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ZNF496 zinc finger protein 496 [ Homo sapiens (human) ]

Gene ID: 84838, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF496provided by HGNC
Official Full Name
zinc finger protein 496provided by HGNC
Primary source
HGNC:HGNC:23713
See related
Ensembl:ENSG00000162714 MIM:613911; AllianceGenome:HGNC:23713
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
NIZP1; ZFP496; ZSCAN49; ZKSCAN17
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein self-association. Predicted to be involved in positive regulation of transcription, DNA-templated and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 3.4), ovary (RPKM 3.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q44
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (247297415..247331867, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (246730535..246764981, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (247460717..247495169, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene vomeronasal 1 receptor 5 (gene/pseudogene) Neighboring gene uncharacterized LOC105373273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247453849-247454367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247462225-247463124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247463125-247464023 Neighboring gene NANOG hESC enhancer GRCh37_chr1:247485935-247486439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247492160-247492662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2044 Neighboring gene Sharpr-MPRA regulatory region 5917 Neighboring gene Sharpr-MPRA regulatory region 7964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247499115-247499615 Neighboring gene uncharacterized LOC124904574 Neighboring gene Sharpr-MPRA regulatory region 1744 Neighboring gene ZNF496 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247525936-247526480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2047 Neighboring gene uncharacterized LOC107985375 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:247556143-247556425

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. KRAB-containing zinc finger protein ZNF496 inhibits breast cancer cell proliferation by selectively repressing ERα activity. Wang J, et al. Biochim Biophys Acta Gene Regul Mech, 2018 Jul 20. PMID 30012466
  2. NSD1 PHD domains bind methylated H3K4 and H3K9 using interactions disrupted by point mutations in human sotos syndrome. Pasillas MP, et al. Hum Mutat, 2011 Mar. PMID 21972110
  3. The NIZP1 KRAB and C2HR domains cross-talk for transcriptional regulation. Losson R, et al. Biochim Biophys Acta, 2010 May-Jun. PMID 20176155
  4. Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif. Nielsen AL, et al. Mol Cell Biol, 2004 Jun. PMID 15169884, Free PMC Article
  5. Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex. Ouyang J, et al. Mol Cell, 2009 Apr 24. PMID 19394292, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC15548

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
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 positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
zinc finger protein 496
Names
NSD1 (nuclear receptor binding SET-domain containing 1)-interacting zinc finger protein 1
zinc finger protein with KRAB and SCAN domains 17

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_001329733.2 → NP_001316662.1  zinc finger protein 496 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC104335
    Conserved Domains (2) summary
    cd07765
    Location:222 → 259
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    pfam02023
    Location:50 → 126
    SCAN; SCAN domain

  2. NM_032752.3 → NP_116141.1  zinc finger protein 496 isoform 1

    See identical proteins and their annotated locations for NP_116141.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC104335, BC007263, BC025794, BU740940, HY023128
    Consensus CDS
    CCDS1631.1
    UniProtKB/Swiss-Prot
    Q8TBS2, Q96IT1
    UniProtKB/TrEMBL
    A0A0C4DGR5
    Related
    ENSP00000507236.1, ENST00000682384.1
    Conserved Domains (6) summary
    cd07765
    Location:222 → 259
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00349
    Location:223 → 275
    KRAB; krueppel associated box
    COG5048
    Location:427 → 586
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:408 → 428
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:463 → 485
    zf-C2H2; Zinc finger, C2H2 type
    pfam02023
    Location:50 → 126
    SCAN; SCAN 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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    247297415..247331867 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791757.1 Reference GRCh38.p14 PATCHES

    Range
    63858..98310 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    246730535..246764981 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96IT1.1 GenPept UniProtKB/Swiss-Prot:Q96IT1

Gene LinkOut

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