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NPHP3 Gene

protein-coding   GIFtS: 55
GCID: GC03M132277

Nephronophthisis 3 (Adolescent)

  See NPHP3-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Nephronophthisis 3 (Adolescent)1 2     Type 71
nephrocystin-31 2     RHPD2
MKS72 5     SLSN32
NPH32 5     Meckel Syndrome, Type 72
RHPD12 5     KIAA20003
Meckel Syndrome1     

External Ids:    HGNC: 79071   Entrez Gene: 270312   Ensembl: ENSG000001139717   OMIM: 6080025   UniProtKB: Q7Z4943   

Export aliases for NPHP3 gene to outside databases

Previous GC identifers: GC03U990139 GC03M133598 GC03M133599 GC03M133760 GC03M133882 GC03M129779


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 renal-hepatic-pancreatic dysplasia, and nphp3-related meckel syndrome. An important paralog of this gene is KLC2.

UniProtKB/Swiss-Prot: NPHP3_HUMAN, Q7Z494
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 Wiki entry for NPHP3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NC_018914.2  NT_005612.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the NPHP3 gene promoter:
         AREB6   STAT1   POU2F1   FOXJ2 (long isoform)   POU2F1a   STAT1beta   FOXJ2   STAT1alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNPHP3 promoter sequence
   Search Chromatin IP Primers for NPHP3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NPHP3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q22.1   Ensembl cytogenetic band:  3q22.1   HGNC cytogenetic band: 3q22

NPHP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPHP3 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M132277:  view genomic region     (about GC identifiers)

Start:
132,276,986 bp from pter      End:
132,441,303 bp from pter
Size:
164,318 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for NPHP3

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: NPHP3_HUMAN, Q7Z494 (See protein sequence)
Recommended Name: Nephrocystin-3  
Size: 1330 amino acids; 150864 Da
Subunit: 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
Sequence caution: Sequence=BAB70891.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC02709.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAC04268.1;
Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q5JPE3 Q5JPE6 Q68D99 Q6NVH3 Q7Z492 Q7Z493 Q8N9R2 Q8NCM5 Q96N70 Q96NK2
Alternative splicing: 7 isoforms:  Q7Z494-1   Q7Z494-2   Q7Z494-3   Q7Z494-4   Q7Z494-5   Q7Z494-6   Q7Z494-7   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NPHP3: NX_Q7Z494

Explore proteomics data for NPHP3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NPHP3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_694972.3  
    ENSEMBL proteins: 
     ENSP00000419763   ENSP00000419907   ENSP00000427666   ENSP00000338766   ENSP00000418664  
     ENSP00000319909   ENSP00000344802   ENSP00000372769  

    NPHP3 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for NPHP3

     
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    antibodies-online proteins for NPHP3 (2 products) 

     
    antibodies-online peptides for NPHP3

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    TTC: Tetratricopeptide (TTC) repeat domain containing

    4 InterPro protein domains:
     IPR011990 TPR-like_helical
     IPR027417 P-loop_NTPase
     IPR013026 TPR-contain_dom
     IPR019734 TPR_repeat

    Graphical View of Domain Structure for InterPro Entry Q7Z494

    ProtoNet protein and cluster: Q7Z494

    UniProtKB/Swiss-Prot: NPHP3_HUMAN, Q7Z494
    Similarity: Contains 11 TPR repeats


    Find genes that share domains with NPHP3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NPHP3_HUMAN, Q7Z494
    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): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI12872122
         
    Find genes that share ontologies with NPHP3           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for NPHP3:
     Decreased cilium length after   Decreased viability of wild-ty 

         12 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Nphp3):
     behavior/neurological  cardiovascular system  craniofacial  embryogenesis  growth/size/body 
     hematopoietic system  homeostasis/metabolism  immune system  mortality/aging  nervous system 
     renal/urinary system  skeleton 

    Find genes that share phenotypes with NPHP3           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for NPHP3

    miRNA
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    miRTarBase miRNAs that target NPHP3:
    hsa-mir-215-5p (MIRT024459), hsa-mir-192-5p (MIRT026854)

    Block miRNA regulation of human, mouse, rat NPHP3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NPHP3 (see all 24):
    hsa-let-7d hsa-miR-202 hsa-miR-25 hsa-let-7c hsa-miR-340 hsa-miR-1304 hsa-let-7g hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidNPHP3 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NPHP3_HUMAN, Q7Z494: 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: 

    CompartmentConfidence
    cytosol3
    endoplasmic reticulum1
    nucleus1
    peroxisome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005929cilium IDA--
    GO:0072372primary cilium IDA--

    Find genes that share ontologies with NPHP3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Pathway & Disease-focused RT2 Profiler PCR Array including NPHP3: 
              Primary Cilia in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for NPHP3

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    5 Interacting proteins for NPHP3 (Q7Z4941, 2, 3 ENSP000003387664) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NPHP1O152593, ENSP000003131694I2D: score=2 STRING: ENSP00000313169
    CEP164Q9UPV01EBI-2804263,EBI-3937015
    UNC119Q134322MINT-8411894
    UNC119BA6NIH72MINT-8411953
    INVSENSP000002624574STRING: ENSP00000262457
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 24):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001822kidney development IMP--
    GO:0001947heart looping IMP18371931
    GO:0003283atrial septum development IMP18371931
    GO:0006629lipid metabolic process IEA--
    GO:0007163establishment or maintenance of cell polarity IEA--

    Find genes that share ontologies with NPHP3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NPHP3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for NPHP3 gene: 
    NM_153240.4  

    Unigene Cluster for NPHP3:

    Nephronophthisis 3 (adolescent)
    Hs.511991  [show with all ESTs]
    Unigene Representative Sequence: NR_037804
    14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000471702(uc003eoz.1 uc003epf.2) ENST00000474871 ENST00000493732
    ENST00000490993 ENST00000465756 ENST00000512094 ENST00000337331 ENST00000515289
    ENST00000469232 ENST00000476742 ENST00000471145 ENST00000326682(uc003epd.2 uc003epe.2)
    ENST00000343113 ENST00000383282
    miRNA
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    Block miRNA regulation of human, mouse, rat NPHP3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NPHP3 (see all 24):
    hsa-let-7d hsa-miR-202 hsa-miR-25 hsa-let-7c hsa-miR-340 hsa-miR-1304 hsa-let-7g hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidNPHP3 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat NPHP3

    Additional mRNA sequence: 

    AK055253.1 AK092910.1 AK094015.1 AY257864.1 BC068082.1 NR_037804.1 

    13 DOTS entries:

    DT.100752365  DT.438581  DT.100027783  DT.70103793  DT.100027784  DT.120924396  DT.91683721  DT.120924324 
    DT.120924382  DT.40196361  DT.100664087  DT.120924344  DT.434373 

    Selected AceView cDNA sequences (see all 249):

    AK092910 AW088130 AU125268 AX803783 BC068082 AI768926 AL832873 BM312074 
    AI288586 CK430577 AA703194 AI056537 BM504752 AL518293 CD245081 CB993596 
    CD514772 BU738360 NM_032169 BQ224852 BU618759 CA411998 NM_153240 AL518294 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for NPHP3 (see all 10)    About this scheme

    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:                                                                                                                                                            

    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:                                                                                                                                                            

    ExUns: 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49
    SP1:                                    
    SP2:                                    
    SP3:                                    
    SP4:                                    
    SP5:                                    


    ECgene alternative splicing isoforms for NPHP3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NPHP3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TATTGATTGT
    NPHP3 Expression
    About this image

    NPHP3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NPHP3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.511991

    UniProtKB/Swiss-Prot: NPHP3_HUMAN, Q7Z494
    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

        Pathway & Disease-focused RT2 Profiler PCR Array including NPHP3: 
              Primary Cilia in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NPHP3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for NPHP3 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nphp31 , 5 nephronophthisis 3 (adolescent)1, 5 84.74(n)1
    88.82(a)1
      9 (56.11 cM)5
    740251  NM_028721.31  NP_082997.31 
     1040025445 
    chicken
    (Gallus gallus)
    Aves NPHP31 nephronophthisis 3 (adolescent) 77.89(n)
    84.66(a)
      420690  XM_418790.3  XP_418790.2 
    lizard
    (Anolis carolinensis)
    Reptilia NPHP36
    nephronophthisis 3 (adolescent)
    81(a)
    1 ↔ 1
    6(38213876-38266274)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.193652 Xenopus laevis transcribed sequences 75.98(n)    BQ385000.1 
    zebrafish
    (Danio rerio)
    Actinopterygii nphp31 nephronophthisis 3 66.38(n)
    71.33(a)
      562601  NM_001202441.1  NP_001189370.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Klc6
    Kinesin light chain
    25(a)
    1 → many
    3L(12739716-12743156)
    worm
    (Caenorhabditis elegans)
    Secernentea klc-26
    klc-16
    Protein KLC-1, isoform b
    24(a)
    21(a)
    many ↔ many
    many ↔ many
    V(5575410-5581713) WBGene00002215
    IV(11083735-11086053) WBGene00002214


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NPHP3 gene
    KLC22  ENSG000002565002  KLC42  KLC32  KLC12  
    5 SIMAP similar genes for NPHP3 using alignment to 5 protein entries:     NPHP3_HUMAN (see all proteins):
    KLC3    KLC1    KLC4    KNS2    KLC2

    Find genes that share paralogs with NPHP3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NPHP3 (see all 24)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0228194
    Nephronophthisis 3 (NPHP3)4--see VAR_0228192 A V mis40--------
    VAR_0441214
    Renal-hepatic-pancreatic dysplasia 1 (RHPD1)4--see VAR_0441212 R Q mis40--------
    VAR_0228184
    Nephronophthisis 3 (NPHP3)4--see VAR_0228182 L P mis40--------
    rs753168021,2,4
    Nephronophthisis 3 (NPHP3)4--see VAR_0228212 mis40--------
    rs1420210491,2,4
    Nephronophthisis 3 (NPHP3)4--see VAR_0228162 mis40--------
    VAR_0228154
    Nephronophthisis 3 (NPHP3)4--see VAR_0228152 S T mis40--------
    VAR_0228174
    Nephronophthisis 3 (NPHP3)4--see VAR_0228172 R H mis40--------
    rs1434517661,2,4
    Nephronophthisis 3 (NPHP3)4--see VAR_0228202 mis40--------
    rs58527061,2
    C--129808210(+) ttttt-/T/T   
      T
    /TTTT
    gagac
    1 -- int11NA 2
    rs117090991,2
    C,H--129821650(+) CGGAAC/GGGGGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for NPHP3 (132276986 - 132441303 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for NPHP3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv4014CNV Insertion18451855

    Human Gene Mutation Database (HGMD): NPHP3
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NPHP3
    DNA2.0 Custom Variant and Variant Library Synthesis for NPHP3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608002   
    OMIM disorders: 604387  208540  267010  
    UniProtKB/Swiss-Prot: NPHP3_HUMAN, Q7Z494
  • 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. 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. 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. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • 10 diseases for NPHP3:    
    About MalaCards
    renal-hepatic-pancreatic dysplasia    nphp3-related meckel syndrome    renal-hepatic-pancreatic dysplasia 1    late-onset autosomal recessive medullary cystic kidney disease
    nephronophthisis 3    meckel syndrome 7    meckel syndrome    senior-loken syndrome 1
    cystic kidney    nephronophthisis

    3 diseases from the University of Copenhagen DISEASES database for NPHP3:
    Nephronophthisis     Cystic kidney     Situs inversus

    Find genes that share disorders with NPHP3           About GenesLikeMe

    4 Novoseek inferred disease relationships for NPHP3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    nphp2 98.6 17 19177160 (4), 17855640 (2), 14750102 (2), 18076122 (1) (see all 7)
    nphp1 96.5 12 18076122 (3), 17855640 (2), 14750102 (2), 11274269 (1) (see all 8)
    cystic kidney disease 87.8 1 19303681 (1)
    polycystic kidney diseases 65.2 1 15381417 (1)

    Genetic Association Database (GAD): NPHP3
    Human Genome Epidemiology (HuGE) Navigator: NPHP3 (2 documents)

    Export disorders for NPHP3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for NPHP3 gene, integrated from 10 sources (see all 34):
    (articles sorted by number of sources associating them with NPHP3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. (PubMed id 12872122)1, 2, 3, 4, 9 Olbrich H.... Omran H. (Nat. Genet. 2003)
    2. Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic- pancreatic dysplasia. (PubMed id 18371931)1, 2, 9 Bergmann C.... Omran H. (Am. J. Hum. Genet. 2008)
    3. 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. (PubMed id 15381417)1, 3, 9 Leipe D.D....Aravind L. (J. Mol. Biol. 2004)
    4. ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3. (PubMed id 23793029)1, 2 Hoff S....Lienkamp S.S. (Nat. Genet. 2013)
    5. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. (PubMed id 22863007)1, 2 Chaki M....Hildebrandt F. (Cell 2012)
    6. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. (PubMed id 21102462)1, 4 Elks C.E....Murray A. (Nat. Genet. 2010)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    9. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PubMed id 12056414)1, 2 Ohara O.... Koseki H. (DNA Res. 2002)
    10. Mutations of NPHP2 and NPHP3 in infantile nephronophthisis. (PubMed id 19177160)1, 9 Tory K....Salomon R. (Kidney Int. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 27031 HGNC: 7907 AceView: FLJ12592andNPHP3 Ensembl:ENSG00000113971 euGenes: HUgn27031
    ECgene: NPHP3 H-InvDB: NPHP3

    (According to HUGE)
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    HUGE: KIAA2000

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NPHP3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NPHP3 gene:
    Search GeneIP for patents involving NPHP3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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