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    GFI1 growth factor independent 1 transcriptional repressor [ Homo sapiens (human) ]

    Gene ID: 2672, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GFI1provided by HGNC
    Official Full Name
    growth factor independent 1 transcriptional repressorprovided by HGNC
    Primary source
    HGNC:HGNC:4237
    See related
    Ensembl:ENSG00000162676 MIM:600871; AllianceGenome:HGNC:4237
    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
    SCN2; GFI-1; GFI1A; ZNF163
    Summary
    This gene encodes a nuclear zinc finger protein that functions as a transcriptional repressor. This protein plays a role in diverse developmental contexts, including hematopoiesis and oncogenesis. It functions as part of a complex along with other cofactors to control histone modifications that lead to silencing of the target gene promoters. Mutations in this gene cause autosomal dominant severe congenital neutropenia, and also dominant nonimmune chronic idiopathic neutropenia of adults, which are heterogeneous hematopoietic disorders that cause predispositions to leukemias and infections. Multiple alternatively spliced variants, encoding the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in bone marrow (RPKM 11.4), lymph node (RPKM 2.0) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GFI1 in Genome Data Viewer
    Location:
    1p22.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (92473043..92486925, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (92317932..92331836, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (92938600..92952482, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1312 Neighboring gene glomulin, FKBP associated protein Neighboring gene Sharpr-MPRA regulatory region 6980 Neighboring gene RNA polymerase II associated protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1313 Neighboring gene RNA, 7SL, cytoplasmic 824, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:92949865-92950465 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:92948665-92949264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:92951066-92951666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1317 Neighboring gene ecotropic viral integration site 5 Neighboring gene succinate dehydrogenase assembly factor 3, mitochondrial-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1076 Neighboring gene high mobility group box 3 pseudogene 9

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DLEU2/EZH2/GFI1 Axis Regulates the Proliferation and Apoptosis of Human Bone Marrow Mesenchymal Stem Cells.
      Title: DLEU2/EZH2/GFI1 Axis Regulates the Proliferation and Apoptosis of Human Bone Marrow Mesenchymal Stem Cells.
    2. Dose-dependent expression of GFI1 alters metabolism in the haematopoietic progenitors and MLL::AF9-induced leukaemic cells.
      Title: Dose-dependent expression of GFI1 alters metabolism in the haematopoietic progenitors and MLL::AF9-induced leukaemic cells.
    3. Hematopoietic transcription factor GFI1 promotes anchorage independence by sustaining ERK activity in cancer cells.
      Title: Hematopoietic transcription factor GFI1 promotes anchorage independence by sustaining ERK activity in cancer cells.
    4. GFI1 regulates chromatin state essential in human endothelial-to-haematopoietic transition.
      Title: GFI1 regulates chromatin state essential in human endothelial-to-haematopoietic transition.
    5. GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia.
      Title: GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia.
    6. DNA methylation of GFI1 as a mediator of the association between prenatal smoking exposure and ADHD symptoms at 6 years: the Hokkaido Study on Environment and Children's Health.
      Title: DNA methylation of GFI1 as a mediator of the association between prenatal smoking exposure and ADHD symptoms at 6 years: the Hokkaido Study on Environment and Children's Health.
    7. GFI1 promotes the proliferation and migration of esophageal squamous cell carcinoma cells through the inhibition of SOCS1 expression.
      Title: GFI1 promotes the proliferation and migration of esophageal squamous cell carcinoma cells through the inhibition of SOCS1 expression.
    8. The transcription factors GFI1 and GFI1B as modulators of the innate and acquired immune response.
      Title: The transcription factors GFI1 and GFI1B as modulators of the innate and acquired immune response.
    9. Epigenetic Regulation of Gfi1 in Endocrine-Related Cancers: a Role Regulating Tumor Growth.
      Title: Epigenetic Regulation of Gfi1 in Endocrine-Related Cancers: a Role Regulating Tumor Growth.
    10. Gfi1 upregulates c-Myc expression and promotes c-Myc-driven cell proliferation.
      Title: Gfi1 upregulates c-Myc expression and promotes c-Myc-driven cell proliferation.
    Submit: New GeneRIF Correction See all GeneRIFs (66)

    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
    Neutropenia, severe congenital, 2, autosomal dominant
    MedGen: C2751288 OMIM: 613107 GeneReviews: Not available
    		not available
    Nonimmune chronic idiopathic neutropenia of adults
    MedGen: C1842930 OMIM: 607847 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2024-07-22)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2024-07-22)

    ClinGen Genome Curation Page

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ94509

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables enzyme-substrate adaptor activity IDA
    Inferred from Direct Assay
    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 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of NF-kappaB transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of calcidiol 1-monooxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of neuron projection development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of vitamin D biosynthetic process IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-6-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of toll-like receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of transcription repressor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger protein Gfi-1
    Names
    growth factor independence-1
    growth factor independent 1 transcription repressor
    growth factor independent protein 1
    zinc finger protein 163

    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_007874.1 RefSeqGene

      Range
      5001..17116
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_63

    mRNA and Protein(s)

    1. NM_001127215.3 → NP_001120687.1  zinc finger protein Gfi-1

      See identical proteins and their annotated locations for NP_001120687.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC104456, AK123009, AK313876, AW086150, BC032751, BQ336135, DA927584
      Consensus CDS
      CCDS30773.1
      UniProtKB/Swiss-Prot
      Q8N564, Q99684
      Related
      ENSP00000359357.1, ENST00000370332.5
      Conserved Domains (2) summary
      COG5048
      Location:254 → 416
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314 → 334
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. NM_001127216.3 → NP_001120688.1  zinc finger protein Gfi-1

      See identical proteins and their annotated locations for NP_001120688.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC104456, AK123009, AW086150, BC032751, BQ336135, DA927584, DA938896
      Consensus CDS
      CCDS30773.1
      UniProtKB/Swiss-Prot
      Q8N564, Q99684
      Related
      ENSP00000399719.1, ENST00000427103.6
      Conserved Domains (2) summary
      COG5048
      Location:254 → 416
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314 → 334
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. NM_005263.5 → NP_005254.2  zinc finger protein Gfi-1

      See identical proteins and their annotated locations for NP_005254.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC104456, AK123009, AW086150, BE242676, BQ336135, DA927584, DB129173
      Consensus CDS
      CCDS30773.1
      UniProtKB/Swiss-Prot
      Q8N564, Q99684
      Related
      ENSP00000294702.5, ENST00000294702.6
      Conserved Domains (2) summary
      COG5048
      Location:254 → 416
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314 → 334
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      92473043..92486925 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541246.3 → XP_011539548.1  zinc finger protein Gfi-1 isoform X1

      See identical proteins and their annotated locations for XP_011539548.1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684
      Conserved Domains (2) summary
      COG5048
      Location:254 → 416
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314 → 334
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. XM_011541245.3 → XP_011539547.1  zinc finger protein Gfi-1 isoform X1

      See identical proteins and their annotated locations for XP_011539547.1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684
      Conserved Domains (2) summary
      COG5048
      Location:254 → 416
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314 → 334
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. XM_005270749.4 → XP_005270806.1  zinc finger protein Gfi-1 isoform X1

      See identical proteins and their annotated locations for XP_005270806.1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684
      Conserved Domains (2) summary
      COG5048
      Location:254 → 416
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314 → 334
      ZF_C2H2; C2H2 Zn finger [structural motif]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      92317932..92331836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335977.1 → XP_054191952.1  zinc finger protein Gfi-1 isoform X1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684

    2. XM_054335978.1 → XP_054191953.1  zinc finger protein Gfi-1 isoform X1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684

    3. XM_054335979.1 → XP_054191954.1  zinc finger protein Gfi-1 isoform X1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684

    4. XM_054335980.1 → XP_054191955.1  zinc finger protein Gfi-1 isoform X1

      UniProtKB/Swiss-Prot
      Q8N564, Q99684
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99684.2 GenPept UniProtKB/Swiss-Prot:Q99684

    Gene LinkOut

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

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