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NPHP1 (nephrocystin 1)

Identity

Alias_namesNPH1
nephronophthisis 1 (juvenile)
Alias_symbol (synonym)JBTS4
SLSN1
Other alias
HGNC (Hugo) NPHP1
LocusID (NCBI) 4867
Atlas_Id 56524
Location 2q13  [Link to chromosome band 2q13]
Location_base_pair Starts at 110123336 and ends at 110205062 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CD109 (6q13) / NPHP1 (2q13)NPHP1 (2q13) / MALL (2q13)NPHP1 (2q13) / PARG (10q11.23)
NPHP1 (2q13) / RAMP2 (17q21.31)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)NPHP1   7905
Cards
Entrez_Gene (NCBI)NPHP1  4867  nephrocystin 1
AliasesJBTS4; NPH1; SLSN1
GeneCards (Weizmann)NPHP1
Ensembl hg19 (Hinxton)ENSG00000144061 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000144061 [Gene_View]  chr2:110123336-110205062 [Contig_View]  NPHP1 [Vega]
ICGC DataPortalENSG00000144061
TCGA cBioPortalNPHP1
AceView (NCBI)NPHP1
Genatlas (Paris)NPHP1
WikiGenes4867
SOURCE (Princeton)NPHP1
Genetics Home Reference (NIH)NPHP1
Genomic and cartography
GoldenPath hg38 (UCSC)NPHP1  -     chr2:110123336-110205062 -  2q13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NPHP1  -     2q13   [Description]    (hg19-Feb_2009)
EnsemblNPHP1 - 2q13 [CytoView hg19]  NPHP1 - 2q13 [CytoView hg38]
Mapping of homologs : NCBINPHP1 [Mapview hg19]  NPHP1 [Mapview hg38]
OMIM256100   266900   607100   609583   
Gene and transcription
Genbank (Entrez)AF023674 AI433852 AJ001815 AK225600 AK299011
RefSeq transcript (Entrez)NM_000272 NM_001128178 NM_001128179 NM_207181
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)NPHP1
Cluster EST : UnigeneHs.280388 [ NCBI ]
CGAP (NCI)Hs.280388
Alternative Splicing GalleryENSG00000144061
Gene ExpressionNPHP1 [ NCBI-GEO ]   NPHP1 [ EBI - ARRAY_EXPRESS ]   NPHP1 [ SEEK ]   NPHP1 [ MEM ]
Gene Expression Viewer (FireBrowse)NPHP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4867
GTEX Portal (Tissue expression)NPHP1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15259   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15259  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15259
Splice isoforms : SwissVarO15259
PhosPhoSitePlusO15259
Domaine pattern : Prosite (Expaxy)SH3 (PS50002)   
Domains : Interpro (EBI)NPHP1_SH3    SH3_domain   
Domain families : Pfam (Sanger)SH3_1 (PF00018)   
Domain families : Pfam (NCBI)pfam00018   
Domain families : Smart (EMBL)SH3 (SM00326)  
Conserved Domain (NCBI)NPHP1
DMDM Disease mutations4867
Blocks (Seattle)NPHP1
PDB (SRS)1S1N   
PDB (PDBSum)1S1N   
PDB (IMB)1S1N   
PDB (RSDB)1S1N   
Structural Biology KnowledgeBase1S1N   
SCOP (Structural Classification of Proteins)1S1N   
CATH (Classification of proteins structures)1S1N   
SuperfamilyO15259
Human Protein AtlasENSG00000144061
Peptide AtlasO15259
HPRD02019
IPIIPI00028739   IPI01015576   IPI00410302   IPI00843954   IPI00924745   IPI00218974   IPI00927075   IPI00927293   
Protein Interaction databases
DIP (DOE-UCLA)O15259
IntAct (EBI)O15259
FunCoupENSG00000144061
BioGRIDNPHP1
STRING (EMBL)NPHP1
ZODIACNPHP1
Ontologies - Pathways
QuickGOO15259
Ontology : AmiGOstructural molecule activity  protein binding  cytosol  cytoskeleton  cell-cell junction  adherens junction  bicellular tight junction  signal transduction  excretion  visual behavior  membrane  single organismal cell-cell adhesion  cell projection organization  actin cytoskeleton organization  motile cilium  photoreceptor connecting cilium  spermatid differentiation  retina development in camera-type eye  ciliary basal body docking  positive regulation of bicellular tight junction assembly  
Ontology : EGO-EBIstructural molecule activity  protein binding  cytosol  cytoskeleton  cell-cell junction  adherens junction  bicellular tight junction  signal transduction  excretion  visual behavior  membrane  single organismal cell-cell adhesion  cell projection organization  actin cytoskeleton organization  motile cilium  photoreceptor connecting cilium  spermatid differentiation  retina development in camera-type eye  ciliary basal body docking  positive regulation of bicellular tight junction assembly  
NDEx NetworkNPHP1
Atlas of Cancer Signalling NetworkNPHP1
Wikipedia pathwaysNPHP1
Orthology - Evolution
OrthoDB4867
GeneTree (enSembl)ENSG00000144061
Phylogenetic Trees/Animal Genes : TreeFamNPHP1
HOVERGENO15259
HOGENOMO15259
Homologs : HomoloGeneNPHP1
Homology/Alignments : Family Browser (UCSC)NPHP1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNPHP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NPHP1
dbVarNPHP1
ClinVarNPHP1
1000_GenomesNPHP1 
Exome Variant ServerNPHP1
ExAC (Exome Aggregation Consortium)NPHP1 (select the gene name)
Genetic variants : HAPMAP4867
Genomic Variants (DGV)NPHP1 [DGVbeta]
DECIPHERNPHP1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNPHP1 
Mutations
ICGC Data PortalNPHP1 
TCGA Data PortalNPHP1 
Broad Tumor PortalNPHP1
OASIS PortalNPHP1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICNPHP1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDNPHP1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Eye diseases - LOVD
BioMutasearch NPHP1
DgiDB (Drug Gene Interaction Database)NPHP1
DoCM (Curated mutations)NPHP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NPHP1 (select a term)
intoGenNPHP1
Cancer3DNPHP1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM256100    266900    607100    609583   
Orphanet2824    3244    18917    12427   
MedgenNPHP1
Genetic Testing Registry NPHP1
NextProtO15259 [Medical]
TSGene4867
GENETestsNPHP1
Target ValidationNPHP1
Huge Navigator NPHP1 [HugePedia]
snp3D : Map Gene to Disease4867
BioCentury BCIQNPHP1
ClinGenNPHP1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4867
Chemical/Pharm GKB GenePA31706
Clinical trialNPHP1
Miscellaneous
canSAR (ICR)NPHP1 (select the gene name)
Probes
Litterature
PubMed69 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNPHP1
EVEXNPHP1
GoPubMedNPHP1
iHOPNPHP1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:47:14 CEST 2017

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