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ZFAT zinc finger and AT-hook domain containing [ Homo sapiens (human) ]

Gene ID: 57623, updated on 3-Apr-2024

Summary

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Official Symbol
ZFATprovided by HGNC
Official Full Name
zinc finger and AT-hook domain containingprovided by HGNC
Primary source
HGNC:HGNC:19899
See related
Ensembl:ENSG00000066827 MIM:610931; AllianceGenome:HGNC:19899
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
AITD3; ZFAT1; ZNF406
Summary
This gene encodes a protein that likely binds DNA and functions as a transcriptional regulator involved in apoptosis and cell survival. This gene resides in a susceptibility locus for autoimmune thyroid disease (AITD) on chromosome 8q24. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Nov 2009]
Expression
Broad expression in placenta (RPKM 4.4), kidney (RPKM 1.1) and 17 other tissues See more
Orthologs
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Genomic context

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See ZFAT in Genome Data Viewer
Location:
8q24.22
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (134477788..134832339, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (135595711..135950237, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (135490031..135725274, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene MIA SH3 domain ER export factor 2 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135180517-135181018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135181019-135181518 Neighboring gene uncharacterized LOC124902070 Neighboring gene Sharpr-MPRA regulatory region 13712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19567 Neighboring gene MPRA-validated peak7183 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135469463-135469963 Neighboring gene NANOG hESC enhancer GRCh37_chr8:135512751-135513262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:135534207-135534774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28013 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:135593335-135594534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28016 Neighboring gene ZFAT antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135697807-135698308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135698309-135698808 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:135698888-135699054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28019 Neighboring gene NANOG hESC enhancer GRCh37_chr8:135721671-135722354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28021 Neighboring gene uncharacterized LOC124902072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28022 Neighboring gene uncharacterized LOC124902071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19568 Neighboring gene uncharacterized LOC101927845 Neighboring gene non-protein coding RNA 250 Neighboring gene microRNA 30b Neighboring gene microRNA 30d

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. ZFAT gene variant association with multiple sclerosis in the Arabian Gulf population: A genetic basis for gender-associated susceptibility. Bourguiba-Hachemi S, et al. Mol Med Rep, 2016 Oct. PMID 27572828, Free PMC Article
  2. Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT. Tochio N, et al. J Struct Funct Genomics, 2015 Jun. PMID 25801860, Free PMC Article
  3. ZFAT is essential for endothelial cell assembly and the branch point formation of capillary-like structures in an angiogenesis model. Yoshida Y, et al. Cell Mol Biol Lett, 2010 Dec. PMID 20645017, Free PMC Article
  4. Recent advances in the association studies of autoimmune thyroid disease and the functional characterization of AITD-related transcription factor ZFAT. Nakabayashi K, et al. Nihon Rinsho Meneki Gakkai Kaishi, 2010. PMID 20453441
  5. ZFAT is an antiapoptotic molecule and critical for cell survival in MOLT-4 cells. Fujimoto T, et al. FEBS Lett, 2009 Feb 4. PMID 19162026

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Death domain-associated protein DAXX regulates noncoding RNA transcription at the centromere through the transcription regulator ZFAT.
    Title: Death domain-associated protein DAXX regulates noncoding RNA transcription at the centromere through the transcription regulator ZFAT.
  2. CENP-B promotes the centromeric localization of ZFAT to control transcription of noncoding RNA.
    Title: CENP-B promotes the centromeric localization of ZFAT to control transcription of noncoding RNA.
  3. Identification of pelvic organ prolapse risk susceptibility gene SNP locus in Xinjiang women.
    Title: Identification of pelvic organ prolapse risk susceptibility gene SNP locus in Xinjiang women.
  4. ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis.
    Title: ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis.
  5. Zfat knockdown partially inhibited CD71(-/low)Ter119(-) to CD71(high)Ter119(-) transition of fetal liver erythroid progenitors with impairment in the elevation of CD71 expression. Zfat plays a critical role for erythropoiesis in the fetal liver
    Title: Zfat Is Indispensable for the Development of Erythroid Cells in the Fetal Liver.
  6. Analysis of PTPN22, ZFAT and MYO9B polymorphisms in Turner Syndrome and risk of autoimmune disease.
    Title: Analysis of PTPN22, ZFAT and MYO9B polymorphisms in Turner Syndrome and risk of autoimmune disease.
  7. The present study observed, for the first time, that in an Arabian Gulf population, the ZFAT rs733254 polymorphism (T>G) is a genderspecific risk marker for multiple sclerosis.
    Title: ZFAT gene variant association with multiple sclerosis in the Arabian Gulf population: A genetic basis for gender-associated susceptibility.
  8. We describe the structural features of the ZFAT ZFs, including the structural differences on the putative DNA recognition surfaces among the ZFAT ZFs, and the unique interaction mode within the tandem ZFs of ZF4 and ZF5
    Title: Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.
  9. ZFAT is paternally expressed in the placenta (as ZFAT-AS1, a non-coding antisense RNA)but biallelic in other tissues.
    Title: A genome-wide approach reveals novel imprinted genes expressed in the human placenta.
  10. ZFAT polymorphism was associated with the Hashimoto disease severity but not with its development.
    Title: Associations between autoimmune thyroid disease prognosis and functional polymorphisms of susceptibility genes, CTLA4, PTPN22, CD40, FCRL3, and ZFAT, previously revealed in genome-wide association studies.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

Associated conditions

Description Tests
Autoimmune thyroid disease, susceptibility to, 3
MedGen: C1842444 OMIM: 608175 GeneReviews: Not available
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EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog
Genome-wide association study of smoking behaviours among Bangladeshi adults.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog
Two-marker association tests yield new disease associations for coronary artery disease and hypertension.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1485, MGC126815, MGC126817

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
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 hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger protein ZFAT
Names
zinc finger gene in autoimmune thyroid disease
zinc finger protein 406
zinc-finger gene in AITD susceptibility region

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_016356.3 RefSeqGene

    Range
    124308..359551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001029939.4 → NP_001025110.2  zinc finger protein ZFAT isoform 2

    See identical proteins and their annotated locations for NP_001025110.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Variants 2, 3, and 6 all encode the same isoform (2).
    Source sequence(s)
    AB167740, AC015599, AC135075, BC098405, BM685256
    Consensus CDS
    CCDS43768.2
    UniProtKB/TrEMBL
    B7Z6H1
    Related
    ENSP00000427831.1, ENST00000520727.5
    Conserved Domains (4) summary
    COG5048
    Location:255 → 414
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:259 → 281
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:273 → 295
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001167583.3 → NP_001161055.1  zinc finger protein ZFAT isoform 2

    See identical proteins and their annotated locations for NP_001161055.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Variants 2, 3, and 6 all encode the same isoform (2).
    Source sequence(s)
    AC015599, AC135075, AK300324, BC098405, BM685256
    Consensus CDS
    CCDS43768.2
    UniProtKB/TrEMBL
    B7Z6H1
    Related
    ENSP00000428483.1, ENST00000520214.5
    Conserved Domains (4) summary
    COG5048
    Location:255 → 414
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:259 → 281
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:273 → 295
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001174157.2 → NP_001167628.1  zinc finger protein ZFAT isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AC015599, AC087045, AK300324, BC143519, BM685256, DC333809
    Consensus CDS
    CCDS55276.1
    UniProtKB/TrEMBL
    B7Z6H1
    Related
    ENSP00000429091.1, ENST00000523399.5
    Conserved Domains (4) summary
    COG5048
    Location:205 → 364
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:211 → 231
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:209 → 231
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:223 → 245
    zf-H2C2_2; Zinc-finger double domain

  4. NM_001174158.2 → NP_001167629.1  zinc finger protein ZFAT isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon, and lacks an in-frame segment in the 3' coding region, compared to variant 1. The resulting isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC015599, AC135075, BC012989, BC098405
    Consensus CDS
    CCDS55275.1
    UniProtKB/TrEMBL
    E9PBN4, Q6PJQ2
    Related
    ENSP00000427879.1, ENST00000520356.5
    Conserved Domains (3) summary
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:259 → 281
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:273 → 295
    zf-H2C2_2; Zinc-finger double domain

  5. NM_001289394.2 → NP_001276323.1  zinc finger protein ZFAT isoform 2

    See identical proteins and their annotated locations for NP_001276323.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) 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. This results in an isoform (2) which has a shorter N-terminus, compared to isoform 1. Variants 2, 3, and 6 all encode the same isoform (2).
    Source sequence(s)
    AB167739, AK300324, AL832066, BM685256
    Consensus CDS
    CCDS43768.2
    UniProtKB/TrEMBL
    B7Z6H1
    Conserved Domains (4) summary
    COG5048
    Location:255 → 414
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:259 → 281
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:273 → 295
    zf-H2C2_2; Zinc-finger double domain

  6. NM_020863.4 → NP_065914.2  zinc finger protein ZFAT isoform 1

    See identical proteins and their annotated locations for NP_065914.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AB040918, AC135075, AL832066, BC046180, BC101768
    Consensus CDS
    CCDS47924.1
    UniProtKB/Swiss-Prot
    B7ZL15, E9PER3, Q3MIM5, Q6PJ01, Q75PJ6, Q75PJ7, Q75PJ9, Q86X64, Q9P243
    UniProtKB/TrEMBL
    B7Z6H1
    Related
    ENSP00000367069.3, ENST00000377838.8
    Conserved Domains (4) summary
    COG5048
    Location:267 → 426
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:273 → 293
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:271 → 293
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:285 → 307
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_110323.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate internal exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB040918, AK300324, AL832066, BC025423, BC101766, BM685256
    Related
    ENST00000523243.5

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    134477788..134832339 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422062.1 → XP_047278018.1  zinc finger protein ZFAT isoform X2

    UniProtKB/Swiss-Prot
    B7ZL15, E9PER3, Q3MIM5, Q6PJ01, Q75PJ6, Q75PJ7, Q75PJ9, Q86X64, Q9P243

  2. XM_047422063.1 → XP_047278019.1  zinc finger protein ZFAT isoform X3

  3. XM_011517204.3 → XP_011515506.1  zinc finger protein ZFAT isoform X4

    UniProtKB/TrEMBL
    B7Z6H1
    Conserved Domains (4) summary
    COG5048
    Location:205 → 364
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:211 → 231
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:209 → 231
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:223 → 245
    zf-H2C2_2; Zinc-finger double domain

  4. XM_011517206.2 → XP_011515508.1  zinc finger protein ZFAT isoform X5

    UniProtKB/TrEMBL
    F8W7M8, Q4KMQ4
    Conserved Domains (3) summary
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:259 → 281
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:273 → 295
    zf-H2C2_2; Zinc-finger double domain

  5. XM_017013716.2 → XP_016869205.1  zinc finger protein ZFAT isoform X1

    UniProtKB/TrEMBL
    B7Z6H1

RNA

  1. XR_007060749.1 RNA Sequence

  2. XR_007060750.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    135595711..135950237 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360941.1 → XP_054216916.1  zinc finger protein ZFAT isoform X2

    UniProtKB/Swiss-Prot
    B7ZL15, E9PER3, Q3MIM5, Q6PJ01, Q75PJ6, Q75PJ7, Q75PJ9, Q86X64, Q9P243

  2. XM_054360940.1 → XP_054216915.1  zinc finger protein ZFAT isoform X2

    UniProtKB/Swiss-Prot
    B7ZL15, E9PER3, Q3MIM5, Q6PJ01, Q75PJ6, Q75PJ7, Q75PJ9, Q86X64, Q9P243

  3. XM_054360942.1 → XP_054216917.1  zinc finger protein ZFAT isoform X3

  4. XM_054360943.1 → XP_054216918.1  zinc finger protein ZFAT isoform X4

  5. XM_054360944.1 → XP_054216919.1  zinc finger protein ZFAT isoform X5

    UniProtKB/TrEMBL
    F8W7M8

  6. XM_054360939.1 → XP_054216914.1  zinc finger protein ZFAT isoform X1

RNA

  1. XR_008487868.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P243.2 GenPept UniProtKB/Swiss-Prot:Q9P243

Gene LinkOut

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