Human Gene NF1 (uc002hgf.2)
  Description: Homo sapiens neurofibromin 1 (NF1), transcript variant 3, mRNA.
RefSeq Summary (NM_001128147): This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:29,421,945-29,549,782 Size: 127,838 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr17:29,422,328-29,549,008 Size: 126,681 Coding Exon Count: 15 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:29,421,945-29,549,782)mRNA (may differ from genome)Protein (593 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NF1
CDC HuGE Published Literature: NF1
Positive Disease Associations: aberrant splicing , autism , intestinal neuronal dysplasia type B (IND B) , Leukemia, Myeloid, Acute , neurofibromatosis 1
Related Studies:
  1. aberrant splicing
    Messiaen LM et al. 1999, Exon 10b of the NF1 gene represents a mutational hotspot and harbors a recurrent missense mutation Y489C associated with aberrant splicing., Genetics in medicine. 1999 Sep-Oct;1(6):248-53. [PubMed 11258625]
    As exon 10b shows the highest mutation rate yet found in any of the 60 NF1 exons, it should be implemented with priority in mutation analysis.
  2. autism
    Marui, T. et al. 2004, Association between the neurofibromatosis-1 (NF1) locus and autism in the Japanese population., American journal of medical genetics Part B, Neuropsychiatric genetics. 2004 Nov;131(1):43-7. [PubMed 15389774]
    This may suggest an involvement of the NF1 locus in susceptibility to autism, although further investigations are recommended.
  3. intestinal neuronal dysplasia type B (IND B)
    Bahuau M et al. 2000, Tandem duplication within the neurofibromatosis type 1 gene (NF1) and reciprocal t(15;16)(q26.3;q12.1) translocation in familial association of NF1 with intestinal neuronal dysplasia type B (IND B), Journal of medical genetics. 2000 Feb;37(2):146-50. [PubMed 10712107]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NF1
Diseases sorted by gene-association score: neurofibromatosis, type 1* (1715), neurofibromatosis-noonan syndrome* (1700), neurofibromatosis, familial spinal* (1300), watson syndrome* (1048), juvenile myelomonocytic leukemia* (924), neurofibroma* (440), autosomal dominant café au lait spots* (419), cafe-au-lait spots, multiple* (400), legius syndrome* (303), juvenile myelomonocytic leukemia, somatic nf1-related* (100), chromosome 17q11.2 deletion syndrome, 1.4-mb* (42), plexiform neurofibroma (38), neurofibrosarcoma (32), pulmonic stenosis (28), nervous system cancer (28), malignant peripheral nerve sheath tumor (24), elephantiasis (23), optic pathway glioma (18), neurilemmoma (18), pseudoarthrosis (18), optic nerve neoplasm (17), pulsating exophthalmos (16), atypical neurofibroma (16), cellular schwannoma (16), vagus nerve neoplasm (15), equatorial staphyloma (15), adult malignant schwannoma (15), autosomal genetic disease (14), neurofibromatosis, type 2 (12), tuberous sclerosis (11), schwannomatosis (11), peripheral nervous system neoplasm (11), pilocytic astrocytoma (11), malignant glandular tumor of peripheral nerve sheath (11), leopard syndrome (11), orbit embryonal rhabdomyosarcoma (10), paraganglioma (10), orbit rhabdomyosarcoma (10), nervous system benign neoplasm (10), astrocytoma (10), ectropion (10), renovascular hypertension (9), intracranial berry aneurysm (9), myelodysplastic syndrome (8), myelodysplastic myeloproliferative cancer (8), malignant triton tumor (8), gliofibroma (8), meningocele (8), von hippel-lindau syndrome (8), phaeochromocytoma (8), childhood pilocytic astrocytoma (8), plexiform schwannoma (8), multiple endocrine neoplasia (7), adult oligodendroglioma (7), pheochromocytoma (7), frey syndrome (7), tolosa-hunt syndrome (7), sporadic pheochromocytoma (7), giant cell reparative granuloma (6), bone structure disease (6), multiple endocrine neoplasia iia (6), osteofibrous dysplasia (6), noonan syndrome 1 (6), scleral staphyloma (6), epithelioid malignant peripheral nerve sheath tumor (6), juvenile pilocytic astrocytoma (6), expressive language disorder (6), chromosome 6pter-p24 deletion syndrome (6), obstructive hydrocephalus (6), pilocytic astrocytoma of cerebellum (6), inflammatory leiomyosarcoma (6), conventional leiomyosarcoma (6), cerebral arterial disease (6), immature cataract (6), optic nerve glioma (5), duodenal somatostatinoma (5), exophthalmos (5), li-fraumeni syndrome (5), malignant spindle cell melanoma (5), subclavian artery aneurysm (5), amyloid tumor (5), chronic polyneuropathy (4), pleomorphic lipoma (4), glaucoma 3a, primary open angle, congenital, juvenile, or adult onset (4), internuclear ophthalmoplegia (4), spinal canal and spinal cord meningioma (4), intraneural perineurioma (4), poland syndrome (4), hypotropia (4), basal cell nevus syndrome (4), spinal cord ependymoma (4), lung sarcoma (4), spinal meningioma (4), nephrogenic adenofibroma (4), brachial plexus lesion (4), brain germinoma (3), gastrointestinal stromal tumor (3), bone marrow cancer (3), colorectal cancer (3), autistic disorder (2), breast cancer (2), autosomal dominant disease (2), meningioma, familial (2), multiple endocrine neoplasia 1 (1), organ system benign neoplasm (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.13 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 208.74 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -154.50383-0.403 Picture PostScript Text
3' UTR -135.72774-0.175 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  ModBase Predicted Comparative 3D Structure on P21359-5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  D12625 - Homo sapiens mRNA for NF1 protein isoform, complete cds.
LF384773 - JP 2014500723-A/192276: Polycomb-Associated Non-Coding RNAs.
AK289936 - Homo sapiens cDNA FLJ76650 complete cds, highly similar to Human mRNA for NF1 N-isoform-exon11.
M82814 - Homo sapiens GAP-related protein (NF1) mRNA, complete cds.
M89914 - Human neurofibromin (NF1) gene, complete cds.
BC144643 - Homo sapiens cDNA clone IMAGE:9053174.
D42072 - Homo sapiens mRNA for NF1 N-isoform-exon11, complete cds.
BC172192 - Synthetic construct Homo sapiens clone IMAGE:9094293 neurofibromin isoform 2 (NF1) gene, partial cds.
BX537850 - Homo sapiens mRNA; cDNA DKFZp686J1293 (from clone DKFZp686J1293).
M38106 - Human neurofibromatosis protein type 1 mRNA, 3' end of cds.
M38107 - Human neurofibromatosis type 1 (NF-1) mRNA, 3' end of cds.
MA620350 - JP 2018138019-A/192276: Polycomb-Associated Non-Coding RNAs.
JD380294 - Sequence 361318 from Patent EP1572962.
JD391439 - Sequence 372463 from Patent EP1572962.
JD390223 - Sequence 371247 from Patent EP1572962.
JD470695 - Sequence 451719 from Patent EP1572962.
JD153917 - Sequence 134941 from Patent EP1572962.
JD099427 - Sequence 80451 from Patent EP1572962.
JD415997 - Sequence 397021 from Patent EP1572962.
LF326870 - JP 2014500723-A/134373: Polycomb-Associated Non-Coding RNAs.
LF326871 - JP 2014500723-A/134374: Polycomb-Associated Non-Coding RNAs.
MA562447 - JP 2018138019-A/134373: Polycomb-Associated Non-Coding RNAs.
MA562448 - JP 2018138019-A/134374: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_hSWI-SNFpathway - Chromatin Remodeling by hSWI/SNF ATP-dependent Complexes

Reactome (by CSHL, EBI, and GO)

Protein P21359 (Reactome details) participates in the following event(s):

R-HSA-5658438 SPRED dimer binds NF1
R-HSA-5658424 KBTBD7:CUL3:RBX1 ubiquitinates NF1
R-HSA-5658435 RAS GAPs bind RAS:GTP
R-HSA-5658231 RAS GAPs stimulate RAS GTPase activity
R-HSA-5658442 Regulation of RAS by GAPs
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-6802953 RAS signaling downstream of NF1 loss-of-function variants
R-HSA-6802949 Signaling by RAS mutants
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-5683057 MAPK family signaling cascades
R-HSA-5663202 Diseases of signal transduction
R-HSA-162582 Signal Transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001128147, NP_001121619, P21359-5
UCSC ID: uc002hgf.2
RefSeq Accession: NM_001128147
Protein: P21359-5, splice isoform of P21359 CCDS: CCDS45645.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NF1:
nf1 (Neurofibromatosis 1)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001128147.2
exon count: 15CDS single in 3' UTR: no RNA size: 2939
ORF size: 1782CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3635.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 835# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.