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

    Gene ID: 57623, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (134477788..134832339, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (135595711..135950237, complement)
    RS_2024_09 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 is an antiapoptotic molecule and critical for cell survival in MOLT-4 cells. Fujimoto T, et al. FEBS Lett, 2009 Feb 4. PMID 19162026
    2. 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
    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. 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
    5. 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

    See all (41) 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
    		Compare labs

    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)

    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_2024_08

    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
      UniProtKB/TrEMBL
      B7Z6H1

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

      UniProtKB/TrEMBL
      B7Z6H1

    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
      UniProtKB/TrEMBL
      B7Z6H1

    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
      UniProtKB/TrEMBL
      B7Z6H1

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

      UniProtKB/TrEMBL
      B7Z6H1

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

      UniProtKB/TrEMBL
      B7Z6H1

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

      UniProtKB/TrEMBL
      F8W7M8, Q4KMQ4

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

      UniProtKB/TrEMBL
      B7Z6H1

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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