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Aliases for NPHS1 Gene

Aliases for NPHS1 Gene

  • Nephrosis 1, Congenital, Finnish Type (Nephrin) 2 3
  • NPHN 3 4 6
  • Renal Glomerulus-Specific Cell Adhesion Receptor 3 4
  • Nephrin 3
  • CNF 3

External Ids for NPHS1 Gene

Summaries for NPHS1 Gene

Entrez Gene Summary for NPHS1 Gene

  • This gene encodes a member of the immunoglobulin family of cell adhesion molecules that functions in the glomerular filtration barrier in the kidney. The gene is primarily expressed in renal tissues, and the protein is a type-1 transmembrane protein found at the slit diaphragm of glomerular podocytes. The slit diaphragm is thought to function as an ultrafilter to exclude albumin and other plasma macromolecules in the formation of urine. Mutations in this gene result in Finnish-type congenital nephrosis 1, characterized by severe proteinuria and loss of the slit diaphragm and foot processes.[provided by RefSeq, Oct 2009]

GeneCards Summary for NPHS1 Gene

NPHS1 (Nephrosis 1, Congenital, Finnish Type (Nephrin)) is a Protein Coding gene. Diseases associated with NPHS1 include nephrotic syndrome, type 1 and congenital nephrotic syndrome finnish type. Among its related pathways are Cell junction organization and Nephrin/Neph1 signaling in the kidney podocyte. GO annotations related to this gene include myosin binding. An important paralog of this gene is KIRREL3.

UniProtKB/Swiss-Prot for NPHS1 Gene

  • Seems to play a role in the development or function of the kidney glomerular filtration barrier. Regulates glomerular vascular permeability. May anchor the podocyte slit diaphragm to the actin cytoskeleton. Plays a role in skeletal muscle formation through regulation of myoblast fusion (By similarity).

Gene Wiki entry for NPHS1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPHS1 Gene

Genomics for NPHS1 Gene

Genomic Location for NPHS1 Gene

35,825,372 bp from pter
35,869,287 bp from pter
43,916 bases
Minus strand

Genomic View for NPHS1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for NPHS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPHS1 Gene

Regulatory Elements for NPHS1 Gene

Proteins for NPHS1 Gene

  • Protein details for NPHS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A6NDH2
    • C3RX61

    Protein attributes for NPHS1 Gene

    1241 amino acids
    Molecular mass:
    134742 Da
    Quaternary structure:
    • Interacts with CD2AP (via C-terminal domain). Interacts with MAGI1 (via PDZ 2 and 3 domains) forming a tripartite complex with IGSF5/JAM4. Interacts with DDN; the interaction is direct. Self-associates (via the Ig-like domains). Also interacts (via the Ig-like domains) with KIRREL/NEPH1 and KIRREL2; the interaction with KIRREL is dependent on KIRREL glycosylation. Forms a complex with ACTN4, CASK, IQGAP1, MAGI2, SPTAN1 and SPTBN1 (By similarity). Interacts with NPHS2.

    Alternative splice isoforms for NPHS1 Gene


neXtProt entry for NPHS1 Gene

Proteomics data for NPHS1 Gene at MOPED

Post-translational modifications for NPHS1 Gene

  • Phosphorylated at Tyr-1193 by FYN, leading to the recruitment and activation of phospholipase C-gamma-1/PLCG1.
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn40, Asn356, Asn401, Asn547, Asn553, Asn564, Asn577, Asn680, Asn708, and Asn908

Other Protein References for NPHS1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for NPHS1 Gene

Domains for NPHS1 Gene

Gene Families for NPHS1 Gene

  • VSET :Immunoglobulin superfamily / V-set domain containing
  • FN3 :Fibronectin type III domain containing
  • IGD :Immunoglobulin superfamily / Immunoglobulin-like domain containing
  • C2SET :Immunoglobulin superfamily / C2-set domain containing

Suggested Antigen Peptide Sequences for NPHS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 fibronectin type-III domain.:
    • O60500
  • Contains 8 Ig-like C2-type (immunoglobulin-like) domains.:
    • O60500
  • Belongs to the immunoglobulin superfamily.:
    • O60500
genes like me logo Genes that share domains with NPHS1: view

Function for NPHS1 Gene

Molecular function for NPHS1 Gene

GENATLAS Biochemistry: nephrin,transmembrane protein of the immunoglobulin family of cell-adhesion molecules,expressed in renal glomeruli with CD2 associated protein CD2AP specifically located at the slit membrane extending between foot processes of the podocytes,mediating filtration through the podocyte filter which sits at the interface of the capillary and the nephron
UniProtKB/Swiss-Prot Function: Seems to play a role in the development or function of the kidney glomerular filtration barrier. Regulates glomerular vascular permeability. May anchor the podocyte slit diaphragm to the actin cytoskeleton. Plays a role in skeletal muscle formation through regulation of myoblast fusion (By similarity).

Gene Ontology (GO) - Molecular Function for NPHS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16525419
GO:0017022 myosin binding IPI 21402783
GO:0019904 protein domain specific binding IEA --
GO:0030507 spectrin binding IEA --
GO:0051393 alpha-actinin binding IEA --
genes like me logo Genes that share ontologies with NPHS1: view
genes like me logo Genes that share phenotypes with NPHS1: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for NPHS1 Gene

Localization for NPHS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPHS1 Gene

Cell membrane; Single-pass type I membrane protein. Note=Predominantly located at podocyte slit diaphragm between podocyte foot processes. Also associated with podocyte apical plasma membrane. {ECO:0000269 PubMed:10393930, ECO:0000269 PubMed:10550324}.

Subcellular locations from

Jensen Localization Image for NPHS1 Gene COMPARTMENTS Subcellular localization image for NPHS1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 2
extracellular 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 1
lysosome 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for NPHS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 9660941
GO:0016020 membrane --
GO:0036057 slit diaphragm ISS --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with NPHS1: view

Pathways for NPHS1 Gene

genes like me logo Genes that share pathways with NPHS1: view

Pathways by source for NPHS1 Gene

1 BioSystems pathway for NPHS1 Gene
2 Reactome pathways for NPHS1 Gene

Gene Ontology (GO) - Biological Process for NPHS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade --
GO:0007155 cell adhesion IEA --
GO:0007254 JNK cascade IEA --
GO:0007519 skeletal muscle tissue development IEA --
GO:0007520 myoblast fusion IEA --
genes like me logo Genes that share ontologies with NPHS1: view

Compounds for NPHS1 Gene

(16) Novoseek inferred chemical compound relationships for NPHS1 Gene

Compound -log(P) Hits PubMed IDs
puromycin aminonucleoside 78.9 8
puromycin 55.5 4
vegf 32.6 21
steroid 27.1 2
tyrosine 22.3 24
genes like me logo Genes that share compounds with NPHS1: view

Transcripts for NPHS1 Gene

mRNA/cDNA for NPHS1 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(12) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NPHS1 Gene

Nephrosis 1, congenital, Finnish type (nephrin):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NPHS1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5
SP2: -

Relevant External Links for NPHS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NPHS1 Gene

mRNA expression in normal human tissues for NPHS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NPHS1 Gene

This gene is overexpressed in Kidney - Cortex (28.1) and Pancreas (19.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for NPHS1 Gene

SOURCE GeneReport for Unigene cluster for NPHS1 Gene Hs.122186

mRNA Expression by UniProt/SwissProt for NPHS1 Gene

Tissue specificity: Specifically expressed in podocytes of kidney glomeruli
genes like me logo Genes that share expressions with NPHS1: view

Orthologs for NPHS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPHS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NPHS1 35
  • 99.06 (n)
  • 99.11 (a)
NPHS1 36
  • 99 (a)
(Bos Taurus)
Mammalia NPHS1 35
  • 86.36 (n)
  • 87.91 (a)
NPHS1 36
  • 88 (a)
(Canis familiaris)
Mammalia NPHS1 35
  • 85.36 (n)
  • 87.11 (a)
NPHS1 36
  • 87 (a)
(Mus musculus)
Mammalia Nphs1 35
  • 82.84 (n)
  • 82.7 (a)
Nphs1 16
Nphs1 36
  • 81 (a)
(Monodelphis domestica)
Mammalia NPHS1 36
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia NPHS1 36
  • 59 (a)
(Rattus norvegicus)
Mammalia Nphs1 35
  • 82.99 (n)
  • 82.66 (a)
(Anolis carolinensis)
Reptilia NPHS1 36
  • 45 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nphs1 35
  • 55.08 (n)
  • 47.92 (a)
(Danio rerio)
Actinopterygii nphs1 35
  • 50.01 (n)
  • 42.12 (a)
nphs1 36
  • 38 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010742 35
  • 44.77 (n)
  • 33.37 (a)
fruit fly
(Drosophila melanogaster)
Insecta hbs 36
  • 27 (a)
sns 35
  • 46.15 (n)
  • 31.97 (a)
sns 36
  • 23 (a)
hbs 37
  • 30 (a)
sns 37
  • 29 (a)
(Caenorhabditis elegans)
Secernentea syg-2 36
  • 21 (a)
C26G2.1 37
  • 23 (a)
Species with no ortholog for NPHS1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 NPHS1 Gene

Gene Tree for NPHS1 (if available)
Gene Tree for NPHS1 (if available)

Paralogs for NPHS1 Gene

Paralogs for NPHS1 Gene

genes like me logo Genes that share paralogs with NPHS1: view

Variants for NPHS1 Gene

Sequence variations from dbSNP and Humsavar for NPHS1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs392702 -- 35,848,161(+) TGGGC(A/G)GGATC reference, synonymous-codon
rs396178 -- 35,851,151(+) GAGTT(C/T)GGTAC intron-variant
rs455322 -- 35,833,688(+) TCATA(C/T)ACCAA intron-variant
rs460560 -- 35,830,623(-) gagac(A/G)agcct intron-variant
rs1137844 -- 35,852,177(-) CCAAG(C/G)TGGGA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for NPHS1 Gene

Variant ID Type Subtype PubMed ID
nsv911638 CNV Loss 21882294
esv2481755 CNV Insertion 19546169
esv1600817 CNV Insertion 17803354
dgv51n68 CNV Loss 17160897

Relevant External Links for NPHS1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPHS1 Gene

Disorders for NPHS1 Gene

(1) OMIM Diseases for NPHS1 Gene (602716)


  • Nephrotic syndrome 1 (NPHS1) [MIM:256300]: 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. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. {ECO:0000269 PubMed:10652016, ECO:0000269 PubMed:11317351, ECO:0000269 PubMed:17290294, ECO:0000269 PubMed:18503012, ECO:0000269 PubMed:18614772, ECO:0000269 PubMed:20172850, ECO:0000269 PubMed:22009864, ECO:0000269 PubMed:22565185, ECO:0000269 PubMed:9660941, ECO:0000269 PubMed:9915943}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(33) Novoseek inferred disease relationships for NPHS1 Gene

Disease -log(P) Hits PubMed IDs
nphs1 98.7 216
nephrotic syndrome 92 115
proteinuria 89.1 108
glomerulosclerosis, focal segmental 86.6 13
glomerulosclerosis 80.8 6

Genatlas disease for NPHS1 Gene

congenital nephrotic syndrome of the Finnish type,autosomal recessive,with mitochondrial dysfunction in the kidneys,characterized by massive proteinuria already present at birth without extrarenal symptoms and anatomically an absence of podocyte foot processes and of slit diaphragm

Relevant External Links for NPHS1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with NPHS1: view

Publications for NPHS1 Gene

  1. Positionally cloned gene for a novel glomerular protein -- nephrin -- is mutated in congenital nephrotic syndrome. (PMID: 9660941) Kestilae M. … Tryggvason K. (Mol. Cell 1998) 2 3 4 23
  2. Nephrin localizes at the podocyte filtration slit area and is characteristically spliced in the human kidney. (PMID: 10550324) Holthoefer H. … Kerjaschki D. (Am. J. Pathol. 1999) 3 4 23
  3. Nephrin is specifically located at the slit diaphragm of glomerular podocytes. (PMID: 10393930) Ruotsalainen V. … Tryggvason K. (Proc. Natl. Acad. Sci. U.S.A. 1999) 3 4 23
  4. Genetic polymorphism of NPHS1 modifies the clinical manifestations of Ig A nephropathy. (PMID: 12920248) Narita I. … Gejyo F. (Lab. Invest. 2003) 3 23 48
  5. Nephrin gene (NPHS1) in patients with minimal change nephrotic syndrome (MCNS). (PMID: 15086927) Lahdenkari A.T. … Jalanko H. (Kidney Int. 2004) 3 23 48

Products for NPHS1 Gene

Sources for NPHS1 Gene

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