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

    Gene ID: 4868, updated on 28-Oct-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
    mouse all
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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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