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NPHS1 NPHS1 adhesion molecule, nephrin [ Homo sapiens (human) ]

Gene ID: 4868, updated on 2-Nov-2024

Summary

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Official Symbol
NPHS1provided by HGNC
Official Full Name
NPHS1 adhesion molecule, nephrinprovided by HGNC
Primary source
HGNC:HGNC:7908
See related
Ensembl:ENSG00000161270 MIM:602716; AllianceGenome:HGNC:7908
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CNF; NPHN; nephrin
Summary
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]
Expression
Biased expression in kidney (RPKM 12.8), pancreas (RPKM 3.0) and 1 other tissue See more
Orthologs
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Genomic context

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See NPHS1 in Genome Data Viewer
Location:
19q13.12
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35825372..35852504, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38370677..38398258, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36316274..36343406, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14503 Neighboring gene testis expressed 14B, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36297835-36298335 Neighboring gene proline dehydrogenase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36336236-36336488 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36339012-36339187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36342052-36342692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36342693-36343334 Neighboring gene kirre like nephrin family adhesion molecule 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36351790-36352542 Neighboring gene uncharacterized LOC107985317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10541 Neighboring gene amyloid beta precursor like protein 1 Neighboring gene uncharacterized LOC124904705 Neighboring gene RNA, 7SL, cytoplasmic 402, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Analysis of the intronic single nucleotide polymorphism rs#466452 of the nephrin gene in patients with diabetic nephropathy. González R, et al. Biol Res, 2009. PMID 19746264
  2. Association of nephrin gene polymorphisms with type 2 diabetes in a Japanese population: The Funagata study. Daimon M, et al. Diabetes Care, 2006 May. PMID 16644649
  3. A familial childhood-onset relapsing nephrotic syndrome. Kitamura A, et al. Kidney Int, 2007 May. PMID 17290294
  4. Nephrin is critical for the action of insulin on human glomerular podocytes. Coward RJ, et al. Diabetes, 2007 Apr. PMID 17395751
  5. Misleading findings of homozygosity mapping resulting from three novel mutations in NPHS1 encoding nephrin in a highly inbred community. Frishberg Y, et al. Genet Med, 2007 Mar. PMID 17413422

See all (162) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Anti-nephrin antibodies in steroid-sensitive nephrotic syndrome in Japanese children.
    Title: Anti-nephrin antibodies in steroid-sensitive nephrotic syndrome in Japanese children.
  2. Loss of S1P Lyase Expression in Human Podocytes Causes a Reduction in Nephrin Expression That Involves PKCdelta Activation.
    Title: Loss of S1P Lyase Expression in Human Podocytes Causes a Reduction in Nephrin Expression That Involves PKCδ Activation.
  3. Clinicopathological Impact of Gene Polymorphism of Nephrin and Glucocorticoid Receptor Genes in Egyptian Children with Nonfamilial Nephrotic Syndrome.
    Title: Clinicopathological Impact of Gene Polymorphism of Nephrin and Glucocorticoid Receptor Genes in Egyptian Children with Nonfamilial Nephrotic Syndrome.
  4. Nephrin expression in human epidermal keratinocytes and its implication in poor wound closure.
    Title: Nephrin expression in human epidermal keratinocytes and its implication in poor wound closure.
  5. Spectrum of NPHS1 and NPHS2 variants in egyptian children with focal segmental glomerular sclerosis: identification of six novel variants and founder effect.
    Title: Spectrum of NPHS1 and NPHS2 variants in egyptian children with focal segmental glomerular sclerosis: identification of six novel variants and founder effect.
  6. Urinary Matrix Metalloproteinase-9 and Nephrin in Idiopathic Membranous Nephropathy: A Cross-Sectional Study.
    Title: Urinary Matrix Metalloproteinase-9 and Nephrin in Idiopathic Membranous Nephropathy: A Cross-Sectional Study.
  7. The association of NPHS1 and ACNT4 gene polymorphisms with pre-eclampsia.
    Title: The association of NPHS1 and ACNT4 gene polymorphisms with pre-eclampsia.
  8. Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function.
    Title: Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function.
  9. Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome.
    Title: Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome.
  10. [Analysis of a sib-pair with Finnish type congenital nephrotic syndrome due to variant of NPHS1 gene].
    Title: [Analysis of a sib-pair with Finnish type congenital nephrotic syndrome due to variant of NPHS1 gene].
Submit: New GeneRIF Correction See all GeneRIFs (128)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat rapidly induces the redistribution and loss of nephrin by engaging vascular endothelial growth factor receptors types 2 and 3 and the integrin alphavbeta3 in cultured human podocytes PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables myosin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in JNK cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in glomerular basement membrane development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in myoblast fusion IEA
Inferred from Electronic Annotation
more info
  
involved_in podocyte development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in positive regulation of actin filament polymerization IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to synapse IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in skeletal muscle tissue development IEA
Inferred from Electronic Annotation
more info
  
involved_in slit diaphragm assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in slit diaphragm assembly TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
is_active_in cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
located_in focal adhesion IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in slit diaphragm ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
nephrin
Names
NPHS1, nephrin
nephrosis 1, congenital, Finnish type (nephrin)
renal glomerulus-specific cell adhesion receptor

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013356.2 RefSeqGene

    Range
    22295..48916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_693

mRNA and Protein(s)

  1. NM_004646.4 → NP_004637.1  nephrin precursor

    See identical proteins and their annotated locations for NP_004637.1

    Status: REVIEWED

    Source sequence(s)
    AC002133, U95090
    Consensus CDS
    CCDS32996.1
    UniProtKB/Swiss-Prot
    A6NDH2, C3RX61, O60500
    Related
    ENSP00000368190.4, ENST00000378910.10
    Conserved Domains (8) summary
    cd05773
    Location:834 → 942
    Ig8_hNephrin_like; Eighth immunoglobulin-like domain of nephrin
    smart00410
    Location:845 → 935
    IG_like; Immunoglobulin like
    pfam07679
    Location:646 → 736
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:942 → 1023
    fn3; Fibronectin type III domain
    pfam07686
    Location:38 → 119
    V-set; Immunoglobulin V-set domain
    pfam08205
    Location:141 → 228
    C2-set_2; CD80-like C2-set immunoglobulin domain
    pfam13927
    Location:739 → 820
    Ig_3; Immunoglobulin domain
    cl11960
    Location:345 → 424
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    35825372..35852504 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    38370677..38398258 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60500.1 GenPept UniProtKB/Swiss-Prot:O60500

Gene LinkOut

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