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NPHP4 nephrocystin 4 [ Homo sapiens (human) ]

Gene ID: 261734, updated on 5-Aug-2018

Summary

Official Symbol
NPHP4provided by HGNC
Official Full Name
nephrocystin 4provided by HGNC
Primary source
HGNC:HGNC:19104
See related
Ensembl:ENSG00000131697 MIM:607215; Vega:OTTHUMG00000000701
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
POC10; SLSN4
Summary
This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Expression
Broad expression in testis (RPKM 3.4), thyroid (RPKM 2.6) and 25 other tissues See more
Orthologs

Genomic context

See NPHP4 in Genome Data Viewer
Location:
1p36.31
Exon count:
36
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (5862808..5992473, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (5922870..6052618, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene AJAP1-NPHP4 intergenic nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene microRNA 4689 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene protein GVQW2-like Neighboring gene uncharacterized LOC105376687 Neighboring gene chromodomain helicase DNA binding protein 5

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Nephronophthisis 4
MedGen: C1847013 OMIM: 606966 GeneReviews: Nephronophthisis
Compare labs
Senior-Loken syndrome 4
MedGen: C1846979 OMIM: 606996 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Common variants at ten loci influence QT interval duration in the QTGEN Study.
NHGRI GWA Catalog
Genetic association with overall survival of taxane-treated lung cancer patients - A genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.
NHGRI GWA Catalog

Pathways from BioSystems

  • 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...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Hippo, organism-specific biosystem (from REACTOME)
    Signaling by Hippo, organism-specific biosystemHuman Hippo signaling is a network of reactions that regulates cell proliferation and apoptosis, centered on a three-step kinase cascade. The cascade was discovered by analysis of Drosophila mutation...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ46306, KIAA0673

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-cell adhesion NAS
Non-traceable Author Statement
more info
PubMed 
ciliary basal body-plasma membrane docking TAS
Traceable Author Statement
more info
 
flagellated sperm motility IEA
Inferred from Electronic Annotation
more info
 
hippo signaling TAS
Traceable Author Statement
more info
 
negative regulation of canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
photoreceptor cell maintenance IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell outer segment organization IEA
Inferred from Electronic Annotation
more info
 
positive regulation of bicellular tight junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
retina development in camera-type eye IEA
Inferred from Electronic Annotation
more info
 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
visual behavior NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
bicellular tight junction IEA
Inferred from Electronic Annotation
more info
 
cell-cell junction IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IEA
Inferred from Electronic Annotation
more info
 
ciliary base IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
photoreceptor connecting cilium IEA
Inferred from Electronic Annotation
more info
 
ribbon synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
nephrocystin-4
Names
POC10 centriolar protein homolog
nephroretinin

NCBI Reference Sequences (RefSeq)

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_011724.2 RefSeqGene

    Range
    4999..134664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291593.1NP_001278522.1  nephrocystin-4 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks three exons and uses an alternate splice site in the 5' region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK124074, AK314326, BC040520, R40620
    UniProtKB/Swiss-Prot
    O75161
    UniProtKB/TrEMBL
    B3KW36
    Conserved Domains (1) summary
    pfam00937
    Location:333424
    Corona_nucleoca; Coronavirus nucleocapsid protein
  2. NM_001291594.1NP_001278523.1  nephrocystin-4 isoform c

    See identical proteins and their annotated locations for NP_001278523.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks four exons in the 5' region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK124074, AK314326, BC040520, R40620
    UniProtKB/Swiss-Prot
    O75161
    UniProtKB/TrEMBL
    B3KW36
    Conserved Domains (1) summary
    pfam00937
    Location:334425
    Corona_nucleoca; Coronavirus nucleocapsid protein
  3. NM_015102.4NP_055917.1  nephrocystin-4 isoform a

    See identical proteins and their annotated locations for NP_055917.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF537130, AK314326, BC040520, BU738621, R40620
    Consensus CDS
    CCDS44052.1
    UniProtKB/Swiss-Prot
    O75161
    Related
    ENSP00000367398.4, OTTHUMP00000000745, ENST00000378156.8, OTTHUMT00000001715

RNA

  1. NR_111987.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains three alternate internal exons and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL356693, BC040520, R40620
    Related
    ENST00000489180.6, OTTHUMT00000001716

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    5862808..5992473 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000999.1XP_016856488.1  nephrocystin-4 isoform X7

  2. XM_006710563.3XP_006710626.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_006710626.1

    UniProtKB/Swiss-Prot
    O75161
  3. XM_011541217.2XP_011539519.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_011539519.1

    UniProtKB/Swiss-Prot
    O75161
  4. XM_011541216.2XP_011539518.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_011539518.1

    UniProtKB/Swiss-Prot
    O75161
  5. XM_017000997.1XP_016856486.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161
  6. XM_011541218.2XP_011539520.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_011539520.1

    UniProtKB/Swiss-Prot
    O75161
  7. XM_011541215.1XP_011539517.1  nephrocystin-4 isoform X4

  8. XM_017000996.1XP_016856485.1  nephrocystin-4 isoform X3

  9. XM_011541213.1XP_011539515.1  nephrocystin-4 isoform X1

  10. XM_011541214.1XP_011539516.1  nephrocystin-4 isoform X2

  11. XM_017001000.2XP_016856489.1  nephrocystin-4 isoform X7

  12. XM_017001001.1XP_016856490.1  nephrocystin-4 isoform X8

  13. XM_017001003.1XP_016856492.1  nephrocystin-4 isoform X10

    Conserved Domains (1) summary
    pfam00937
    Location:333424
    Corona_nucleoca; Coronavirus nucleocapsid protein
  14. XM_017000998.1XP_016856487.1  nephrocystin-4 isoform X6

  15. XM_017001002.1XP_016856491.1  nephrocystin-4 isoform X9

    Related
    ENSP00000481831.2, ENST00000622020.4

RNA

  1. XR_001737115.1 RNA Sequence

  2. XR_001737114.1 RNA Sequence

    Related
    ENST00000478423.6
  3. XR_946605.1 RNA Sequence

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