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    NFIX nuclear factor I X [ Homo sapiens (human) ]

    Gene ID: 4784, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NFIXprovided by HGNC
    Official Full Name
    nuclear factor I Xprovided by HGNC
    Primary source
    HGNC:HGNC:7788
    See related
    Ensembl:ENSG00000008441 MIM:164005; AllianceGenome:HGNC:7788
    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
    CTF; NF1A; MALNS; NF1-X; MRSHSS; NF-I/X; SOTOS2
    Summary
    The protein encoded by this gene is a transcription factor that binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3 in viral and cellular promoters. The encoded protein can also stimulate adenovirus replication in vitro. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]
    Expression
    Ubiquitous expression in brain (RPKM 36.5), fat (RPKM 32.4) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NFIX in Genome Data Viewer
    Location:
    19p13.13
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12995475..13098796)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13120686..13224010)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13106289..13209610)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:13063321-13064520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13067513-13068385 Neighboring gene GADD45G interacting protein 1 Neighboring gene RAD23 homolog A, nucleotide excision repair protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13079936-13080539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13080540-13081142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13085246-13085752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10187 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13095227-13095752 Neighboring gene DAN domain BMP antagonist family member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13106570-13107158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13121583-13122126 Neighboring gene uncharacterized LOC107985286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13134224-13134736 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13135703-13136522 Neighboring gene VISTA enhancer hs1900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13168092-13168678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13170695-13171596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13171597-13172496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13187265-13188200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13206733-13207596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13210189-13211052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14106 Neighboring gene CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element Neighboring gene Sharpr-MPRA regulatory region 14065 Neighboring gene uncharacterized LOC105372282 Neighboring gene LYL1 basic helix-loop-helix family member

    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. Nuclear factor IA is expressed in astrocytomas and is associated with improved survival. Song HR, et al. Neuro Oncol, 2010 Feb. PMID 20150379, Free PMC Article
    2. Two nuclear localization signals are required for nuclear translocation of nuclear factor 1-A. Imagawa M, et al. FEBS Lett, 2000 Nov 3. PMID 11068044
    3. Parental gonadal but not somatic mosaicism leading to de novo NFIX variants shared by two brothers with Malan syndrome. Hancarova M, et al. Am J Med Genet A, 2019 Oct. PMID 31369202
    4. NFIX downregulation independently predicts poor prognosis in lung adenocarcinoma, but not in squamous cell carcinoma. Ge J, et al. Future Oncol, 2018 Dec. PMID 30418046
    5. Nuclear Factor One X in Development and Disease. Piper M, et al. Trends Cell Biol, 2019 Jan. PMID 30287093

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circular RNA NFIX Functions as an Oncogene in Non-Small Cell Lung Cancer by Modulating the miR-214-3p/TRIAP1 Axis.
      Title: Circular RNA NFIX Functions as an Oncogene in Non-Small Cell Lung Cancer by Modulating the miR-214-3p/TRIAP1 Axis.
    2. [NFIX gene mutation causes Marshall-Smith syndrome in a pair of identical twins and literature review].
      Title: [NFIX gene mutation causes Marshall-Smith syndrome in a pair of identical twins and literature review].
    3. m6A-modified circNFIX promotes ovarian cancer progression and immune escape via activating IL-6R/JAK1/STAT3 signaling by sponging miR-647.
      Title: m6A-modified circNFIX promotes ovarian cancer progression and immune escape via activating IL-6R/JAK1/STAT3 signaling by sponging miR-647.
    4. A rare cause of intellectual disability: Novel mutations of NFIX gene in two patients with clinical features of Marshall-Smith syndrome and Malan syndrome.
      Title: A rare cause of intellectual disability: Novel mutations of NFIX gene in two patients with clinical features of Marshall-Smith syndrome and Malan syndrome.
    5. NFIXing Cancer: The Role of NFIX in Oxidative Stress Response and Cell Fate.
      Title: NFIXing Cancer: The Role of NFIX in Oxidative Stress Response and Cell Fate.
    6. CircNFIX stimulates the proliferation, invasion, and stemness properties of ovarian cancer cells by enhancing SH3RF3 mRNA stability via binding LIN28B.
      Title: CircNFIX stimulates the proliferation, invasion, and stemness properties of ovarian cancer cells by enhancing SH3RF3 mRNA stability via binding LIN28B.
    7. A Novel Tumor-Promoting Role for Nuclear Factor IX in Glioblastoma Is Mediated through Transcriptional Activation of GINS1.
      Title: A Novel Tumor-Promoting Role for Nuclear Factor IX in Glioblastoma Is Mediated through Transcriptional Activation of GINS1.
    8. CircNFIX regulates chondrogenesis and cartilage homeostasis by targeting the miR758-3p/KDM6A axis.
      Title: CircNFIX regulates chondrogenesis and cartilage homeostasis by targeting the miR758-3p/KDM6A axis.
    9. A novel miRNA-762/NFIX pathway modulates LPS-induced acute lung injury.
      Title: A novel miRNA-762/NFIX pathway modulates LPS-induced acute lung injury.
    10. Pathogenic variant in NFIX gene affecting three sisters due to paternal mosaicism.
      Title: Pathogenic variant in NFIX gene affecting three sisters due to paternal mosaicism.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    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
    Malan overgrowth syndrome
    MedGen: C3553660 OMIM: 614753 GeneReviews: NFIX-Related Malan Syndrome
    		Compare labs
    Marshall-Smith syndrome
    MedGen: C0265211 OMIM: 602535 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2022-04-12)

    ClinGen Genome Curation PagePubMed
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2022-04-12)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder.
    EBI GWAS Catalog
    Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
    EBI GWAS Catalog
    Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.
    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    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 factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    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 
    Process Evidence Code Pubs
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II 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
    		  
    involved_in transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    nuclear factor 1 X-type
    Names
    CCAAT-box-binding transcription factor
    TGGCA-binding protein
    nuclear factor 1/X

    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_032925.2 RefSeqGene

      Range
      4706..108027
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271043.2 → NP_001257972.1  nuclear factor 1 X-type isoform 1

      See identical proteins and their annotated locations for NP_001257972.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC007787, AK295290, KF456509
      Consensus CDS
      CCDS92532.1
      UniProtKB/TrEMBL
      B4DHW2
      Related
      ENSP00000502554.1, ENST00000676441.1
      Conserved Domains (3) summary
      pfam10524
      Location:18 → 54
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:221 → 510
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:76 → 178
      MH1; N-terminal Mad Homology 1 (MH1) domain

    2. NM_001271044.3 → NP_001257973.1  nuclear factor 1 X-type isoform 3

      See identical proteins and their annotated locations for NP_001257973.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks an alternate 3' exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has shorter and distinct N- and C-termini compared to isoform 1.
      Source sequence(s)
      AC007787, BP228658, KF456509, U18759
      Consensus CDS
      CCDS59359.1
      UniProtKB/TrEMBL
      Q7Z3K7
      Related
      ENSP00000466389.1, ENST00000587760.5
      Conserved Domains (3) summary
      pfam10524
      Location:2 → 38
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:205 → 410
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:60 → 162
      MH1; N-terminal Mad Homology 1 (MH1) domain

    3. NM_001365902.3 → NP_001352831.1  nuclear factor 1 X-type isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      Consensus CDS
      CCDS92530.1
      UniProtKB/Swiss-Prot
      B4DM25, O60413, Q0VG09, Q12859, Q13050, Q13052, Q14938, Q5U094, Q9UPH1, Q9Y6R8
      Related
      ENSP00000467512.1, ENST00000592199.6
      Conserved Domains (3) summary
      pfam10524
      Location:9 → 46
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:213 → 502
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68 → 170
      MH1; N-terminal Mad Homology 1 (MH1) domain

    4. NM_001365982.2 → NP_001352911.1  nuclear factor 1 X-type isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      UniProtKB/TrEMBL
      Q7Z3K7
      Related
      ENSP00000353219.4, ENST00000360105.8
      Conserved Domains (3) summary
      pfam10524
      Location:9 → 46
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:213 → 377
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68 → 170
      MH1; N-terminal Mad Homology 1 (MH1) domain

    5. NM_001365983.2 → NP_001352912.1  nuclear factor 1 X-type isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      UniProtKB/TrEMBL
      Q7Z3K7
      Conserved Domains (2) summary
      pfam00859
      Location:166 → 371
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:21 → 123
      MH1; N-terminal Mad Homology 1 (MH1) domain

    6. NM_001365984.2 → NP_001352913.1  nuclear factor 1 X-type isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      Related
      ENSP00000466735.1, ENST00000588228.5
      Conserved Domains (3) summary
      pfam10524
      Location:8 → 45
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:212 → 501
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:67 → 169
      MH1; N-terminal Mad Homology 1 (MH1) domain

    7. NM_001365985.2 → NP_001352914.1  nuclear factor 1 X-type isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      Consensus CDS
      CCDS92533.1
      UniProtKB/TrEMBL
      Q7Z3K7
      Related
      ENSP00000467785.1, ENST00000587260.1
      Conserved Domains (3) summary
      pfam10524
      Location:8 → 45
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:212 → 417
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:67 → 169
      MH1; N-terminal Mad Homology 1 (MH1) domain

    8. NM_001378404.1 → NP_001365333.1  nuclear factor 1 X-type isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      Consensus CDS
      CCDS92531.1
      UniProtKB/TrEMBL
      D2DXM9
      Related
      ENSP00000468794.1, ENST00000585575.5
      Conserved Domains (3) summary
      pfam10524
      Location:2 → 38
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:205 → 494
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:60 → 162
      MH1; N-terminal Mad Homology 1 (MH1) domain

    9. NM_001378405.1 → NP_001365334.1  nuclear factor 1 X-type isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      Conserved Domains (3) summary
      pfam10524
      Location:26 → 62
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:229 → 518
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:84 → 186
      MH1; N-terminal Mad Homology 1 (MH1) domain

    10. NM_002501.4 → NP_002492.2  nuclear factor 1 X-type isoform 2

      See identical proteins and their annotated locations for NP_002492.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate 3' exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has shorter and distinct N- and C-termini compared to isoform 1.
      Source sequence(s)
      AC007787, AC138474, BF115883, KF456509, U18759
      Consensus CDS
      CCDS45996.1
      UniProtKB/TrEMBL
      Q7Z3K7
      Related
      ENSP00000380781.2, ENST00000397661.6
      Conserved Domains (3) summary
      pfam10524
      Location:9 → 46
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:213 → 418
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68 → 170
      MH1; N-terminal Mad Homology 1 (MH1) domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      12995475..13098796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438864.1 → XP_047294820.1  nuclear factor 1 X-type isoform X3

    2. XM_047438865.1 → XP_047294821.1  nuclear factor 1 X-type isoform X4

    3. XM_005259917.5 → XP_005259974.2  nuclear factor 1 X-type isoform X1

      Related
      ENSP00000351354.5, ENST00000358552.8

    4. XM_047438863.1 → XP_047294819.1  nuclear factor 1 X-type isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      13120686..13224010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321074.1 → XP_054177049.1  nuclear factor 1 X-type isoform X3

    2. XM_054321075.1 → XP_054177050.1  nuclear factor 1 X-type isoform X4

    3. XM_054321072.1 → XP_054177047.1  nuclear factor 1 X-type isoform X1

    4. XM_054321073.1 → XP_054177048.1  nuclear factor 1 X-type isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14938.2 GenPept UniProtKB/Swiss-Prot:Q14938

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