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Aliases for NPHS2 Gene

Aliases for NPHS2 Gene

  • NPHS2, Podocin 2 3 5
  • Nephrosis 2, Idiopathic, Steroid-Resistant (Podocin) 2 3
  • Podocin 3
  • PDCN 3
  • SRN1 3

External Ids for NPHS2 Gene

Previous GeneCards Identifiers for NPHS2 Gene

  • GC01M177044
  • GC01M174948
  • GC01M176039
  • GC01M176759
  • GC01M176251
  • GC01M177786
  • GC01M150746

Summaries for NPHS2 Gene

Entrez Gene Summary for NPHS2 Gene

  • 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]

GeneCards Summary for NPHS2 Gene

NPHS2 (NPHS2, Podocin) is a Protein Coding gene. Diseases associated with NPHS2 include Nephrotic Syndrome, Type 2 and Nephrotic Syndrome, Idiopathic, Steroid-Resistant. Among its related pathways are Primary Focal Segmental Glomerulosclerosis FSGS and Nephrin/Neph1 signaling in the kidney podocyte. An important paralog of this gene is STOM.

UniProtKB/Swiss-Prot for NPHS2 Gene

  • Plays a role in the regulation of glomerular permeability, acting probably as a linker between the plasma membrane and the cytoskeleton.

Gene Wiki entry for NPHS2 Gene

Additional gene information for NPHS2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPHS2 Gene

Genomics for NPHS2 Gene

GeneHancer (GH) Regulatory Elements for NPHS2 Gene

Promoters and enhancers for NPHS2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I179575 Promoter 0.7 EPDnew 550.8 +0.0 13 0.1 CTCF SUZ12 EZH2 RNU5F-2P NPHS2 GC01P179577 TDRD5 PIRC5
GH01I179550 Enhancer 0.7 ENCODE 0.3 +24.9 24900 1 ATF1 ZBTB21 MAX BACH1 EBF1 CEBPG BATF FOSL1 ZNF316 SCRT2 TDRD5 LOC126860 ENSG00000261060 AXDND1 ENSG00000261250 NPHS2 PIRC5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NPHS2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NPHS2 gene promoter:

Genomic Locations for NPHS2 Gene

Genomic Locations for NPHS2 Gene
chr1:179,550,539-179,575,976
(GRCh38/hg38)
Size:
25,438 bases
Orientation:
Minus strand
chr1:179,519,674-179,545,087
(GRCh37/hg19)

Genomic View for NPHS2 Gene

Genes around NPHS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPHS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPHS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPHS2 Gene

Proteins for NPHS2 Gene

  • Protein details for NPHS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NP85-PODO_HUMAN
    Recommended name:
    Podocin
    Protein Accession:
    Q9NP85
    Secondary Accessions:
    • B1AM32
    • B1AM33
    • Q8N6Q5

    Protein attributes for NPHS2 Gene

    Size:
    383 amino acids
    Molecular mass:
    42201 Da
    Quaternary structure:
    • Interacts with nephrin/NPHS1 and KIRREL1. Interacts directly with CD2AP. Interacts with DDN (By similarity).

    Alternative splice isoforms for NPHS2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NPHS2 Gene

Post-translational modifications for NPHS2 Gene

Other Protein References for NPHS2 Gene

No data available for DME Specific Peptides for NPHS2 Gene

Domains & Families for NPHS2 Gene

Gene Families for NPHS2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for NPHS2 Gene

Suggested Antigen Peptide Sequences for NPHS2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NP85

UniProtKB/Swiss-Prot:

PODO_HUMAN :
  • Belongs to the band 7/mec-2 family.
Family:
  • Belongs to the band 7/mec-2 family.
genes like me logo Genes that share domains with NPHS2: view

Function for NPHS2 Gene

Molecular function for NPHS2 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the regulation of glomerular permeability, acting probably as a linker between the plasma membrane and the cytoskeleton.

Gene Ontology (GO) - Molecular Function for NPHS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12424224
genes like me logo Genes that share ontologies with NPHS2: view
genes like me logo Genes that share phenotypes with NPHS2: view

Human Phenotype Ontology for NPHS2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NPHS2 Gene

MGI Knock Outs for NPHS2:

Animal Model Products

miRNA for NPHS2 Gene

miRTarBase miRNAs that target NPHS2

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for NPHS2 Gene

Localization for NPHS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPHS2 Gene

Isoform 1: Cell membrane; Peripheral membrane protein.
Isoform 2: Endoplasmic reticulum.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NPHS2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 4
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for NPHS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IEA,TAS --
GO:0005911 cell-cell junction IDA 17675666
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with NPHS2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NPHS2 Gene

Pathways & Interactions for NPHS2 Gene

genes like me logo Genes that share pathways with NPHS2: view

Pathways by source for NPHS2 Gene

Gene Ontology (GO) - Biological Process for NPHS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007588 excretion IEA --
GO:0031532 actin cytoskeleton reorganization IDA 17675666
GO:0072249 metanephric glomerular visceral epithelial cell development IEP 11786407
genes like me logo Genes that share ontologies with NPHS2: view

No data available for SIGNOR curated interactions for NPHS2 Gene

Drugs & Compounds for NPHS2 Gene

(5) Drugs for NPHS2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for NPHS2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NPHS2: view

Transcripts for NPHS2 Gene

Unigene Clusters for NPHS2 Gene

Nephrosis 2, idiopathic, steroid-resistant (podocin):
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPHS2 Gene

No ASD Table

Relevant External Links for NPHS2 Gene

GeneLoc Exon Structure for
NPHS2
ECgene alternative splicing isoforms for
NPHS2

Expression for NPHS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NPHS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NPHS2 Gene

This gene is overexpressed in Kidney - Cortex (x52.2).

Protein differential expression in normal tissues from HIPED for NPHS2 Gene

This gene is overexpressed in Urine (64.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NPHS2 Gene



Protein tissue co-expression partners for NPHS2 Gene

NURSA nuclear receptor signaling pathways regulating expression of NPHS2 Gene:

NPHS2

SOURCE GeneReport for Unigene cluster for NPHS2 Gene:

Hs.412710

mRNA Expression by UniProt/SwissProt for NPHS2 Gene:

Q9NP85-PODO_HUMAN
Tissue specificity: Almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli.

Evidence on tissue expression from TISSUES for NPHS2 Gene

  • Kidney(4.9)
  • Intestine(4.1)
  • Urine(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NPHS2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • head
Thorax:
  • heart
  • lung
Abdomen:
  • duodenum
  • intestine
  • kidney
  • liver
  • small intestine
General:
  • blood
  • blood vessel
  • coagulation system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with NPHS2: view

Primer Products

Orthologs for NPHS2 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPHS2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPHS2 33 34
  • 97.35 (n)
cow
(Bos Taurus)
Mammalia NPHS2 33 34
  • 88.86 (n)
dog
(Canis familiaris)
Mammalia NPHS2 33 34
  • 88.25 (n)
mouse
(Mus musculus)
Mammalia Nphs2 33 16 34
  • 85.91 (n)
rat
(Rattus norvegicus)
Mammalia Nphs2 33
  • 84.35 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NPHS2 34
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NPHS2 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPHS2 33 34
  • 66.39 (n)
lizard
(Anolis carolinensis)
Reptilia NPHS2 34
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nphs2 33
  • 62.02 (n)
zebrafish
(Danio rerio)
Actinopterygii nphs2 33 34
  • 53.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG42540 34
  • 27 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sto-1 35
  • 40 (a)
sto-3 35
  • 39 (a)
sto-2 34
  • 36 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
ManyToMany
-- 34
  • 43 (a)
ManyToMany
-- 34
  • 42 (a)
ManyToMany
Species where no ortholog for NPHS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NPHS2 Gene

ENSEMBL:
Gene Tree for NPHS2 (if available)
TreeFam:
Gene Tree for NPHS2 (if available)

Paralogs for NPHS2 Gene

Paralogs for NPHS2 Gene

(2) SIMAP similar genes for NPHS2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NPHS2: view

Variants for NPHS2 Gene

Sequence variations from dbSNP and Humsavar for NPHS2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1008739528 uncertain-significance, Steroid-resistant nephrotic syndrome 179,550,833(-) G/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1057516395 likely-pathogenic, Nephrotic syndrome, idiopathic, steroid-resistant 179,564,699(-) G/ coding_sequence_variant, frameshift, intron_variant
rs1057516414 likely-pathogenic, Nephrotic syndrome, idiopathic, steroid-resistant 179,557,080(-) G/A/T coding_sequence_variant, intron_variant, stop_gained, synonymous_variant
rs1057516523 likely-pathogenic, Nephrotic syndrome, idiopathic, steroid-resistant 179,552,682(-) C/T splice_acceptor_variant
rs1057516680 likely-pathogenic, Nephrotic syndrome, idiopathic, steroid-resistant 179,575,862(-) C/A/T initiator_codon_variant, missense_variant

Variation tolerance for NPHS2 Gene

Residual Variation Intolerance Score: 65% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.02; 60.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPHS2 Gene

Human Gene Mutation Database (HGMD)
NPHS2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPHS2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for NPHS2 Gene

Disorders for NPHS2 Gene

MalaCards: The human disease database

(31) MalaCards diseases for NPHS2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
nephrotic syndrome, type 2
  • nphs2
nephrotic syndrome, idiopathic, steroid-resistant
  • nephrotic syndrome, steroid-resistant, autosomal recessive
focal segmental glomerulosclerosis
  • fgs
sporadic idiopathic steroid-resistant nephrotic syndrome with minimal changes
sporadic idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis
  • sporadic idiopathic steroid-resistant nephrotic syndrome with focal segmental glomerulosclerosis
- elite association - COSMIC cancer census association via MalaCards
Search NPHS2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PODO_HUMAN
  • Nephrotic syndrome 2 (NPHS2) [MIM:600995]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as 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. {ECO:0000269 PubMed:10742096, ECO:0000269 PubMed:12464671, ECO:0000269 PubMed:15253708, ECO:0000269 PubMed:17899208, ECO:0000269 PubMed:20798252, ECO:0000269 PubMed:20947785, ECO:0000269 PubMed:22565185, ECO:0000269 PubMed:22578956, ECO:0000269 PubMed:23242530, ECO:0000269 PubMed:23800802, ECO:0000269 PubMed:23913389, ECO:0000269 PubMed:24072147, ECO:0000269 PubMed:24227627, ECO:0000269 PubMed:26420286}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NPHS2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NPHS2: view

No data available for Genatlas for NPHS2 Gene

Publications for NPHS2 Gene

  1. NPHS2 (podicin) mutations in Turkish children with idiopathic nephrotic syndrome. (PMID: 17899208) Berdeli A … Cakar N (Pediatric nephrology (Berlin, Germany) 2007) 3 4 22 44 58
  2. Identification of podocin (NPHS2) gene mutations in African Americans with nondiabetic end-stage renal disease. (PMID: 15954915) Dusel JA … Freedman BI (Kidney international 2005) 3 4 22 44 58
  3. NPHS2 mutations in sporadic steroid-resistant nephrotic syndrome in Japanese children. (PMID: 12687458) Maruyama K … Yoshikawa N (Pediatric nephrology (Berlin, Germany) 2003) 3 4 22 44 58
  4. NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome. (PMID: 10742096) Boute N … Antignac C (Nature genetics 2000) 2 3 4 22 58
  5. Genetic effect of the NPHS2 gene variants on proteinuria in minimal change disease and immunoglobulin A nephropathy. (PMID: 20025681) Zhu L … Wang HY (Nephrology (Carlton, Vic.) 2009) 3 22 44 58

Products for NPHS2 Gene

Sources for NPHS2 Gene

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