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    GLIS3 GLIS family zinc finger 3 [ Homo sapiens (human) ]

    Gene ID: 169792, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GLIS3provided by HGNC
    Official Full Name
    GLIS family zinc finger 3provided by HGNC
    Primary source
    HGNC:HGNC:28510
    See related
    Ensembl:ENSG00000107249 MIM:610192; AllianceGenome:HGNC:28510
    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
    NDH; ZNF515
    Summary
    This gene is a member of the GLI-similar zinc finger protein family and encodes a nuclear protein with five C2H2-type zinc finger domains. This protein functions as both a repressor and activator of transcription and is specifically involved in the development of pancreatic beta cells, the thyroid, eye, liver and kidney. Mutations in this gene have been associated with neonatal diabetes and congenital hypothyroidism (NDH). Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only two have been determined. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in thyroid (RPKM 8.8), gall bladder (RPKM 2.6) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GLIS3 in Genome Data Viewer
    Location:
    9p24.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (3824127..4490465, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (3828153..4494104, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (3824127..4300068, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:3674142-3675341 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:3696328-3696940 Neighboring gene RFX3 divergent transcript Neighboring gene uncharacterized LOC105375962 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:3862633-3863832 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:3927295-3928494 Neighboring gene GLIS3 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr9:3954464-3954984 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:3968328-3969527 Neighboring gene uncharacterized LOC105375964 Neighboring gene uncharacterized LOC124902111 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:4136663-4137862 Neighboring gene GLIS3 intron CAGE-defined low expression enhancer Neighboring gene NANOG hESC enhancer GRCh37_chr9:4237960-4238479 Neighboring gene Sharpr-MPRA regulatory region 13837 Neighboring gene Sharpr-MPRA regulatory region 3194 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:4329035-4330234 Neighboring gene Sharpr-MPRA regulatory region 3538 Neighboring gene GLIS3 antisense RNA 2 Neighboring gene Sharpr-MPRA regulatory region 14111 Neighboring gene RNA, U6 small nuclear 694, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28147 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:4514651-4515591 Neighboring gene solute carrier family 1 member 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:4605494-4606693 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:4630798-4631350 Neighboring gene spermatogenesis associated 6 like Neighboring gene ribosomal protein S6 pseudogene 11

    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. GLIS family zinc finger 3 promoting cell malignant behaviors and NF-κB signaling in glioma. Liu Z, et al. Brain Res, 2021 Nov 1. PMID 34403660
    2. Polymorphism of the GLIS3 gene in a Caucasian population and among individuals with carbohydrate metabolism disorders in Russia. Shakhtshneider EV, et al. BMC Res Notes, 2018 Apr 2. PMID 29606121, Free PMC Article
    3. A novel variant in GLIS3 is associated with osteoarthritis. Casalone E, et al. Ann Rheum Dis, 2018 Apr. PMID 29436472, Free PMC Article
    4. Evaluation of the association between five genetic variants and primary open-angle glaucoma in a Han Chinese population. Li K, et al. Ophthalmic Genet, 2020 Jun. PMID 32281515
    5. Mutations in GLIS3 are responsible for a rare syndrome with neonatal diabetes mellitus and congenital hypothyroidism. Senée V, et al. Nat Genet, 2006 Jun. PMID 16715098

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Variations in the LINGO2 and GLIS3 Genes and Gene-Environment Interactions Increase Gestational Diabetes Mellitus Risk in Chinese Women.
      Title: Variations in the LINGO2 and GLIS3 Genes and Gene-Environment Interactions Increase Gestational Diabetes Mellitus Risk in Chinese Women.
    2. CircGLIS3 promotes gastric cancer progression by regulating the miR-1343-3p/PGK1 pathway and inhibiting vimentin phosphorylation.
      Title: CircGLIS3 promotes gastric cancer progression by regulating the miR-1343-3p/PGK1 pathway and inhibiting vimentin phosphorylation.
    3. Pathogenic monoallelic variants in GLIS3 increase type 2 diabetes risk and identify a subgroup of patients sensitive to sulfonylureas.
      Title: Pathogenic monoallelic variants in GLIS3 increase type 2 diabetes risk and identify a subgroup of patients sensitive to sulfonylureas.
    4. GLIS3, a novel prognostic indicator of gastric adenocarcinoma, contributes to the malignant biological behaviors of tumor cells via modulating TGF-beta1/TGFbetaR1/Smad1/5 signaling pathway.
      Title: GLIS3, a novel prognostic indicator of gastric adenocarcinoma, contributes to the malignant biological behaviors of tumor cells via modulating TGF-β1/TGFβR1/Smad1/5 signaling pathway.
    5. GLIS Family Zinc Finger 3 Promotes Triple-Negative Breast Cancer Progression by Inducing Cell Proliferation, Migration and Invasion, and Activating the NF-kappaB Signaling Pathway.
      Title: GLIS Family Zinc Finger 3 Promotes Triple-Negative Breast Cancer Progression by Inducing Cell Proliferation, Migration and Invasion, and Activating the NF-κB Signaling Pathway.
    6. Gli-similar 3 (GLIS3) rs7020763 (C>G) polymorphism in patients with type 2 diabetes mellitus.
      Title: Gli-similar 3 (GLIS3) rs7020763 (C>G) polymorphism in patients with type 2 diabetes mellitus.
    7. A circular RNA derived from GLIS3 accelerates the proliferation of glioblastoma cells through competitively binding with miR-449c-5p to upregulate CAPG and GLIS3.
      Title: A circular RNA derived from GLIS3 accelerates the proliferation of glioblastoma cells through competitively binding with miR-449c-5p to upregulate CAPG and GLIS3.
    8. GLIS family zinc finger 3 promoting cell malignant behaviors and NF-kappaB signaling in glioma.
      Title: GLIS family zinc finger 3 promoting cell malignant behaviors and NF-κB signaling in glioma.
    9. Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene.
      Title: Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene.
    10. GLIS3: A Critical Transcription Factor in Islet beta-Cell Generation.
      Title: GLIS3: A Critical Transcription Factor in Islet β-Cell Generation.
    Submit: New GeneRIF Correction See all GeneRIFs (48)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neonatal diabetes mellitus with congenital hypothyroidism
    MedGen: C1857775 OMIM: 610199 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    EBI GWAS Catalog
    A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
    EBI GWAS Catalog
    A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
    EBI GWAS Catalog
    Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes.
    EBI GWAS Catalog
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
    EBI GWAS Catalog
    Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
    EBI GWAS Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    EBI GWAS Catalog
    Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects.
    EBI GWAS Catalog
    GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
    EBI GWAS Catalog
    New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.
    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

    • FLJ38999, FLJ90578, MGC33662

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    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 negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    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 GLIS3
    Names
    GLI-similar 3
    OK/KNS-cl.4
    zinc finger protein 515

    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_011782.3 RefSeqGene

      Range
      195397..671338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001042413.2 → NP_001035878.1  zinc finger protein GLIS3 isoform a

      See identical proteins and their annotated locations for NP_001035878.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AA933816, AK075059, AL133283, AL137071, AL162419, BC033899, DQ438886
      Consensus CDS
      CCDS43784.1
      UniProtKB/Swiss-Prot
      Q8NEA6
      UniProtKB/TrEMBL
      Q1PHJ8
      Related
      ENSP00000371398.3, ENST00000381971.8
      Conserved Domains (2) summary
      COG5189
      Location:558 → 652
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:569 → 591
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. NM_152629.4 → NP_689842.3  zinc finger protein GLIS3 isoform b

      See identical proteins and their annotated locations for NP_689842.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (b) has a shorter N-terminus when compared to isoform 1.
      Source sequence(s)
      AA933816, AL133283, AL137071, BC033899
      Consensus CDS
      CCDS6451.1
      UniProtKB/Swiss-Prot
      B1AL19, Q1PHK5, Q8NEA6
      UniProtKB/TrEMBL
      A0A0S2Z649, A0A0S2Z689
      Related
      ENSP00000325494.10, ENST00000324333.14
      Conserved Domains (2) summary
      COG5189
      Location:403 → 497
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:414 → 436
      ZF_C2H2; C2H2 Zn finger [structural motif]

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      3824127..4490465 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422890.1 → XP_047278846.1  zinc finger protein GLIS3 isoform X2

    2. XM_011517763.3 → XP_011516065.1  zinc finger protein GLIS3 isoform X1

      See identical proteins and their annotated locations for XP_011516065.1

      UniProtKB/Swiss-Prot
      Q8NEA6
      Conserved Domains (2) summary
      COG5189
      Location:558 → 652
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:569 → 591
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. XM_005251386.5 → XP_005251443.1  zinc finger protein GLIS3 isoform X3

      See identical proteins and their annotated locations for XP_005251443.1

      UniProtKB/Swiss-Prot
      B1AL19, Q1PHK5, Q8NEA6
      UniProtKB/TrEMBL
      A0A0S2Z649, A0A0S2Z689
      Related
      ENSP00000507306.1, ENST00000682749.1
      Conserved Domains (2) summary
      COG5189
      Location:403 → 497
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:414 → 436
      ZF_C2H2; C2H2 Zn finger [structural motif]

    4. XM_011517764.3 → XP_011516066.1  zinc finger protein GLIS3 isoform X1

      See identical proteins and their annotated locations for XP_011516066.1

      UniProtKB/Swiss-Prot
      Q8NEA6
      Conserved Domains (2) summary
      COG5189
      Location:558 → 652
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:569 → 591
      ZF_C2H2; C2H2 Zn finger [structural motif]

    5. XM_047422889.1 → XP_047278845.1  zinc finger protein GLIS3 isoform X1

    6. XM_011517766.3 → XP_011516068.1  zinc finger protein GLIS3 isoform X3

      See identical proteins and their annotated locations for XP_011516068.1

      UniProtKB/Swiss-Prot
      B1AL19, Q1PHK5, Q8NEA6
      UniProtKB/TrEMBL
      A0A0S2Z649, A0A0S2Z689
      Conserved Domains (2) summary
      COG5189
      Location:403 → 497
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:414 → 436
      ZF_C2H2; C2H2 Zn finger [structural motif]

    7. XM_017014361.2 → XP_016869850.1  zinc finger protein GLIS3 isoform X3

      UniProtKB/Swiss-Prot
      B1AL19, Q1PHK5, Q8NEA6
      UniProtKB/TrEMBL
      A0A0S2Z649, A0A0S2Z689
      Conserved Domains (2) summary
      COG5189
      Location:403 → 497
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:414 → 436
      ZF_C2H2; C2H2 Zn finger [structural motif]

    8. XM_047422892.1 → XP_047278848.1  zinc finger protein GLIS3 isoform X5

    9. XM_047422891.1 → XP_047278847.1  zinc finger protein GLIS3 isoform X4

    10. XM_047422893.1 → XP_047278849.1  zinc finger protein GLIS3 isoform X6

    RNA

    1. XR_007061257.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      3828153..4494104 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362214.1 → XP_054218189.1  zinc finger protein GLIS3 isoform X2

    2. XM_054362211.1 → XP_054218186.1  zinc finger protein GLIS3 isoform X1

    3. XM_054362215.1 → XP_054218190.1  zinc finger protein GLIS3 isoform X3

    4. XM_054362213.1 → XP_054218188.1  zinc finger protein GLIS3 isoform X1

    5. XM_054362212.1 → XP_054218187.1  zinc finger protein GLIS3 isoform X1

    6. XM_054362217.1 → XP_054218192.1  zinc finger protein GLIS3 isoform X3

    7. XM_054362216.1 → XP_054218191.1  zinc finger protein GLIS3 isoform X3

    8. XM_054362218.1 → XP_054218193.1  zinc finger protein GLIS3 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NEA6.5 GenPept UniProtKB/Swiss-Prot:Q8NEA6

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