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Aliases for NPHP3 Gene

Aliases for NPHP3 Gene

  • Nephronophthisis 3 (Adolescent) 2 3
  • Cilia And Flagella Associated Protein 31 2 3
  • Nephrocystin-3 2 3
  • RHPD1 3 6
  • MKS7 3 6
  • NPH3 3 6
  • Meckel Syndrome, Type 7 3
  • Meckel Syndrome 2
  • KIAA2000 4
  • Type 7 2
  • CFAP31 3
  • SLSN3 3
  • RHPD 3

External Ids for NPHP3 Gene

Previous GeneCards Identifiers for NPHP3 Gene

  • GC03U990139
  • GC03M133598
  • GC03M133599
  • GC03M133760
  • GC03M133882
  • GC03M132277
  • GC03M129779

Summaries for NPHP3 Gene

Entrez Gene Summary for NPHP3 Gene

  • 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]

GeneCards Summary for NPHP3 Gene

NPHP3 (Nephronophthisis 3 (Adolescent)) is a Protein Coding gene. Diseases associated with NPHP3 include nephronophthisis 3 and renal-hepatic-pancreatic dysplasia 1. An important paralog of this gene is KLC4.

UniProtKB/Swiss-Prot for NPHP3 Gene

  • Required for normal ciliary development and function. Inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling which regulates planar cell polarity. Probably acts as a molecular switch between different Wnt signaling pathways. Required for proper convergent extension cell movements.

Gene Wiki entry for NPHP3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPHP3 Gene

Genomics for NPHP3 Gene

Regulatory Elements for NPHP3 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for NPHP3 Gene

Start:
132,680,609 bp from pter
End:
132,722,459 bp from pter
Size:
41,851 bases
Orientation:
Minus strand

Genomic View for NPHP3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for NPHP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPHP3 Gene

Proteins for NPHP3 Gene

  • Protein details for NPHP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z494-NPHP3_HUMAN
    Recommended name:
    Nephrocystin-3
    Protein Accession:
    Q7Z494
    Secondary Accessions:
    • Q5JPE3
    • Q5JPE6
    • Q68D99
    • Q6NVH3
    • Q7Z492
    • Q7Z493
    • Q8N9R2
    • Q8NCM5
    • Q96N70
    • Q96NK2

    Protein attributes for NPHP3 Gene

    Size:
    1330 amino acids
    Molecular mass:
    150864 Da
    Quaternary structure:
    • Interacts with NPHP1 and INVS/NPHP2. Interacts (when myristoylated) with UNC119 and UNC119B; interaction is required for localization to cilium. Interacts with CEP164. Component of a complex containing at least ANKS6, INVS, NEK8 and NPHP3. ANKS6 may organize complex assembly by linking INVS and NPHP3 to NEK8 and INVS may target the complex to the proximal ciliary axoneme.
    SequenceCaution:
    • Sequence=BAB70891.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC02709.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAC04268.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for NPHP3 Gene

neXtProt entry for NPHP3 Gene

Proteomics data for NPHP3 Gene at MOPED

Post-translational modifications for NPHP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NPHP3 Gene

Antibody Products

No data available for DME Specific Peptides for NPHP3 Gene

Domains for NPHP3 Gene

Gene Families for NPHP3 Gene

HGNC:
  • TTC :Tetratricopeptide (TTC) repeat domain containing

Protein Domains for NPHP3 Gene

Suggested Antigen Peptide Sequences for NPHP3 Gene

Graphical View of Domain Structure for InterPro Entry

Q7Z494

UniProtKB/Swiss-Prot:

NPHP3_HUMAN :
  • Q7Z494
Similarity:
  • Contains 11 TPR repeats.
genes like me logo Genes that share domains with NPHP3: view

Function for NPHP3 Gene

Molecular function for NPHP3 Gene

UniProtKB/Swiss-Prot Function:
Required for normal ciliary development and function. Inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling which regulates planar cell polarity. Probably acts as a molecular switch between different Wnt signaling pathways. Required for proper convergent extension cell movements.

Gene Ontology (GO) - Molecular Function for NPHP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12872122
genes like me logo Genes that share ontologies with NPHP3: view
genes like me logo Genes that share phenotypes with NPHP3: view

miRNA for NPHP3 Gene

miRTarBase miRNAs that target NPHP3

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for NPHP3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for NPHP3 Gene

Localization for NPHP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPHP3 Gene

Cell projection, cilium. Note=Localization to cilium is mediated via interaction with UNC119 and UNC119B, which bind to the myristoyl moiety of the N-terminus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NPHP3 Gene COMPARTMENTS Subcellular localization image for NPHP3 gene
Compartment Confidence
cytosol 3
endoplasmic reticulum 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for NPHP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005929 cilium IDA 20462968
GO:0072372 primary cilium TAS --
genes like me logo Genes that share ontologies with NPHP3: view

Pathways for NPHP3 Gene

SuperPathways for NPHP3 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for NPHP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001822 kidney development IMP 20007846
GO:0001947 heart looping IMP 18371931
GO:0003283 atrial septum development IMP 18371931
GO:0006996 organelle organization TAS --
GO:0007368 determination of left/right symmetry IMP 18371931
genes like me logo Genes that share ontologies with NPHP3: view

No data available for Pathways by source for NPHP3 Gene

Transcripts for NPHP3 Gene

mRNA/cDNA for NPHP3 Gene

Unigene Clusters for NPHP3 Gene

Nephronophthisis 3 (adolescent):
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for NPHP3

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPHP3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
SP1: - -
SP2:
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

ExUns: 25a · 25b ^ 26 ^ 27 ^ 28a · 28b · 28c ^ 29a · 29b ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35a · 35b ^ 36 ^ 37 ^ 38 ^ 39 ^ 40a · 40b ^ 41 ^ 42a · 42b ^ 43 ^
SP1: -
SP2: - -
SP3: - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: - - - - -

ExUns: 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for NPHP3 Gene

GeneLoc Exon Structure for
NPHP3
ECgene alternative splicing isoforms for
NPHP3

Expression for NPHP3 Gene

mRNA expression in normal human tissues for NPHP3 Gene

Protein differential expression in normal tissues for NPHP3 Gene

This gene is overexpressed in Nasal epithelium (46.1) and Cerebrospinal fluid (16.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for NPHP3 Gene

SOURCE GeneReport for Unigene cluster for NPHP3 Gene Hs.511991

mRNA Expression by UniProt/SwissProt for NPHP3 Gene

Q7Z494-NPHP3_HUMAN
Tissue specificity: Widely expressed at low level. Expressed in heart, placenta, liver, skeletal muscle, kidney and pancreas. Expressed at very low level in brain and lung.
genes like me logo Genes that share expressions with NPHP3: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Expression partners for NPHP3 Gene

Orthologs for NPHP3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPHP3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia NPHP3 35
  • 92.08 (n)
  • 95.34 (a)
NPHP3 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NPHP3 35
  • 92.65 (n)
  • 95.33 (a)
NPHP3 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nphp3 35
  • 84.74 (n)
  • 88.82 (a)
Nphp3 16
Nphp3 36
  • 89 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia NPHP3 35
  • 99.47 (n)
  • 99.52 (a)
NPHP3 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nphp3 35
  • 83.94 (n)
  • 88.22 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia NPHP3 36
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPHP3 35
  • 77.89 (n)
  • 84.66 (a)
NPHP3 36
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPHP3 36
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nphp3 35
  • 72.27 (n)
  • 79.22 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19365 35
zebrafish
(Danio rerio)
Actinopterygii nphp3 35
  • 66.38 (n)
  • 71.33 (a)
nphp3 36
  • 71 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Klc 36
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea klc-1 36
  • 21 (a)
ManyToMany
klc-2 36
  • 24 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.801 36
  • 37 (a)
OneToOne
Species with no ortholog for NPHP3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NPHP3 Gene

ENSEMBL:
Gene Tree for NPHP3 (if available)
TreeFam:
Gene Tree for NPHP3 (if available)

Paralogs for NPHP3 Gene

Paralogs for NPHP3 Gene

Selected SIMAP similar genes for NPHP3 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with NPHP3: view

Variants for NPHP3 Gene

Sequence variations from dbSNP and Humsavar for NPHP3 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
VAR_022815 Nephronophthisis 3 (NPHP3)
VAR_022816 Nephronophthisis 3 (NPHP3)
VAR_022817 Nephronophthisis 3 (NPHP3)
VAR_022818 Nephronophthisis 3 (NPHP3)
VAR_022819 Nephronophthisis 3 (NPHP3)

Structural Variations from Database of Genomic Variants (DGV) for NPHP3 Gene

Variant ID Type Subtype PubMed ID
nsv4014 CNV Insertion 18451855

Relevant External Links for NPHP3 Gene

HapMap Linkage Disequilibrium report
NPHP3
Human Gene Mutation Database (HGMD)
NPHP3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPHP3 Gene

Disorders for NPHP3 Gene

(3) OMIM Diseases for NPHP3 Gene (608002)

UniProtKB/Swiss-Prot

NPHP3_HUMAN
  • Nephronophthisis 3 (NPHP3) [MIM:604387]: An autosomal recessive disorder resulting in end-stage renal disease. It is characterized by polyuria, polydipsia, anemia. Onset of terminal renal failure occurr significantly later (median age, 19 years) than in juvenile nephronophthisis. Renal pathology is characterized by alterations of tubular basement membranes, tubular atrophy and dilation, sclerosing tubulointerstitial nephropathy, and renal cyst development predominantly at the corticomedullary junction. {ECO:0000269 PubMed:12872122}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Renal-hepatic-pancreatic dysplasia 1 (RHPD1) [MIM:208540]: A disease characterized by cystic malformations of the kidneys, liver, and pancreas. The pathological findings consist of multicystic dysplastic kidneys, dilated and dysgenetic bile ducts, a dysplastic pancreas with dilated ducts, cysts, fibrosis and inflammatory infiltrates. {ECO:0000269 PubMed:18371931}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Meckel syndrome 7 (MKS7) [MIM:267010]: A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269 PubMed:18371931}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for NPHP3 Gene

(4) Novoseek inferred disease relationships for NPHP3 Gene

Disease -log(P) Hits PubMed IDs
nphp2 98.6 12
nphp1 96.5 12
cystic kidney disease 87.8 1
polycystic kidney diseases 65.2 1

Relevant External Links for NPHP3

Genetic Association Database (GAD)
NPHP3
Human Genome Epidemiology (HuGE) Navigator
NPHP3
genes like me logo Genes that share disorders with NPHP3: view

No data available for Genatlas for NPHP3 Gene

Publications for NPHP3 Gene

  1. Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. (PMID: 12872122) Olbrich H. … Omran H. (Nat. Genet. 2003) 2 3 4 23 48
  2. STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. (PMID: 15381417) Leipe D.D. … Aravind L. (J. Mol. Biol. 2004) 2 3 23
  3. Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic- pancreatic dysplasia. (PMID: 18371931) Bergmann C. … Omran H. (Am. J. Hum. Genet. 2008) 3 4 23
  4. Mutations of NPHP2 and NPHP3 in infantile nephronophthisis. (PMID: 19177160) Tory K. … Salomon R. (Kidney Int. 2009) 3 23
  5. Lethal cystic kidney disease in Amish neonates associated with homozygous nonsense mutation of NPHP3. (PMID: 19303681) Simpson M.A. … Crosby A.H. (Am. J. Kidney Dis. 2009) 3 23

Products for NPHP3 Gene

Sources for NPHP3 Gene

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