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    NPHP3 nephrocystin 3 [ Homo sapiens (human) ]

    Gene ID: 27031, updated on 9-Jul-2021

    Summary

    Official Symbol
    NPHP3provided by HGNC
    Official Full Name
    nephrocystin 3provided by HGNC
    Primary source
    HGNC:HGNC:7907
    See related
    Ensembl:ENSG00000113971 MIM:608002
    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
    MKS7; NPH3; RHPD; RHPD1; SLSN3; CFAP31
    Summary
    This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in ovary (RPKM 12.5), endometrium (RPKM 10.4) and 25 other tissues See more
    Orthologs
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    Genomic context

    See NPHP3 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (132680609..132722409, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (132399453..132441253, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NPHP3-ACAD11 readthrough (NMD candidate) Neighboring gene acyl-CoA dehydrogenase family member 11 Neighboring gene heat shock protein family A (Hsp70) member pseudogene 19 Neighboring gene ubiquitin like modifier activating enzyme 5 Neighboring gene NPHP3 antisense RNA 1 Neighboring gene uncharacterized LOC105374115 Neighboring gene Sharpr-MPRA regulatory region 13907

    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
    Meckel syndrome type 7
    MedGen: C2673885 OMIM: 267010 GeneReviews: Not available
    Compare labs
    Nephronophthisis 3
    MedGen: C1858392 OMIM: 604387 GeneReviews: Nephronophthisis
    Compare labs
    Renal-hepatic-pancreatic dysplasia 1
    MedGen: C3715199 OMIM: 208540 GeneReviews: Not available
    Compare labs
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of nephronophthisis 3 (NPHP3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough NPHP3-ACAD11

    Readthrough gene: NPHP3-ACAD11, Included gene: ACAD11

    Homology

    Clone Names

    • FLJ30691, FLJ36696, KIAA2000, MGC78666, DKFZp667K242, DKFZp781K1312

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in atrial septum development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in convergent extension involved in gastrulation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in determination of intestine left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of left/right symmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of liver left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of pancreatic left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in determination of stomach left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in epithelial cilium movement involved in determination of left/right asymmetry IC
    Inferred by Curator
    more info
     
    involved_in heart looping IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in kidney development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in kidney morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lung development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in maintenance of animal organ identity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of Wnt signaling pathway, planar cell polarity pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of planar cell polarity pathway involved in neural tube closure IC
    Inferred by Curator
    more info
    PubMed 
    involved_in ureter development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    nephrocystin-3
    Names
    Meckel syndrome, type 7
    cilia and flagella associated protein 31
    nephronophthisis 3 (adolescent)

    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_008130.2 RefSeqGene

      Range
      5024..46824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_153240.5NP_694972.3  nephrocystin-3

      See identical proteins and their annotated locations for NP_694972.3

      Status: REVIEWED

      Source sequence(s)
      AC055732, AY257864, DB114822, EB387619
      Consensus CDS
      CCDS3078.1
      UniProtKB/Swiss-Prot
      Q7Z494
      Related
      ENSP00000338766.5, ENST00000337331.10
      Conserved Domains (6) summary
      sd00006
      Location:11351163
      TPR; TPR repeat [structural motif]
      pfam03938
      Location:124206
      OmpH; Outer membrane protein (OmpH-like)
      pfam04871
      Location:117203
      Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region
      pfam12711
      Location:80149
      Kinesin-relat_1; Kinesin motor
      pfam13374
      Location:11351174
      TPR_10; Tetratricopeptide repeat
      pfam13424
      Location:11311209
      TPR_12; Tetratricopeptide repeat

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

      Range
      132680609..132722409 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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