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    NPHP1 nephrocystin 1 [ Homo sapiens (human) ]

    Gene ID: 4867, updated on 9-Jul-2017
    Official Symbol
    NPHP1provided by HGNC
    Official Full Name
    nephrocystin 1provided by HGNC
    Primary source
    HGNC:HGNC:7905
    See related
    Ensembl:ENSG00000144061 MIM:607100; Vega:OTTHUMG00000131195
    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
    NPH1; JBTS4; SLSN1
    Summary
    This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    2q13
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (110123336..110205062, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (110880913..110962639, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene microRNA 4267 Neighboring gene microRNA 4436b-1 Neighboring gene mal, T-cell differentiation protein like Neighboring gene ARP1 actin related protein 1 homolog A pseudogene Neighboring gene long intergenic non-protein coding RNA 116 Neighboring gene two pore channel 3 pseudogene

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
      Anchoring of the basal body to the plasma membrane, organism-specific biosystemCilium biogenesis is initiated by the docking of basal bodies, a centriole-derived organelle, to the plasma membrane (reviewed in Reiter et al, 2012). The centriole consists of a multiprotein core su...
    • Cilium Assembly, organism-specific biosystem (from REACTOME)
      Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
    • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
      Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ97602

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    structural molecule activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    actin cytoskeleton organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell projection organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ciliary basal body-plasma membrane docking TAS
    Traceable Author Statement
    more info
     
    excretion TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of bicellular tight junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    retina development in camera-type eye ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    single organismal cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    spermatid differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    visual behavior NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    adherens junction IEA
    Inferred from Electronic Annotation
    more info
     
    bicellular tight junction IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    motile cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    photoreceptor connecting cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Preferred Names
    nephrocystin-1
    Names
    juvenile nephronophthisis 1 protein
    nephronophthisis 1 (juvenile)

    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_008287.1 RefSeqGene

      Range
      5001..86727
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000272.3NP_000263.2  nephrocystin-1 isoform 1

      See identical proteins and their annotated locations for NP_000263.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF023674, AJ001815, BC062574, DB454094
      Consensus CDS
      CCDS2086.1
      UniProtKB/Swiss-Prot
      O15259
      Related
      ENSP00000313169.4, OTTHUMP00000161841, ENST00000316534.8, OTTHUMT00000253920
      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    2. NM_001128178.1NP_001121650.1  nephrocystin-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice donor site in the mid-coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AJ001815, AK225600, BC062574, DB454094
      Consensus CDS
      CCDS46386.1
      UniProtKB/Swiss-Prot
      O15259
      Related
      ENSP00000389879.2, OTTHUMP00000225199, ENST00000445609.6, OTTHUMT00000376064
      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    3. NM_001128179.1NP_001121651.1  nephrocystin-1 isoform 4

      See identical proteins and their annotated locations for NP_001121651.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame segment in the 5' coding region, and uses two alternate in-frame splice sites in the mid-coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      AJ001815, BC062574, DB454094
      Consensus CDS
      CCDS46384.1
      UniProtKB/Swiss-Prot
      O15259
      Related
      ENSP00000347452.4, OTTHUMP00000207141, ENST00000355301.8, OTTHUMT00000338098
      Conserved Domains (1) summary
      cd11770
      Location:94147
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    4. NM_207181.2NP_997064.2  nephrocystin-1 isoform 2

      See identical proteins and their annotated locations for NP_997064.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice acceptor site in the mid-coding region, compared to variant 1, resulting in an isoform (2) that lacks a residue, compared to isoform 1.
      Source sequence(s)
      AJ001815, BC062574, DB454094
      Consensus CDS
      CCDS46385.1
      UniProtKB/Swiss-Prot
      O15259
      Related
      ENSP00000376953.3, OTTHUMP00000161840, ENST00000393272.7, OTTHUMT00000253919
      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

      Range
      110123336..110205062 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005263679.1XP_005263736.1  nephrocystin-1 isoform X6

      See identical proteins and their annotated locations for XP_005263736.1

      UniProtKB/TrEMBL
      B4DQY0
      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    2. XM_005263677.1XP_005263734.1  nephrocystin-1 isoform X4

      UniProtKB/TrEMBL
      C9JNM7
      Related
      ENSP00000402176.1, OTTHUMP00000207142, ENST00000417665.5, OTTHUMT00000338101
      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    3. XM_005263676.1XP_005263733.1  nephrocystin-1 isoform X3

      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    4. XM_017004218.1XP_016859707.1  nephrocystin-1 isoform X7

    5. XM_006712551.1XP_006712614.1  nephrocystin-1 isoform X1

      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
    6. XM_005263678.2XP_005263735.1  nephrocystin-1 isoform X5

      Conserved Domains (2) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
      cl09111
      Location:10105
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
    7. XM_011511244.1XP_011509546.1  nephrocystin-1 isoform X2

      Conserved Domains (2) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
      cl09111
      Location:10105
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
    8. XM_006712552.2XP_006712615.1  nephrocystin-1 isoform X8

      Conserved Domains (1) summary
      cd11770
      Location:156209
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

    Alternate CHM1_1.1

    Genomic

    1. NC_018913.2 Alternate CHM1_1.1

      Range
      110885220..110966946 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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