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Aliases for NPHS1 Gene

Aliases for NPHS1 Gene

  • NPHS1, Nephrin 2 3 5
  • Renal Glomerulus-Specific Cell Adhesion Receptor 3 4
  • Nephrosis 1, Congenital, Finnish Type (Nephrin) 2 3
  • Nephrin 3 3
  • NPHN 3 4
  • Truncated NPHS1 3
  • CNF 3

External Ids for NPHS1 Gene

Previous GeneCards Identifiers for NPHS1 Gene

  • GC19M036956
  • GC19M036740
  • GC19M040968
  • GC19M041008
  • GC19M040983
  • GC19M040984
  • GC19M036290
  • GC19M036316
  • GC19M032820

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 (NPHS1, Nephrin) is a Protein Coding gene. Diseases associated with NPHS1 include Nephrotic Syndrome, Type 1 and Familial Idiopathic Steroid-Resistant Nephrotic Syndrome With Diffuse Mesangial Proliferation. Among its related pathways are Nephrin interactions and Cell junction organization. Gene Ontology (GO) annotations related to this gene include protein domain specific binding and myosin binding. An important paralog of this gene is KIRREL2.

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

Additional gene information for NPHS1 Gene

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

Genomics for NPHS1 Gene

GeneHancer (GH) Regulatory Elements for NPHS1 Gene

Promoters and enhancers for NPHS1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J035868 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 0.0 -30 2.6 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 ZBTB7B E2F8 KLF13 SP3 APLP1 NPHS1 TMEM147-AS1 ZNF345 KMT2B ZNF850 HAUS5 PROSER3 ZNF567 U2AF1L4
GH19J035845 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 650.3 +23.3 23296 1.5 PKNOX1 ATF1 FOXA2 SIN3A DMAP1 ZNF2 ZNF121 GLIS2 ZNF143 KLF7 NPHS1 RBM42 ZNF792 ZNF850 ZNF146 KIRREL2 PRODH2
GH19J035910 Enhancer 1.1 FANTOM5 Ensembl ENCODE 10.8 -42.3 -42314 1.6 CTCF NFIB RAD21 ZNF121 ZNF335 ZNF366 ZBTB48 SCRT2 ZNF143 PRDM10 LRFN3 ZNF345 ZNF567 RBM42 PROSER3 ZNF850 ZNF790-AS1 ZNF461 ZNF529-AS1 ZNF790
GH19J035766 Enhancer 1 ENCODE dbSUPER 11.3 +101.4 101436 2.5 ARID4B SIN3A KLF14 THRB ZNF48 ZSCAN9 RARA GLIS2 THAP11 EGR2 ARHGAP33 PRODH2 LINC01529 KIRREL2 NPHS1 UPK1A ENSG00000267049 PROSER3 GC19M039149
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPHS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NPHS1 gene promoter:
  • p53
  • NRSF form 1
  • NRSF form 2
  • E2F-4
  • E2F
  • E2F-1
  • E2F-2

Genomic Locations for NPHS1 Gene

Genomic Locations for NPHS1 Gene
43,916 bases
Minus strand
43,916 bases
Minus strand

Genomic View for NPHS1 Gene

Genes around NPHS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPHS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPHS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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 KIRREL1/NEPH1 and KIRREL2; the interaction with KIRREL1 is dependent on KIRREL1 glycosylation. Interacts with KIRREL3. Forms a complex with ACTN4, CASK, IQGAP1, MAGI2, SPTAN1 and SPTBN1 (By similarity). Interacts with NPHS2 (PubMed:11562357).

    Three dimensional structures from OCA and Proteopedia for NPHS1 Gene

    Alternative splice isoforms for NPHS1 Gene


neXtProt entry for NPHS1 Gene

Post-translational modifications for NPHS1 Gene

  • Phosphorylated at Tyr-1193 by FYN, leading to the recruitment and activation of phospholipase C-gamma-1/PLCG1.
  • Glycosylation at isoforms=2908, isoforms=2708, Asn680, isoforms=2577, isoforms=2564, isoforms=2553, Asn547, Asn401, Asn356, and isoforms=240
  • Modification sites at PhosphoSitePlus

Other Protein References for NPHS1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for NPHS1
  • Boster Bio Antibodies for NPHS1

No data available for DME Specific Peptides for NPHS1 Gene

Domains & Families for NPHS1 Gene

Gene Families for NPHS1 Gene

Suggested Antigen Peptide Sequences for NPHS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the immunoglobulin superfamily.
  • Belongs to the immunoglobulin superfamily.
genes like me logo Genes that share domains with NPHS1: view

Function for NPHS1 Gene

Molecular function for NPHS1 Gene

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).
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

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
genes like me logo Genes that share ontologies with NPHS1: view
genes like me logo Genes that share phenotypes with NPHS1: view

Human Phenotype Ontology for NPHS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NPHS1 Gene

MGI Knock Outs for NPHS1:

Animal Model Products

Clone Products

  • Addgene plasmids for NPHS1

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

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 NPHS1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
mitochondrion 2
nucleus 2
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for NPHS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 9660941
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NPHS1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NPHS1 Gene

Pathways & Interactions for NPHS1 Gene

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

Pathways by source for NPHS1 Gene

SIGNOR curated interactions for NPHS1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for NPHS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,TAS --
GO:0007254 JNK cascade IEA --
GO:0007275 multicellular organism development IEA --
GO:0007411 axon guidance TAS --
GO:0007517 muscle organ development IEA --
genes like me logo Genes that share ontologies with NPHS1: view

Drugs & Compounds for NPHS1 Gene

(11) Drugs for NPHS1 Gene - From: PharmGKB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Losartan Approved Pharma Antagonist 295

(6) Additional Compounds for NPHS1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

Clone Products

  • Addgene plasmids for NPHS1

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x28.1) and Pancreas (x19.7).

Protein differential expression in normal tissues from HIPED for NPHS1 Gene

This gene is overexpressed in Plasma (43.9), Urine (11.0), and Peripheral blood mononuclear cells (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NPHS1 Gene

Protein tissue co-expression partners for NPHS1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NPHS1 Gene:


SOURCE GeneReport for Unigene cluster for NPHS1 Gene:


mRNA Expression by UniProt/SwissProt for NPHS1 Gene:

Tissue specificity: Specifically expressed in podocytes of kidney glomeruli.

Evidence on tissue expression from TISSUES for NPHS1 Gene

  • Blood(4.4)
  • Kidney(3.9)
  • Urine(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NPHS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • urinary
Head and neck:
  • brain
  • ear
  • eye
  • head
  • hypothalamus
  • neck
  • pituitary gland
  • thyroid
  • esophagus
  • heart
  • lung
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • stomach
  • ureter
  • urinary bladder
  • uterus
  • blood
  • blood vessel
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns 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 34 33
  • 99.06 (n)
(Bos Taurus)
Mammalia NPHS1 34 33
  • 86.36 (n)
(Canis familiaris)
Mammalia NPHS1 34 33
  • 85.36 (n)
(Rattus norvegicus)
Mammalia Nphs1 33
  • 82.99 (n)
(Mus musculus)
Mammalia Nphs1 16 34 33
  • 82.84 (n)
(Monodelphis domestica)
Mammalia NPHS1 34
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia NPHS1 34
  • 59 (a)
(Anolis carolinensis)
Reptilia NPHS1 34
  • 45 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nphs1 33
  • 55.08 (n)
(Danio rerio)
Actinopterygii nphs1 34 33
  • 50.01 (n)
fruit fly
(Drosophila melanogaster)
Insecta sns 34 35 33
  • 46.15 (n)
hbs 34 35
  • 27 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010742 33
  • 44.77 (n)
(Caenorhabditis elegans)
Secernentea C26G2.1 35
  • 23 (a)
syg-2 34
  • 21 (a)
Species where no ortholog for NPHS1 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for NPHS1: view image

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 Variation AA Info Type
rs1054950770 likely-pathogenic, Finnish congenital nephrotic syndrome 35,851,260(-) A/G splice_donor_variant
rs1057516637 likely-pathogenic, Finnish congenital nephrotic syndrome 35,835,756(-) GG/GGG coding_sequence_variant, frameshift
rs1057516776 likely-pathogenic, Finnish congenital nephrotic syndrome 35,848,147(-) C/T coding_sequence_variant, stop_gained
rs1057516918 likely-pathogenic, Finnish congenital nephrotic syndrome 35,848,112(-) CCC/CC coding_sequence_variant, frameshift
rs1057516942 likely-pathogenic, Finnish congenital nephrotic syndrome 35,851,557(-) A/ coding_sequence_variant, frameshift

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

Variant ID Type Subtype PubMed ID
dgv51n68 CNV loss 17160897
esv1600817 CNV insertion 17803354
esv2481755 CNV insertion 19546169
nsv478254 CNV novel sequence insertion 20440878
nsv953286 CNV deletion 24416366

Variation tolerance for NPHS1 Gene

Residual Variation Intolerance Score: 62.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.61; 91.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPHS1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NPHS1 Gene

MalaCards: The human disease database

(29) MalaCards diseases for NPHS1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards


  • 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:11726550, ECO:0000269 PubMed:17290294, ECO:0000269 PubMed:18503012, ECO:0000269 PubMed:18614772, ECO:0000269 PubMed:20172850, ECO:0000269 PubMed:20798252, ECO:0000269 PubMed:22009864, ECO:0000269 PubMed:22565185, ECO:0000269 PubMed:22732337, ECO:0000269 PubMed:25804400, ECO:0000269 PubMed:26560236, ECO:0000269 PubMed:9660941, ECO:0000269 PubMed:9915943}. Note=The disease is caused by mutations affecting the gene represented in this entry.

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

Additional Disease Information for NPHS1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NPHS1: view

Publications for NPHS1 Gene

  1. Association between genetic polymorphisms of the NPHS1 gene and membranous glomerulonephritis in the Taiwanese population. (PMID: 20138859) Lo WY … Tsai FJ (Clinica chimica acta; international journal of clinical chemistry 2010) 3 22 44 58
  2. Clinical features and long-term outcome of nephrotic syndrome associated with heterozygous NPHS1 and NPHS2 mutations. (PMID: 19406966) Caridi G … Ghiggeri GM (Clinical journal of the American Society of Nephrology : CJASN 2009) 3 22 44 58
  3. [Association of NPHS1 gene polymorphism with IgA nephropathy]. (PMID: 19671286) Yu L … Zhang H (Zhonghua yi xue za zhi 2009) 3 22 44 58
  4. Thirteen novel NPHS1 mutations in a large cohort of children with congenital nephrotic syndrome. (PMID: 18503012) Heeringa SF … Members of the APN Study Group (Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2008) 3 4 22 58
  5. Nephrin mutations can cause childhood-onset steroid-resistant nephrotic syndrome. (PMID: 18614772) Philippe A … Antignac C (Journal of the American Society of Nephrology : JASN 2008) 3 4 22 58

Products for NPHS1 Gene

  • Addgene plasmids for NPHS1

Sources for NPHS1 Gene

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