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    ZNHIT3 zinc finger HIT-type containing 3 [ Homo sapiens (human) ]

    Gene ID: 9326, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZNHIT3provided by HGNC
    Official Full Name
    zinc finger HIT-type containing 3provided by HGNC
    Primary source
    HGNC:HGNC:12309
    See related
    Ensembl:ENSG00000273611 MIM:604500; AllianceGenome:HGNC:12309
    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
    Hit1; PEHO; TRIP3
    Summary
    Predicted to enable nuclear thyroid hormone receptor binding activity. Predicted to be involved in box C/D snoRNP assembly; maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); and snoRNA localization. Located in cytoplasm and nucleus. Implicated in PEHO syndrome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 10.5), testis (RPKM 10.1) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See ZNHIT3 in Genome Data Viewer
    Location:
    17q12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (36486681..36499312)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (37472439..37485065)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (34842525..34855156)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:34495357-34496016 Neighboring gene TBC1 domain family member 3J, pseudogene Neighboring gene uncharacterized LOC105371749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:34842246-34843179 Neighboring gene RNA, 5S ribosomal pseudogene 439 Neighboring gene myosin XIX Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:34889386-34890061 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class W Neighboring gene gametogenetin binding protein 2 Neighboring gene ribosomal protein S2 pseudogene 50

    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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    Related articles in PubMed

    1. Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome. Brakta S, et al. Mol Cell Endocrinol, 2024 Aug 1. PMID 38599276
    2. [Relationship between expression of GYPC and TRIP3 genes and prognosis of acute lymphoblastic leukemia in children]. Zhang JB, et al. Zhongguo Dang Dai Er Ke Za Zhi, 2009 Jan. PMID 19149918
    3. Thyroid hormone receptor interacting protein 3 (trip3) is a novel coactivator of hepatocyte nuclear factor-4alpha. Iwahashi H, et al. Diabetes, 2002 Apr. PMID 11916906
    4. TRIB3 promotes MYC-associated lymphoma development through suppression of UBE3B-mediated MYC degradation. Li K, et al. Nat Commun, 2020 Dec 9. PMID 33298911, Free PMC Article
    5. ZNHIT3 is defective in PEHO syndrome, a severe encephalopathy with cerebellar granule neuron loss. Anttonen AK, et al. Brain, 2017 May 1. PMID 28335020

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome.
      Title: Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome.
    2. results suggest that loss-of-function missense mutation of znhit3 underlies PEHO syndrome.
      Title: ZNHIT3 is defective in PEHO syndrome, a severe encephalopathy with cerebellar granule neuron loss.
    3. Results solve the structure of a complex resulting from interaction between protein fragments of human NUFIP1 and its cofactor ZNHIT3, and emphasize their imbrication. Also, it seems that the complexes involving NUFIP1, ZNHIT3, and SNU13 share strong structural similarities between human and yeast, suggesting that the initial steps of the box C/D snoRNP assembly process are conserved among species.
      Title: Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species.
    4. Results identify TRIP3 as a novel regulator of PPARgamma-mediated adipocyte differentiation.
      Title: Nuclear receptor-coregulator interaction profiling identifies TRIP3 as a novel peroxisome proliferator-activated receptor gamma cofactor.
    5. A high GYPC gene expression is associated with an unfavorable outcome, in contrast, a high TRIP3 gene expression is associated with a favorable outcome in childhood ALL.
      Title: [Relationship between expression of GYPC and TRIP3 genes and prognosis of acute lymphoblastic leukemia in children].
    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

    Associated conditions

    Description Tests
    PEHO syndrome
    MedGen: C1850055 OMIM: 260565 GeneReviews: Not available
    		Compare labs

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear thyroid hormone receptor binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in box C/D snoRNP assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in snoRNA localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of pre-snoRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger HIT domain-containing protein 3
    Names
    HNF-4a coactivator
    TR-interacting protein 3
    TRIP-3
    thyroid hormone receptor interactor 3
    thyroid receptor interacting protein 3
    zinc finger, HIT domain containing 3
    zinc finger, HIT type 3

    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_001281432.2 → NP_001268361.1  zinc finger HIT domain-containing protein 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 3' terminal exon, which results in a frame-shift compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC233698, AK096494, AK308583, BI767446, HY045632
      Consensus CDS
      CCDS62156.1
      UniProtKB/Swiss-Prot
      Q15649
      Related
      ENSP00000479727.1, ENST00000620324.4
      Conserved Domains (1) summary
      pfam04438
      Location:7 → 36
      zf-HIT; HIT zinc finger

    2. NM_001281433.2 → NP_001268362.1  zinc finger HIT domain-containing protein 3 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate acceptor splice site at the penultimate coding exon, which results in a frame-shift compared to variant 1. The resulting isoform (4) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AF400652, BG032116, BQ009986, HY045632
      UniProtKB/Swiss-Prot
      Q15649
      Conserved Domains (1) summary
      pfam04438
      Location:7 → 36
      zf-HIT; HIT zinc finger

    3. NM_001281434.2 → NP_001268363.1  zinc finger HIT domain-containing protein 3 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two consecutive in-frame coding exons compared to variant 1. The resulting isoform (3) is shorter, missing an internal protein segment, compared to isoform 1.
      Source sequence(s)
      AF400652, BE260293, BQ009986, HY045632
      UniProtKB/TrEMBL
      A0A087WY54, A0A0G2JNV1
      Related
      ENSP00000481522.1, ENST00000616269.1
      Conserved Domains (1) summary
      pfam04438
      Location:7 → 36
      zf-HIT; HIT zinc finger

    4. NM_004773.4 → NP_004764.1  zinc finger HIT domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_004764.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF400652, BQ009986
      Consensus CDS
      CCDS11312.1
      UniProtKB/Swiss-Prot
      A8K493, K7EQP1, Q15649, Q8WVJ3
      Related
      ENSP00000484687.1, ENST00000617429.5
      Conserved Domains (1) summary
      pfam04438
      Location:7 → 36
      zf-HIT; HIT zinc finger

    RNA

    1. NR_104009.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate acceptor splice site at an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF400652, BM457955, BQ009986, HY045632
      Related
      ENST00000620863.4

    2. NR_104010.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an exon in the 5' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF400652, BC105608, BQ009986
      Related
      ENST00000619730.4

    3. NR_104011.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks an exon in the 5' region and contains an alternate 3' terminal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC233698, AK096494, AK308583, HY045632
      Related
      ENST00000612728.4

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      36486681..36499312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      721585..734216
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      37472439..37485065
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001033577.1: Suppressed sequence

      Description
      NM_001033577.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15649.2 GenPept UniProtKB/Swiss-Prot:Q15649

    Gene LinkOut

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

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