Human Gene NPHS2 (uc009wxi.3)
  Description: Homo sapiens nephrosis 2, idiopathic, steroid-resistant (podocin) (NPHS2), mRNA.
RefSeq Summary (NM_014625): This gene encodes a protein that plays a role in the regulation of glomerular permeability. Mutations in this gene cause steroid-resistant nephrotic syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014].
Transcript (Including UTRs)
   Position: hg19 chr1:179,519,674-179,545,084 Size: 25,411 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:179,520,308-179,544,999 Size: 24,692 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:179,519,674-179,545,084)mRNA (may differ from genome)Protein (315 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIOMIM
PubMedReactomeTreefamUniProtKBWikipediaBioGrid 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): NPHS2
CDC HuGE Published Literature: NPHS2
Positive Disease Associations: microalbuniuria , nephrosis , nephrotic syndrome
Related Studies:
  1. microalbuniuria
    Pereira, A. C. et al. 2004, NPHS2 R229Q functional variant is associated with microalbuminuria in the general population., Kidney international. 2004 Mar;65(3):1026-30. [PubMed 14871423]
    These data have important implications for the understanding of microalbuminuria in the general population and may contribute to better ways of disease prediction and prevention.
  2. nephrosis
    Yu, Z. et al. 2005, Mutations in NPHS2 in sporadic steroid-resistant nephrotic syndrome in Chinese children., Nephrology, dialysis, transplantation. 2005 May;20(5):902-8. [PubMed 15769810]
    The results demonstrate that NPHS2 mutations are also present in Chinese sporadic SRNS. Our investigation supports the necessity of searching for mutations in NPHS2 in Chinese children with sporadic SRNS.
  3. nephrotic syndrome
    Hinkes, B. G. et al. 2007, Nephrotic Syndrome in the First Year of Life, Pediatrics 2007. [PubMed 17371932]
    First, two thirds of nephrotic syndrome manifesting in the first year of life can be explained by mutations in 4 genes only (NPHS1, NPHS2, WT1, or LAMB2).
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NPHS2
Diseases sorted by gene-association score: nephrotic syndrome, type 2* (1225), nephrotic syndrome, idiopathic, steroid-resistant* (425), sporadic idiopathic steroid-resistant nephrotic syndrome with minimal changes* (350), sporadic idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis* (247), familial idiopathic steroid-resistant nephrotic syndrome with minimal changes* (247), glomerulosclerosis, focal segmental, 1* (111), nephrotic syndrome (73), steroid-resistant nephrotic syndrome, nphs2-related* (71), focal segmental glomerulosclerosis (21), nail-patella syndrome (20), congenital nephrotic syndrome finnish type (15), lipoid nephrosis (15), frasier syndrome (13), galloway-mowat syndrome (12), denys-drash syndrome (11), hypoparathyroidism, sensorineural deafness, and renal dysplasia (11), membranous nephropathy (11), familial nephrotic syndrome (11), end stage renal failure (10), nephrosclerosis (10), pierson syndrome (9), diffuse mesangial sclerosis (9), atrial septal defect 3 (9), crescentic glomerulonephritis (7), kidney disease (7), iga glomerulonephritis (6), kidney hypertrophy (6), discrete subaortic stenosis (6), chronic kidney failure (5), urinary system disease (4), glomerulonephritis (4), wilms tumor susceptibility-5 (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: 51.01 RPKM in Kidney - Cortex
Total median expression: 51.89 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 -31.9085-0.375 Picture PostScript Text
3' UTR -172.64634-0.272 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 Q9NP85-2
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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    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  LF383648 - JP 2014500723-A/191151: Polycomb-Associated Non-Coding RNAs.
MA619225 - JP 2018138019-A/191151: Polycomb-Associated Non-Coding RNAs.
BC029141 - Homo sapiens nephrosis 2, idiopathic, steroid-resistant (podocin), mRNA (cDNA clone MGC:34362 IMAGE:5187188), complete cds.
AJ279254 - Homo sapiens mRNA for podocin (NPHS2 gene).
JD172262 - Sequence 153286 from Patent EP1572962.
JD055669 - Sequence 36693 from Patent EP1572962.
JD261513 - Sequence 242537 from Patent EP1572962.
JD226579 - Sequence 207603 from Patent EP1572962.
JD547237 - Sequence 528261 from Patent EP1572962.
JD418051 - Sequence 399075 from Patent EP1572962.
JD130216 - Sequence 111240 from Patent EP1572962.
JD394378 - Sequence 375402 from Patent EP1572962.
JD172592 - Sequence 153616 from Patent EP1572962.
JD217116 - Sequence 198140 from Patent EP1572962.
KJ901849 - Synthetic construct Homo sapiens clone ccsbBroadEn_11243 NPHS2 gene, encodes complete protein.
KJ905342 - Synthetic construct Homo sapiens clone ccsbBroadEn_14885 NPHS2 gene, encodes complete protein.
JD142066 - Sequence 123090 from Patent EP1572962.
JD406902 - Sequence 387926 from Patent EP1572962.
JD126504 - Sequence 107528 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC029141, NM_014625, NP_055440, Q9NP85-2
UCSC ID: uc009wxi.3
RefSeq Accession: NM_014625
Protein: Q9NP85-2, splice isoform of Q9NP85

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC029141.1
exon count: 7CDS single in 3' UTR: no RNA size: 1692
ORF size: 948CDS single in intron: no Alignment % ID: 99.70
txCdsPredict score: 2096.00frame shift in genome: no % Coverage: 98.52
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: 0# 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.