Format

Send to:

Choose Destination

NPHP1 nephrocystin 1 [ Homo sapiens (human) ]

Gene ID: 4867, updated on 20-Feb-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, centractin alpha (yeast) pseudogene Neighboring gene long intergenic non-protein coding RNA 116 Neighboring gene two pore channel 3 pseudogene

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 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, OTTHUMP00000161841, ENST00000316534, 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, OTTHUMP00000225199, ENST00000445609, 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, OTTHUMP00000207141, ENST00000355301, 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, OTTHUMP00000161840, ENST00000393272, 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, OTTHUMP00000207142, ENST00000417665, 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)
Support Center