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    NPHP4 nephrocystin 4 [ Homo sapiens (human) ]

    Gene ID: 261734, updated on 5-Aug-2022

    Summary

    Official Symbol
    NPHP4provided by HGNC
    Official Full Name
    nephrocystin 4provided by HGNC
    Primary source
    HGNC:HGNC:19104
    See related
    Ensembl:ENSG00000131697 MIM:607215; AllianceGenome:HGNC:19104
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NPHP4 in Genome Data Viewer
    Location:
    1p36.31
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (5862811..5992425, complement)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (5387041..5518251, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (5922871..6052485, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9093 Neighboring gene microRNA 4689 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene uncharacterized LOC124903831 Neighboring gene Sharpr-MPRA regulatory region 11871 Neighboring gene chromodomain helicase DNA binding protein 5

    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?

    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

    EBI GWAS Catalog

    Description
    Common variants at ten loci influence QT interval duration in the QTGEN Study.
    EBI GWAS 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.
    EBI GWAS Catalog

    Pathways from PubChem

    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
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural molecule activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in bicellular tight junction IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell-cell junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in centriole IEA
    Inferred from Electronic Annotation
    more info
     
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in ciliary base IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in ciliary transition zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    is_active_in non-motile cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in photoreceptor distal connecting cilium IEA
    Inferred from Electronic Annotation
    more info
     
    located_in 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)

    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_011724.2 RefSeqGene

      Range
      5047..134661
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291593.2NP_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
      UniProtKB/Swiss-Prot
      O75161
      UniProtKB/TrEMBL
      B3KW36
    2. NM_001291594.2NP_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
      UniProtKB/Swiss-Prot
      O75161
      UniProtKB/TrEMBL
      B3KW36
      Related
      ENST00000478423.6
    3. NM_015102.5NP_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, BU738621, R40620
      Consensus CDS
      CCDS44052.1
      UniProtKB/Swiss-Prot
      O75161, Q8IWC0
      Related
      ENSP00000367398.4, ENST00000378156.9

    RNA

    1. NR_111987.2 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

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      5862811..5992425 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      See identical proteins and their annotated locations for XP_006710626.1

      UniProtKB/Swiss-Prot
      O75161, Q8IWC0
    2. XM_017000999.2XP_016856488.1  nephrocystin-4 isoform X10

    3. XM_047417537.1XP_047273493.1  nephrocystin-4 isoform X5

      UniProtKB/Swiss-Prot
      Q8IWC0
    4. XM_047417599.1XP_047273555.1  nephrocystin-4 isoform X10

    5. XM_047417546.1XP_047273502.1  nephrocystin-4 isoform X5

      UniProtKB/Swiss-Prot
      Q8IWC0
    6. XM_047417538.1XP_047273494.1  nephrocystin-4 isoform X5

      UniProtKB/Swiss-Prot
      Q8IWC0
    7. XM_047417590.1XP_047273546.1  nephrocystin-4 isoform X10

    8. XM_011541217.3XP_011539519.1  nephrocystin-4 isoform X5

      See identical proteins and their annotated locations for XP_011539519.1

      UniProtKB/Swiss-Prot
      O75161, Q8IWC0
    9. XM_047417589.1XP_047273545.1  nephrocystin-4 isoform X10

    10. XM_047417535.1XP_047273491.1  nephrocystin-4 isoform X5

      UniProtKB/Swiss-Prot
      Q8IWC0
    11. XM_047417581.1XP_047273537.1  nephrocystin-4 isoform X10

    12. XM_011541216.3XP_011539518.1  nephrocystin-4 isoform X5

      See identical proteins and their annotated locations for XP_011539518.1

      UniProtKB/Swiss-Prot
      O75161, Q8IWC0
    13. XM_047417585.1XP_047273541.1  nephrocystin-4 isoform X10

    14. XM_047417593.1XP_047273549.1  nephrocystin-4 isoform X10

    15. XM_011541215.2XP_011539517.1  nephrocystin-4 isoform X4

    16. XM_047417565.1XP_047273521.1  nephrocystin-4 isoform X7

    17. XM_017000996.2XP_016856485.1  nephrocystin-4 isoform X3

    18. XM_011541213.2XP_011539515.1  nephrocystin-4 isoform X1

    19. XM_047417555.1XP_047273511.1  nephrocystin-4 isoform X6

    20. XM_011541214.2XP_011539516.1  nephrocystin-4 isoform X2

    21. XM_017001000.3XP_016856489.1  nephrocystin-4 isoform X10

    22. XM_047417607.1XP_047273563.1  nephrocystin-4 isoform X12

    23. XM_017001001.2XP_016856490.1  nephrocystin-4 isoform X11

    24. XM_047417574.1XP_047273530.1  nephrocystin-4 isoform X8

    25. XM_017000998.1XP_016856487.1  nephrocystin-4 isoform X9

    26. XM_017001002.2XP_016856491.1  nephrocystin-4 isoform X13

      Related
      ENSP00000481831.2, ENST00000622020.4
    27. XM_047417617.1XP_047273573.1  nephrocystin-4 isoform X14

    RNA

    1. XR_007058632.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      5387041..5518251 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)