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    NFIA nuclear factor I A [ Homo sapiens (human) ]

    Gene ID: 4774, updated on 5-Mar-2024

    Summary

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    Official Symbol
    NFIAprovided by HGNC
    Official Full Name
    nuclear factor I Aprovided by HGNC
    Primary source
    HGNC:HGNC:7784
    See related
    Ensembl:ENSG00000162599 MIM:600727; AllianceGenome:HGNC:7784
    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; NF1-A; NFI-A; NFI-L; BRMUTD; NF-I/A; DEL1P32P31; C1DELp32p31
    Summary
    This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
    Expression
    Ubiquitous expression in fat (RPKM 9.2), thyroid (RPKM 8.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p31.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (61077227..61462788)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (60956019..61341601)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (61542899..61928460)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:61368907-61369440 Neighboring gene NFIA antisense RNA 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:61520031-61520904 Neighboring gene Sharpr-MPRA regulatory region 5981 Neighboring gene Sharpr-MPRA regulatory region 2485 Neighboring gene NFE2L2 motif-containing MPRA enhancer 286 Neighboring gene Sharpr-MPRA regulatory region 4387 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:61713056-61713264 Neighboring gene NANOG hESC enhancer GRCh37_chr1:61715889-61716390 Neighboring gene NFIA antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:61766471-61767069 Neighboring gene MPRA-validated peak260 silencer Neighboring gene Sharpr-MPRA regulatory region 1245 Neighboring gene MPRA-validated peak261 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:61902263-61902764 Neighboring gene VISTA enhancer hs1309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:61942976-61943490 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:61946773-61947972 Neighboring gene uncharacterized LOC105378766 Neighboring gene VISTA enhancer hs1484 Neighboring gene VISTA enhancer hs1450 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:62071813-62073012 Neighboring gene uncharacterized LOC107984964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1113

    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. Nuclear factor I A promotes temozolomide resistance in glioblastoma via activation of nuclear factor κB pathway. Yu X, et al. Life Sci, 2019 Nov 1. PMID 31614149
    2. NFIA-Related Disorder. Adam MP, et al. , 1993. PMID 31194316
    3. Loss-of-function variants in NFIA provide further support that NFIA is a critical gene in 1p32-p31 deletion syndrome: A four patient series. Revah-Politi A, et al. Am J Med Genet A, 2017 Dec. PMID 28941020
    4. Truncating mutation in NFIA causes brain malformation and urinary tract defects. Negishi Y, et al. Hum Genome Var, 2015. PMID 27081522, Free PMC Article
    5. Familial craniosynostosis associated with a microdeletion involving the NFIA gene. Nyboe D, et al. Clin Dysmorphol, 2015 Jul. PMID 25714559

    See all (95) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CNS erythroblastic sarcoma: a potential emerging pediatric tumor type characterized by NFIA::RUNX1T1/3 fusions.
      Title: CNS erythroblastic sarcoma: a potential emerging pediatric tumor type characterized by NFIA::RUNX1T1/3 fusions.
    2. Cell-specific NFIA upregulation promotes epileptogenesis by TRPV4-mediated astrocyte reactivity.
      Title: Cell-specific NFIA upregulation promotes epileptogenesis by TRPV4-mediated astrocyte reactivity.
    3. SOX9/NFIA promotes human ovarian cancer metastasis through the Wnt/beta-catenin signaling pathway.
      Title: SOX9/NFIA promotes human ovarian cancer metastasis through the Wnt/β-catenin signaling pathway.
    4. Spatial control of astrogenesis progression by cortical arealization genes.
      Title: Spatial control of astrogenesis progression by cortical arealization genes.
    5. HIF-1alpha and NFIA-AS2 Polymorphisms as Potential Determinants of Total Hemoglobin Mass in Endurance Athletes.
      Title: HIF-1α and NFIA-AS2 Polymorphisms as Potential Determinants of Total Hemoglobin Mass in Endurance Athletes.
    6. The miR-223/nuclear factor I-A axis regulates inflammation and cellular functions in intestinal tissues with necrotizing enterocolitis.
      Title: The miR-223/nuclear factor I-A axis regulates inflammation and cellular functions in intestinal tissues with necrotizing enterocolitis.
    7. Nuclear Factor IA Is Down-regulated in Muscle-invasive and High-grade Bladder Cancers.
      Title: Nuclear Factor IA Is Down-regulated in Muscle-invasive and High-grade Bladder Cancers.
    8. Recurrent NFIA K125E substitution represents a loss-of-function allele: Sensitive in vitro and in vivo assays for nontruncating alleles.
      Title: Recurrent NFIA K125E substitution represents a loss-of-function allele: Sensitive in vitro and in vivo assays for nontruncating alleles.
    9. Genome-wide association study identifies susceptibility loci of brain atrophy to NFIA and ST18 in Alzheimer's disease.
      Title: Genome-wide association study identifies susceptibility loci of brain atrophy to NFIA and ST18 in Alzheimer's disease.
    10. NFIA enhances cell radiosensitivity by downregulating p-AKT and p-ERK in non-small cell lung cancer
      Title: A novel role for NFIA in restoring radiosensitivity in radioresistant NSCLC cells by downregulating the AKT and ERK pathways.
    Submit: New GeneRIF Correction See all GeneRIFs (48)

    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
    Brain malformations with or without urinary tract defects
    MedGen: CN322312 OMIM: 613735 GeneReviews: NFIA-Related Disorder
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2017-01-12)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2017-01-12)

    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
    A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
    EBI GWAS Catalog
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    EBI GWAS Catalog
    Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk.
    EBI GWAS Catalog
    Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes.
    EBI GWAS Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    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

    Clone Names

    • FLJ39164, KIAA1439, DKFZp434L0422, DKFZp686J23256

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity NAS
    Non-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 DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cartilage development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in exit from mitosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glial cell fate specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron fate specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to wounding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synapse maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ureter development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in viral genome replication NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_011787.2 RefSeqGene

      Range
      10288..390515
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001134673.4 → NP_001128145.1  nuclear factor 1 A-type isoform 1

      See identical proteins and their annotated locations for NP_001128145.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
      Source sequence(s)
      AA974652, AB037860, AL096888
      Consensus CDS
      CCDS44156.1
      UniProtKB/Swiss-Prot
      B4DRJ3, B4DS53, F5H0R0, F8W8W3, Q12857, Q8TA97, Q9H3X9, Q9P2A9
      UniProtKB/TrEMBL
      B4DRN9
      Related
      ENSP00000384523.3, ENST00000403491.8
      Conserved Domains (3) summary
      pfam10524
      Location:9 → 46
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:214 → 508
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68 → 172
      MH1; N-terminal Mad Homology 1 (MH1) domain

    2. NM_001145511.2 → NP_001138983.1  nuclear factor 1 A-type isoform 3

      See identical proteins and their annotated locations for NP_001138983.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AA974652, AB037860, AC096534, AK024964, AK299289, AL096888, AW014151, BC022264, CA398137, CN372139, DB544485
      Consensus CDS
      CCDS53321.1
      UniProtKB/TrEMBL
      B4DRN9
      Related
      ENSP00000384680.2, ENST00000407417.7
      Conserved Domains (3) summary
      pfam10524
      Location:2 → 38
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:206 → 500
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam03165
      Location:60 → 164
      MH1; MH1 domain

    3. NM_001145512.2 → NP_001138984.1  nuclear factor 1 A-type isoform 4

      See identical proteins and their annotated locations for NP_001138984.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding region compared to variant 1. The resulting protein (isoform 4) has a longer and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AA974652, AB037860, AC096534, AK024964, AK299579, AL096888, AW014151, BC022264, CA398137, CN372139, DB544485
      Consensus CDS
      CCDS53322.1
      UniProtKB/TrEMBL
      B4DRN9
      Related
      ENSP00000360231.3, ENST00000371189.8
      Conserved Domains (3) summary
      pfam10524
      Location:54 → 91
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      cl00055
      Location:113 → 217
      MH1; N-terminal Mad Homology 1 (MH1) domain
      pfam00859
      Location:259 → 546
      CTF_NFI; CTF/NF-I family transcription modulation region

    4. NM_005595.5 → NP_005586.1  nuclear factor 1 A-type isoform 2

      See identical proteins and their annotated locations for NP_005586.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment in the 3' UTR, which shifts the reading frame, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus when it is compared to isoform 1.
      Source sequence(s)
      AA974652, AC096534, AL096888, BC022264
      Consensus CDS
      CCDS615.1
      UniProtKB/TrEMBL
      S4R3W2
      Related
      ENSP00000360229.3, ENST00000371187.7
      Conserved Domains (3) summary
      pfam10524
      Location:9 → 46
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:214 → 473
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68 → 172
      MH1; N-terminal Mad Homology 1 (MH1) domain

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      61077227..61462788
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      60956019..61341601
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12857.2 GenPept UniProtKB/Swiss-Prot:Q12857

    Gene LinkOut

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

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