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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
  • NPHN 3 4
  • Truncated NPHS1 3
  • Nephrin 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 Congenital Nephrotic Syndrome Finnish Type. Among its related pathways are Primary Focal Segmental Glomerulosclerosis FSGS and Nephrin interactions. Gene Ontology (GO) annotations related to this gene include protein domain specific binding and 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

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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I035868 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 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
GH19I035912 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.3 -44.5 -44514 2.4 HDGF PKNOX1 EBF1 BATF ZNF121 ZNF302 ZNF366 ATF7 FOS IKZF2 APLP1 ZNF566 TYROBP LRFN3 ZNF529 ZNF790 ZNF260 ZNF30 ZNF461 NPHS1
GH19I035910 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
GH19I035766 Enhancer 1 ENCODE dbSUPER 11.3 +101.4 101436 2.5 ARID4B SIN3A THRB ZNF48 ZSCAN9 RARA GLIS2 THAP11 EGR2 SP5 ARHGAP33 PRODH2 LINC01529 KIRREL2 NPHS1 UPK1A ENSG00000267049 GC19M038853 PROSER3
GH19I035693 Enhancer 1 ENCODE 10.7 +175.3 175333 0.2 FOXA2 PKNOX1 ARID4B SIN3A YBX1 ZNF2 IRF4 SLC30A9 CBX5 ZNF207 TMEM147-AS1 ZNF792 KMT2B HAUS5 RBM42 PROSER3 ZNF567 ENSG00000271032 ZNF599 U2AF1L4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NPHS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NPHS1 gene promoter:

Genomic Locations for NPHS1 Gene

Genomic Locations for NPHS1 Gene
chr19:35,825,372-35,869,287
(GRCh38/hg38)
Size:
43,916 bases
Orientation:
Minus strand
chr19:36,316,274-36,360,189
(GRCh37/hg19)

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:
    O60500-NPHN_HUMAN
    Recommended name:
    Nephrin
    Protein Accession:
    O60500
    Secondary Accessions:
    • A6NDH2
    • C3RX61

    Protein attributes for NPHS1 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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 Asn40, Asn356, isoforms=2401, Asn547, Asn553, isoforms=2564, isoforms=2577, isoforms=2680, Asn708, and isoforms=2908

Other Protein References for NPHS1 Gene

ENSEMBL proteins:
REFSEQ proteins:

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

O60500

UniProtKB/Swiss-Prot:

NPHN_HUMAN :
  • Belongs to the immunoglobulin superfamily.
Family:
  • 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

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
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:

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

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 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
SP1:
SP2: -

Relevant External Links for NPHS1 Gene

GeneLoc Exon Structure for
NPHS1
ECgene alternative splicing isoforms for
NPHS1

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, PaxDb, and MOPED for NPHS1 Gene



Protein tissue co-expression partners for NPHS1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NPHS1 Gene:

NPHS1

SOURCE GeneReport for Unigene cluster for NPHS1 Gene:

Hs.122186

mRNA Expression by UniProt/SwissProt for NPHS1 Gene:

O60500-NPHN_HUMAN
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(2.3)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • eye
  • head
  • hypothalamus
  • neck
  • pituitary gland
  • thyroid
Thorax:
  • esophagus
  • heart
  • lung
Abdomen:
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • stomach
Pelvis:
  • ureter
  • urinary bladder
  • uterus
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia NPHS1 33 34
  • 99.06 (n)
cow
(Bos Taurus)
Mammalia NPHS1 33 34
  • 86.36 (n)
dog
(Canis familiaris)
Mammalia NPHS1 33 34
  • 85.36 (n)
rat
(Rattus norvegicus)
Mammalia Nphs1 33
  • 82.99 (n)
mouse
(Mus musculus)
Mammalia Nphs1 33 16 34
  • 82.84 (n)
oppossum
(Monodelphis domestica)
Mammalia NPHS1 34
  • 63 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NPHS1 34
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPHS1 34
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nphs1 33
  • 55.08 (n)
zebrafish
(Danio rerio)
Actinopterygii nphs1 33 34
  • 50.01 (n)
fruit fly
(Drosophila melanogaster)
Insecta sns 35 33 34
  • 46.15 (n)
hbs 35 34
  • 30 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010742 33
  • 44.77 (n)
worm
(Caenorhabditis elegans)
Secernentea C26G2.1 35
  • 23 (a)
syg-2 34
  • 21 (a)
OneToOne
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

ENSEMBL:
Gene Tree for NPHS1 (if available)
TreeFam:
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 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)
NPHS1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPHS1

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

UniProtKB/Swiss-Prot

NPHN_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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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