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

Gene ID: 169792, updated on 3-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (3824127..4490465, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (3828153..4494104, complement)
105.20220307 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
  • 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 Promotes Triple-Negative Breast Cancer Progression by Inducing Cell Proliferation, Migration and Invasion, and Activating the NF-κB Signaling Pathway. Li C, et al. Biol Pharm Bull, 2023. PMID 36724950
  2. Gli-similar 3 (GLIS3) rs7020763 (C>G) polymorphism in patients with type 2 diabetes mellitus. Mohamed LE, et al. Egypt J Immunol, 2022 Oct. PMID 36206155
  3. A circular RNA derived from GLIS3 accelerates the proliferation of glioblastoma cells through competitively binding with miR-449c-5p to upregulate CAPG and GLIS3. Zhou Q, et al. BMC Neurosci, 2022 Sep 16. PMID 36114444, Free PMC Article
  4. 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
  5. Case Report: Neonatal Diabetes Mellitus Caused by a Novel GLIS3 Mutation in Twins. London S, et al. Front Endocrinol (Lausanne), 2021. PMID 34093443, Free PMC Article

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. GLIS3: A Critical Transcription Factor in Islet beta-Cell Generation.
    Title: GLIS3: A Critical Transcription Factor in Islet β-Cell Generation.
  10. Case Report: Neonatal Diabetes Mellitus Caused by a Novel GLIS3 Mutation in Twins.
    Title: Case Report: Neonatal Diabetes Mellitus Caused by a Novel GLIS3 Mutation in Twins.
Submit: New GeneRIF Correction See all GeneRIFs (47)

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
Neonatal diabetes mellitus with congenital hypothyroidism
MedGen: C1857775 OMIM: 610199 GeneReviews: Not available
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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)

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

  • 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_2023_10

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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