Human Gene SCNN1A (uc001qnw.3) Description and Page Index
  Description: Homo sapiens sodium channel, non-voltage-gated 1 alpha subunit (SCNN1A), transcript variant 2, mRNA.
RefSeq Summary (NM_001159576): Nonvoltage-gated, amiloride-sensitive, sodium channels control fluid and electrolyte transport across epithelia in many organs. These channels are heteromeric complexes consisting of 3 subunits: alpha, beta, and gamma. This gene encodes the alpha subunit, and mutations in this gene have been associated with pseudohypoaldosteronism type 1 (PHA1), a rare salt wasting disease resulting from target organ unresponsiveness to mineralocorticoids. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2009].
Transcript (Including UTRs)
   Position: hg19 chr12:6,456,009-6,484,390 Size: 28,382 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr12:6,457,039-6,484,126 Size: 27,088 Coding Exon Count: 12 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:6,456,009-6,484,390)mRNA (may differ from genome)Protein (728 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHuman Cortex Gene ExpressionLynxMGIOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SCNN1A
CDC HuGE Published Literature: SCNN1A
Positive Disease Associations: Asthma , blood pressure , Inflammation|Premature Birth , Parkinson Disease
Related Studies:
  1. Asthma
    C Ober et al. American journal of human genetics 2000, A second-generation genomewide screen for asthma-susceptibility alleles in a founder population., American journal of human genetics. [PubMed 11022011]
  2. blood pressure
    Iwai, N. et al. 2002, Association of a sodium channel alpha subunit promoter variant with blood pressure., Journal of the American Society of Nephrology. 2002 Jan;13(1):80-5. [PubMed 11752024]
    Therefore, possession of the SCNN1A G(2139) allele significantly increased the risk of hypertension. A lower level of SCNN1A subunit expression among subjects with the AA genotype might lead to lower levels of sodium reabsorption in the kidney and might provide protection against the development of hypertension.
  3. Inflammation|Premature Birth
    Velez DR et al. 2008, Preterm birth in Caucasians is associated with coagulation and inflammation pathway gene variants., PloS one 3(9) : e3283 2008. [PubMed 18818748]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SCNN1A
Diseases sorted by gene-association score: bronchiectasis with or without elevated sweat chloride 2* (1331), pseudohypoaldosteronism, type i* (1184), idiopathic bronchiectasis* (202), pseudohypoaldosteronism (39), bronchiectasis (26), liddle syndrome (16), pseudohypoaldosteronism type i, autosomal dominant (9), cystic fibrosis (8), brugada syndrome (2)
* = 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: 86.23 RPKM in Kidney - Cortex
Total median expression: 640.28 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -82.20264-0.311 Picture PostScript Text
3' UTR -358.521030-0.348 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
  Pfam Domains:
PF00858 - Amiloride-sensitive sodium channel

ModBase Predicted Comparative 3D Structure on P37088-2
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Descriptions from all associated GenBank mRNAs
  BC006526 - Homo sapiens sodium channel, nonvoltage-gated 1 alpha, mRNA (cDNA clone IMAGE:3936903), partial cds.
AK025536 - Homo sapiens cDNA: FLJ21883 fis, clone HEP02841, highly similar to HSLASNA Homo sapiens mRNA for lung amiloride sensitive Na+ channel protein.
BC037417 - Homo sapiens sodium channel, nonvoltage-gated 1 alpha, mRNA (cDNA clone IMAGE:5112163), containing frame-shift errors.
BC062613 - Homo sapiens sodium channel, nonvoltage-gated 1 alpha, mRNA (cDNA clone MGC:75136 IMAGE:5186683), complete cds.
AK172792 - Homo sapiens cDNA FLJ23953 fis, clone HEP10547, highly similar to Amiloride-sensitive sodium channel alpha-subunit.
X76180 - H.sapiens mRNA for lung amiloride sensitive Na+ channel protein.
JD119791 - Sequence 100815 from Patent EP1572962.
JD149934 - Sequence 130958 from Patent EP1572962.
JD559063 - Sequence 540087 from Patent EP1572962.
JD262324 - Sequence 243348 from Patent EP1572962.
JD158278 - Sequence 139302 from Patent EP1572962.
JD261295 - Sequence 242319 from Patent EP1572962.
JD464436 - Sequence 445460 from Patent EP1572962.
JD494423 - Sequence 475447 from Patent EP1572962.
JD301142 - Sequence 282166 from Patent EP1572962.
JD511054 - Sequence 492078 from Patent EP1572962.
JD123011 - Sequence 104035 from Patent EP1572962.
JD354221 - Sequence 335245 from Patent EP1572962.
JD131955 - Sequence 112979 from Patent EP1572962.
JD254226 - Sequence 235250 from Patent EP1572962.
JD325001 - Sequence 306025 from Patent EP1572962.
JD333449 - Sequence 314473 from Patent EP1572962.
JD060541 - Sequence 41565 from Patent EP1572962.
JD190294 - Sequence 171318 from Patent EP1572962.
JD127659 - Sequence 108683 from Patent EP1572962.
JD274036 - Sequence 255060 from Patent EP1572962.
JD310868 - Sequence 291892 from Patent EP1572962.
AK304379 - Homo sapiens cDNA FLJ56208 complete cds, highly similar to Amiloride-sensitive sodium channel subunit alpha.
JD469379 - Sequence 450403 from Patent EP1572962.
JD414129 - Sequence 395153 from Patent EP1572962.
JD183088 - Sequence 164112 from Patent EP1572962.
JD468984 - Sequence 450008 from Patent EP1572962.
DQ402522 - Homo sapiens nasal epithelial sodium channel alpha subunit mRNA, complete cds.
AB527714 - Synthetic construct DNA, clone: pF1KB6217, Homo sapiens SCNN1A gene for sodium channel, nonvoltage-gated 1 alpha, without stop codon, in Flexi system.
AY365119 - Homo sapiens amiloride-sensitive epithelial sodium channel alpha subunit (SCNN1A) mRNA, partial cds; alternatively spliced.
JD439770 - Sequence 420794 from Patent EP1572962.
JD337810 - Sequence 318834 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04742 - Taste transduction
hsa04960 - Aldosterone-regulated sodium reabsorption

Reactome (by CSHL, EBI, and GO)

Protein P37088 (Reactome details) participates in the following event(s):

R-HSA-2682349 RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels
R-HSA-2672334 SCNN channels transport extracellular Na+ to cytosol
R-HSA-2672351 Stimuli-sensing channels
R-HSA-983712 Ion channel transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001159576, NP_001029, P37088-2, SCNN1
UCSC ID: uc001qnw.3
RefSeq Accession: NM_001159576
Protein: P37088-2, splice isoform of P37088 CCDS: CCDS53738.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001159576.1
exon count: 12CDS single in 3' UTR: no RNA size: 3497
ORF size: 2187CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4548.00frame shift in genome: no % Coverage: 99.54
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: 387# 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.