U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
nuclear factor 1 A-type
Names
CCAAT-box-binding transcription factor
TGGCA-binding protein

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous