Human Gene NPHS2 (ENST00000367615.9_6) from GENCODE V47lift37
  Description: NPHS2 stomatin family member, podocin, transcript variant 1 (from RefSeq NM_014625.4)
Gencode Transcript: ENST00000367615.9_6
Gencode Gene: ENSG00000116218.13_8
Transcript (Including UTRs)
   Position: hg19 chr1:179,519,674-179,545,083 Size: 25,410 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:179,520,308-179,544,999 Size: 24,692 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:179,519,674-179,545,083)mRNA (may differ from genome)Protein (383 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PODO_HUMAN
DESCRIPTION: RecName: Full=Podocin;
FUNCTION: Plays a role in the regulation of glomerular permeability, acting probably as a linker between the plasma membrane and the cytoskeleton.
SUBUNIT: Interacts with nephrin/NPHS1 and KIRREL. Interacts directly with CD2AP. Interacts with DDN (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein (Potential).
TISSUE SPECIFICITY: Almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli.
DISEASE: Defects in NPHS2 are the cause of nephrotic syndrome type 2 (NPHS2) [MIM:600995]. It is a renal disorder characterized clinically by childhood onset of proteinuria, hypoalbuminemia, hyperlipidemia, and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. The disorder is resistant to steroid treatment and progresses to end-stage renal failure in the first or second decades. Some patients show later onset of the disorder.
SIMILARITY: Belongs to the band 7/mec-2 family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/NPHS2";

-  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


-  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 -28.2084-0.336 Picture PostScript Text
3' UTR -160.00634-0.252 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
  InterPro Domains: Graphical view of domain structure
IPR001107 - Band_7
IPR018080 - Band_7/stomatin-like_CS
IPR001972 - Stomatin

Pfam Domains:
PF01145 - SPFH domain / Band 7 family

SCOP Domains:
117892 - Band 7/SPFH domain

ModBase Predicted Comparative 3D Structure on Q9NP85
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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007588 excretion
GO:0031532 actin cytoskeleton reorganization
GO:0072249 metanephric glomerular visceral epithelial cell development

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane
GO:0032991 macromolecular complex
GO:0036057 slit diaphragm
GO:0045121 membrane raft
GO:0070062 extracellular exosome


-  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: B1AM32, B1AM33, ENST00000367615.1, ENST00000367615.2, ENST00000367615.3, ENST00000367615.4, ENST00000367615.5, ENST00000367615.6, ENST00000367615.7, ENST00000367615.8, NM_014625, PODO_HUMAN, Q8N6Q5, Q9NP85, uc318gbn.1, uc318gbn.2
UCSC ID: ENST00000367615.9_6
RefSeq Accession: NM_014625.4
Protein: Q9NP85 (aka PODO_HUMAN)

-  Gene Model Information
  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.