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Aliases for NPHP1 Gene

Aliases for NPHP1 Gene

  • Nephronophthisis 1 (Juvenile) 2 3 5
  • Juvenile Nephronophthisis 1 Protein 3 4
  • NPH1 3 4
  • Nephrocystin-1 2
  • Nephrocystin 1 3
  • JBTS4 3
  • SLSN1 3

External Ids for NPHP1 Gene

Previous HGNC Symbols for NPHP1 Gene

  • NPH1

Previous GeneCards Identifiers for NPHP1 Gene

  • GC02M108543
  • GC02M109144
  • GC02M110427
  • GC02M110616
  • GC02M110237
  • GC02M110879
  • GC02M104021

Summaries for NPHP1 Gene

Entrez Gene Summary for NPHP1 Gene

  • This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for NPHP1 Gene

NPHP1 (Nephronophthisis 1 (Juvenile)) is a Protein Coding gene. Diseases associated with NPHP1 include nephronophthisis 1, juvenile and senior-loken syndrome-1. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition. GO annotations related to this gene include structural molecule activity.

UniProtKB/Swiss-Prot for NPHP1 Gene

  • Together with BCAR1 it may play a role in the control of epithelial cell polarity. Involved in the organization of apical junctions in kidney cells together with NPHP4 and RPGRIP1L/NPHP8 (By similarity). Does not seem to be strictly required for ciliogenesis (By similarity). Seems to help to recruit PTK2B/PYK2 to cell matrix adhesions, thereby initiating phosphorylation of PTK2B/PYK2 and PTK2B/PYK2-dependent signaling. May play a role in the regulation of intraflagellar transport (IFT) during cilia assembly. Required for normal retina development. In connecting photoreceptor cilia influences the movement of some IFT proteins such as IFT88 and WDR19. Involved in spermatogenesis (By similarity).

Gene Wiki entry for NPHP1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPHP1 Gene

Genomics for NPHP1 Gene

Regulatory Elements for NPHP1 Gene

Promoters for NPHP1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around NPHP1 on UCSC Golden Path with GeneCards custom track

Genomic Location for NPHP1 Gene

Chromosome:
2
Start:
110,122,311 bp from pter
End:
110,205,066 bp from pter
Size:
82,756 bases
Orientation:
Minus strand

Genomic View for NPHP1 Gene

Genes around NPHP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPHP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPHP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPHP1 Gene

Proteins for NPHP1 Gene

  • Protein details for NPHP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15259-NPHP1_HUMAN
    Recommended name:
    Nephrocystin-1
    Protein Accession:
    O15259
    Secondary Accessions:
    • O14837

    Protein attributes for NPHP1 Gene

    Size:
    732 amino acids
    Molecular mass:
    83299 Da
    Quaternary structure:
    • Interacts with BCAR1, PTK2B/PYK2 and tensin. Interacts with INVS and NPHP3. Interacts with PACS1; the interaction is dependent on NPHP1 phosphorylation by CK2. Interacts with KIF7. Interacts with AHI1 and TNK2. Interacts with NPHP4 in a complex containing NPHP1, NPHP4 and RPGRIP1L. Interacts with IQCB1; the interaction likely requires additional interactors. Interacts with ANKS3 (By similarity).
    Miscellaneous:
    • Nephronophthisis type 1 patients deficient for NPHP1 show normal overall integrity of respiratory cilia.

    Three dimensional structures from OCA and Proteopedia for NPHP1 Gene

    Alternative splice isoforms for NPHP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NPHP1 Gene

Proteomics data for NPHP1 Gene at MOPED

Post-translational modifications for NPHP1 Gene

  • Phosphorylation by CK2 is required for the interaction with PACS1 and the targeting to the base region of cilia.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for NPHP1 Gene

Domains & Families for NPHP1 Gene

Protein Domains for NPHP1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for NPHP1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15259

UniProtKB/Swiss-Prot:

NPHP1_HUMAN :
  • The SH3 domain mediates the stable interaction with Cas.
  • Belongs to the nephrocystin-1 family.
Domain:
  • The SH3 domain mediates the stable interaction with Cas.
  • Contains 1 SH3 domain.
Family:
  • Belongs to the nephrocystin-1 family.
genes like me logo Genes that share domains with NPHP1: view

No data available for Gene Families for NPHP1 Gene

Function for NPHP1 Gene

Molecular function for NPHP1 Gene

GENATLAS Biochemistry:
gene of unknown function,maybe a component of tubular basal membrane
UniProtKB/Swiss-Prot Function:
Together with BCAR1 it may play a role in the control of epithelial cell polarity. Involved in the organization of apical junctions in kidney cells together with NPHP4 and RPGRIP1L/NPHP8 (By similarity). Does not seem to be strictly required for ciliogenesis (By similarity). Seems to help to recruit PTK2B/PYK2 to cell matrix adhesions, thereby initiating phosphorylation of PTK2B/PYK2 and PTK2B/PYK2-dependent signaling. May play a role in the regulation of intraflagellar transport (IFT) during cilia assembly. Required for normal retina development. In connecting photoreceptor cilia influences the movement of some IFT proteins such as IFT88 and WDR19. Involved in spermatogenesis (By similarity).

Gene Ontology (GO) - Molecular Function for NPHP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity NAS 12006559
genes like me logo Genes that share ontologies with NPHP1: view
genes like me logo Genes that share phenotypes with NPHP1: view

Human Phenotype Ontology for NPHP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NPHP1 Gene

MGI Knock Outs for NPHP1:

Animal Model Products

  • Taconic Biosciences Mouse Models for NPHP1

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for NPHP1 Gene

Localization for NPHP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPHP1 Gene

Cell junction, adherens junction. Cell projection, cilium. Cytoplasm, cytoskeleton, cilium axoneme. Cell junction, tight junction. Note=Colocalizes with E-cadherin and BCAR1 at or near the cell-cell adherens junctions (By similarity). Localized to respiratory cilia axoneme. Localized to the transition zone of respiratory cilia, photoreceptor-connecting cilia and renal monocilia. In cultured renal cells, it localizes diffusely in the cytoplasm but, as cells approach confluence, it accumulates to basolateral tight junctions. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NPHP1 Gene COMPARTMENTS Subcellular localization image for NPHP1 gene
Compartment Confidence
cytosol 5
cytoskeleton 4
nucleus 2
endoplasmic reticulum 1
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for NPHP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005856 cytoskeleton IEA --
GO:0005911 cell-cell junction IDA 21565611
GO:0005923 bicellular tight junction IEA --
GO:0031514 motile cilium IDA 16885411
genes like me logo Genes that share ontologies with NPHP1: view

Pathways & Interactions for NPHP1 Gene

genes like me logo Genes that share pathways with NPHP1: view

SIGNOR curated interactions for NPHP1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for NPHP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006996 organelle organization TAS --
GO:0007588 excretion TAS 9361039
GO:0007632 visual behavior NAS 12205563
GO:0016337 single organismal cell-cell adhesion NAS 12006559
genes like me logo Genes that share ontologies with NPHP1: view

Drugs & Compounds for NPHP1 Gene

(2) Drugs for NPHP1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with NPHP1: view

Transcripts for NPHP1 Gene

Unigene Clusters for NPHP1 Gene

Nephronophthisis 1 (juvenile):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NPHP1 Gene

No ASD Table

Relevant External Links for NPHP1 Gene

GeneLoc Exon Structure for
NPHP1
ECgene alternative splicing isoforms for
NPHP1

Expression for NPHP1 Gene

mRNA expression in normal human tissues for NPHP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NPHP1 Gene

This gene is overexpressed in Testis (x4.4).

Protein differential expression in normal tissues from HIPED for NPHP1 Gene

This gene is overexpressed in Ovary (56.0) and Serum (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NPHP1 Gene



SOURCE GeneReport for Unigene cluster for NPHP1 Gene Hs.280388

mRNA Expression by UniProt/SwissProt for NPHP1 Gene

O15259-NPHP1_HUMAN
Tissue specificity: Widespread expression, with highest levels in pituitary gland, spinal cord, thyroid gland, testis, skeletal muscle, lymph node and trachea. Weakly expressed in heart, kidney and pancreas. Expressed in nasal epithelial cells (at protein level).
genes like me logo Genes that share expression patterns with NPHP1: view

Protein tissue co-expression partners for NPHP1 Gene

Primer Products

In Situ Assay Products

Orthologs for NPHP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPHP1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia NPHP1 35
  • 84.1 (n)
  • 82.67 (a)
NPHP1 36
  • 81 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NPHP1 35
  • 87 (n)
  • 84.05 (a)
NPHP1 36
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nphp1 35
  • 79.39 (n)
  • 78.99 (a)
Nphp1 16
Nphp1 36
  • 79 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia NPHP1 35
  • 99.06 (n)
  • 98.67 (a)
NPHP1 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nphp1 35
  • 84.56 (n)
  • 87.33 (a)
oppossum
(Monodelphis domestica)
Mammalia NPHP1 36
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 71 (a)
OneToMany
-- 36
  • 58 (a)
OneToMany
-- 36
  • 70 (a)
OneToMany
chicken
(Gallus gallus)
Aves NPHP1 35
  • 67.57 (n)
  • 61.62 (a)
NPHP1 36
  • 60 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPHP1 36
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nphp1 35
  • 64.19 (n)
  • 58.61 (a)
Str.19365 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.9955 35
zebrafish
(Danio rerio)
Actinopterygii nphp1 35
  • 56.98 (n)
  • 49.3 (a)
nphp1 36
  • 47 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea nphp-1 36
  • 21 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 42 (a)
OneToOne
Species with no ortholog for NPHP1:
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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 NPHP1 Gene

ENSEMBL:
Gene Tree for NPHP1 (if available)
TreeFam:
Gene Tree for NPHP1 (if available)

Paralogs for NPHP1 Gene

(1) SIMAP similar genes for NPHP1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with NPHP1: view

No data available for Paralogs for NPHP1 Gene

Variants for NPHP1 Gene

Sequence variations from dbSNP and Humsavar for NPHP1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs121907899 Nephronophthisis 1 (NPHP1) 110,163,048(-) AGGAA(A/G)GTAAT reference, missense
rs906815 -- 110,184,919(-) GATGG(C/T)GAACA intron-variant
rs1154652 -- 110,177,146(-) cttga(C/T)atagg intron-variant
rs881302 -- 110,184,573(+) TCAGG(A/G)CTTTG intron-variant
rs979376 -- 110,161,731(-) TTTCT(A/T)TGTAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NPHP1 Gene

Variant ID Type Subtype PubMed ID
nsv510884 CNV Complex 20534489
esv2751812 CNV Loss 17911159
dgv4263n71 CNV Gain 21882294
nsv834329 CNV Gain 17160897
nsv874799 CNV Gain 21882294
nsv458751 CNV Loss 19166990
dgv471n27 CNV Gain 19166990
dgv472n27 CNV Loss 19166990
nsv470479 CNV Gain 18288195
nsv515996 CNV Gain+Loss 19592680
nsv818076 CNV Loss 17921354
dgv4268n71 CNV Gain 21882294
dgv154e55 CNV Loss 17911159
dgv155e55 CNV Gain 17911159
essv3631 CNV CNV 17122850
nsv874809 CNV Gain+Loss 21882294
esv33999 CNV Loss 18971310
dgv473n27 CNV Gain 19166990
nsv874813 CNV Gain 21882294
nsv874814 CNV Gain 21882294
nsv2875 CNV Loss 18451855
nsv874820 CNV Gain 21882294
dgv4271n71 CNV Gain 21882294
nsv458973 CNV Loss 19166990
nsv458984 CNV Loss 19166990
nsv874832 CNV Gain 21882294
esv2663887 CNV Deletion 23128226

Variation tolerance for NPHP1 Gene

Residual Variation Intolerance Score: 38.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.06; 50.58% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NPHP1 Gene

HapMap Linkage Disequilibrium report
NPHP1
Human Gene Mutation Database (HGMD)
NPHP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPHP1 Gene

Disorders for NPHP1 Gene

MalaCards: The human disease database

(26) MalaCards diseases for NPHP1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
nephronophthisis 1, juvenile
  • nephronophthisis 1
senior-loken syndrome-1
  • senior-loken syndrome
joubert syndrome 4
  • jbts4
joubert syndrome with renal anomalies
  • joubert syndrome 4
nphp1-related joubert syndrome
  • joubert syndrome 4
- elite association - COSMIC cancer census association via MalaCards
Search NPHP1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NPHP1_HUMAN
  • Joubert syndrome 4 (JBTS4) [MIM:609583]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. Joubert syndrome type 4 is a phenotypically mild form. {ECO:0000269 PubMed:15138899, ECO:0000269 PubMed:26477546}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Nephronophthisis 1 (NPHP1) [MIM:256100]: An autosomal recessive inherited disease characterized by anemia, polyuria, polydipsia, isosthenuria and death in uremia. Symmetrical destruction of the kidneys involving both tubules and glomeruli occurs. The underlying pathology is a chronic tubulo-interstitial nephropathy with characteristic tubular basement membrane thickening and medullary cyst formation. Associations with extrarenal symptoms, especially ocular lesions, are frequent. The age at death ranges from about 4 to 15 years. {ECO:0000269 PubMed:10839884}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Senior-Loken syndrome 1 (SLSN1) [MIM:266900]: A renal-retinal disorder characterized by progressive wasting of the filtering unit of the kidney (nephronophthisis), with or without medullary cystic renal disease, and progressive eye disease. Typically this disorder becomes apparent during the first year of life. {ECO:0000269 PubMed:9856524}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for NPHP1 Gene

nephronophthisis,juvenile,autosomal recessive,characterized by progressive insidious polyuria due to reduced urinary concentrating ability preceding the decline of renal function and associated with an irregularly thickened tubular basement membrane (TBM) and focal interstitial fibrosis and later diffuse tubular-intersitial changes and medullary cystis,leading to renal failure and death in childhood unless treated with dialysis or renal transplantation

Relevant External Links for NPHP1

Genetic Association Database (GAD)
NPHP1
Human Genome Epidemiology (HuGE) Navigator
NPHP1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NPHP1
genes like me logo Genes that share disorders with NPHP1: view

Publications for NPHP1 Gene

  1. The NPHP1 gene deletion associated with juvenile nephronophthisis is present in a subset of individuals with Joubert syndrome. (PMID: 15138899) Parisi M.A. … Glass I.A. (Am. J. Hum. Genet. 2004) 3 4 23 48 67
  2. Alternative splicing of ADAM15 regulates its interactions with cellular SH3 proteins. (PMID: 19718658) Kleino I. … Saksela K. (J. Cell. Biochem. 2009) 3 23
  3. DNA analysis of AHI1, NPHP1 and CYCLIN D1 in Joubert syndrome patients from the Netherlands. (PMID: 18054307) Kroes H.Y. … Sinke R.J. (Eur J Med Genet 2008) 3 23
  4. Nephrocystin-1 interacts directly with Ack1 and is expressed in human collecting duct. (PMID: 18477472) Eley L. … Sayer J.A. (Biochem. Biophys. Res. Commun. 2008) 3 23
  5. Nephronophthisis-like nephritis associated with fibrous dysplasia of bone. (PMID: 18512082) Bacchetta J. … Cochat P. (Pediatr. Nephrol. 2008) 3 23

Products for NPHP1 Gene

Sources for NPHP1 Gene

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