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

Gene ID: 9658, updated on 7-Jul-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (76357682..76496419, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (76587498..76725258, complement)
105.20220307 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
  • 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. 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. Brebi P, et al. Epigenetics, 2014 Feb. PMID 24241165, Free PMC Article
  2. Gene-gene interaction between RBMS3 and ZNF516 influences bone mineral density. Yang TL, et al. J Bone Miner Res, 2013 Apr. PMID 23045156, Free PMC Article
  3. A genome-wide association study of recipient genotype and medium-term kidney allograft function. O'Brien RP, et al. Clin Transplant, 2013 May-Jun. PMID 23432519
  4. A pathogenic CtBP1 missense mutation causes altered cofactor binding and transcriptional activity. Beck DB, et al. Neurogenetics, 2019 Aug. PMID 31041561, Free PMC Article
  5. Cold-inducible Zfp516 activates UCP1 transcription to promote browning of white fat and development of brown fat. Dempersmier J, et al. Mol Cell, 2015 Jan 22. PMID 25578880, Free PMC Article

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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_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
    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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