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NPHP3 nephrocystin 3 [ Homo sapiens (human) ]

Gene ID: 27031, updated on 12-Jan-2019

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

Genomic context

See NPHP3 in Genome Data Viewer
Location:
3q22.1
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (132680609..132722459, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (132399453..132441303, 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 transmembrane protein 108 Neighboring gene TMEM108 antisense RNA 1

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Adolescent nephronophthisis
MedGen: C1858392 OMIM: 604387 GeneReviews: Nephronophthisis
Compare labs
Meckel syndrome type 7
MedGen: C2673885 OMIM: 267010 GeneReviews: Not available
Compare labs
Renal-hepatic-pancreatic dysplasia
MedGen: C3715199 OMIM: 208540 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog

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

Pathways from BioSystems

  • Cargo trafficking to the periciliary membrane, organism-specific biosystem (from REACTOME)
    Cargo trafficking to the periciliary membrane, organism-specific biosystemProteomic studies suggest that the cilium is home to approximately a thousand proteins, and has a unique protein and lipid make up relative to the bulk cytoplasm and plasma membrane (Pazour et al, 20...
  • 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...
  • Trafficking of myristoylated proteins to the cilium, organism-specific biosystem (from REACTOME)
    Trafficking of myristoylated proteins to the cilium, organism-specific biosystemA number of myristoylated proteins have been shown to traffic to the cilium in a myristoyl- and UNC119B:ARL3:RP2-dependent fashion. These include the ciliary proteins Nephrocystin 3 (NPHP3) and Cyst...

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

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
    4974..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, ENST00000337331.9
    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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    132680609..132722459 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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