Neighboring gene long intergenic non-protein coding RNA 1927

    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. MiR-371-5p regulates trophoblast cell proliferation, migration, and invasion by directly targeting ZNF516.
      Title: MiR-371-5p regulates trophoblast cell proliferation, migration, and invasion by directly targeting ZNF516.
    2. ZNF516 represses EGFR transcription through the interaction with the CtBP/LSD1/CoREST complex.
      Title: ZNF516 suppresses EGFR by targeting the CtBP/LSD1/CoREST complex to chromatin.
    3. one interacting gene pair (RBMS3 versus ZNF516) which, even after Bonferroni correction for multiple testing, showed consistently significant effects on hip bone mineral density.
      Title: Gene-gene interaction between RBMS3 and ZNF516 influences bone mineral density.
    4. ZNF516 promoter methylation was the best biomarker, with both sensitivity and specificity of 90% (AUC = 0.92), results subsequently corroborated in a Prevalence cohort.
      Title: Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.
    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

    EBI GWAS Catalog

    Description
    A genome-wide association study of recipient genotype and medium-term kidney allograft function.
    EBI GWAS Catalog
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    EBI GWAS Catalog
    GWAS of dental caries patterns in the permanent dentition.
    EBI GWAS Catalog
    Joint influence of small-effect genetic variants on human longevity.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of zinc finger protein 516 (ZNF516) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    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 adipose tissue development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in brown fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to cold IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 516

    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_032949.2 RefSeqGene

      Range
      6177..143737
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014643.4 → NP_055458.1  zinc finger protein 516

      See identical proteins and their annotated locations for NP_055458.1

      Status: REVIEWED

      Source sequence(s)
      AC009716, AC018413, BC108287, D86975
      Consensus CDS
      CCDS74234.1
      UniProtKB/Swiss-Prot
      Q92618
      Related
      ENSP00000394757.2, ENST00000443185.7
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double 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
      76357682..76496419 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437953.1 → XP_047293909.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    2. XM_047437952.1 → XP_047293908.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    3. XM_011526273.4 → XP_011524575.1  zinc finger protein 516 isoform X1

      See identical proteins and their annotated locations for XP_011524575.1

      UniProtKB/Swiss-Prot
      Q92618
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double domain

    4. XM_011526274.4 → XP_011524576.1  zinc finger protein 516 isoform X1

      See identical proteins and their annotated locations for XP_011524576.1

      UniProtKB/Swiss-Prot
      Q92618
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double domain

    5. XM_017026097.3 → XP_016881586.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double domain

    6. XM_047437956.1 → XP_047293912.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    7. XM_011526275.3 → XP_011524577.1  zinc finger protein 516 isoform X1

      See identical proteins and their annotated locations for XP_011524577.1

      UniProtKB/Swiss-Prot
      Q92618
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double domain

    8. XM_011526269.3 → XP_011524571.1  zinc finger protein 516 isoform X1

      See identical proteins and their annotated locations for XP_011524571.1

      UniProtKB/Swiss-Prot
      Q92618
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double domain

    9. XM_047437951.1 → XP_047293907.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    10. XM_011526270.4 → XP_011524572.1  zinc finger protein 516 isoform X1

      See identical proteins and their annotated locations for XP_011524572.1

      UniProtKB/Swiss-Prot
      Q92618
      Conserved Domains (4) summary
      COG5048
      Location:32 → 90
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:36 → 56
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:34 → 56
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:48 → 73
      zf-H2C2_2; Zinc-finger double domain

    11. XM_047437950.1 → XP_047293906.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    12. XM_047437957.1 → XP_047293913.1  zinc finger protein 516 isoform X2

    13. XM_047437955.1 → XP_047293911.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    14. XM_047437954.1 → XP_047293910.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    RNA

    1. XR_007066258.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      76587498..76725258 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319389.1 → XP_054175364.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    2. XM_054319388.1 → XP_054175363.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    3. XM_054319380.1 → XP_054175355.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    4. XM_054319382.1 → XP_054175357.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    5. XM_054319383.1 → XP_054175358.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    6. XM_054319386.1 → XP_054175361.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    7. XM_054319379.1 → XP_054175354.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    8. XM_054319381.1 → XP_054175356.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    9. XM_054319390.1 → XP_054175365.1  zinc finger protein 516 isoform X2

    10. XM_054319387.1 → XP_054175362.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    11. XM_054319385.1 → XP_054175360.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    12. XM_054319384.1 → XP_054175359.1  zinc finger protein 516 isoform X1

      UniProtKB/Swiss-Prot
      Q92618

    RNA

    1. XR_008485035.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92618.1 GenPept UniProtKB/Swiss-Prot:Q92618

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