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

    Gene ID: 4868, updated on 25-Jan-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NPHS1 in Genome Data Viewer
    Location:
    19q13.12
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35825372..35852504, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38370677..38398258, complement)
    105.20220307 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 long intergenic non-protein coding RNA 1529 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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_004646.4NP_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:834942
      Ig8_hNephrin_like; Eighth immunoglobulin-like domain of nephrin
      smart00410
      Location:845935
      IG_like; Immunoglobulin like
      pfam07679
      Location:646736
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:9421023
      fn3; Fibronectin type III domain
      pfam07686
      Location:38119
      V-set; Immunoglobulin V-set domain
      pfam08205
      Location:141228
      C2-set_2; CD80-like C2-set immunoglobulin domain
      pfam13927
      Location:739820
      Ig_3; Immunoglobulin domain
      cl11960
      Location:345424
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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)