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Aliases for NPHP4 Gene

Aliases for NPHP4 Gene

  • Nephrocystin 4 2 3 5
  • Nephroretinin 2 3 4
  • Nephronophthisis 4 2 3
  • POC10 Centriolar Protein Homolog (Chlamydomonas) 2
  • POC10 Centriolar Protein Homolog 3
  • Nephrocystin-4 3
  • KIAA0673 4
  • POC10 3
  • SLSN4 3

External Ids for NPHP4 Gene

Previous GeneCards Identifiers for NPHP4 Gene

  • GC01U990494
  • GC01M005731
  • GC01M005519
  • GC01M005632
  • GC01M005858
  • GC01M005071
  • GC01M005922

Summaries for NPHP4 Gene

Entrez Gene Summary for NPHP4 Gene

  • This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

GeneCards Summary for NPHP4 Gene

NPHP4 (Nephrocystin 4) is a Protein Coding gene. Diseases associated with NPHP4 include Nephronophthisis 4 and Senior-Loken Syndrome 4. Among its related pathways are Signaling by GPCR and Regulation of PLK1 Activity at G2/M Transition. GO annotations related to this gene include structural molecule activity.

UniProtKB/Swiss-Prot for NPHP4 Gene

  • Involved in the organization of apical junctions in kidney cells together with NPHP1 and RPGRIP1L/NPHP8. Does not seem to be strictly required for ciliogenesis.

Gene Wiki entry for NPHP4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPHP4 Gene

Genomics for NPHP4 Gene

Regulatory Elements for NPHP4 Gene

Enhancers for NPHP4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around NPHP4 on UCSC Golden Path with GeneCards custom track

Promoters for NPHP4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for NPHP4 Gene

Chromosome:
1
Start:
5,862,808 bp from pter
End:
5,992,505 bp from pter
Size:
129,698 bases
Orientation:
Minus strand

Genomic View for NPHP4 Gene

Genes around NPHP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPHP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPHP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPHP4 Gene

Proteins for NPHP4 Gene

  • Protein details for NPHP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75161-NPHP4_HUMAN
    Recommended name:
    Nephrocystin-4
    Protein Accession:
    O75161
    Secondary Accessions:
    • Q8IWC0

    Protein attributes for NPHP4 Gene

    Size:
    1426 amino acids
    Molecular mass:
    157598 Da
    Quaternary structure:
    • Interacts with NPHP1 and RPGRIP1L/NPHP8, and can bridge the interaction between those two proteins. Interacts with IQCB1; the interaction likely requires additional interactors. Interacts with RPGRIP1. Weakly interacts with CEP164.

    Alternative splice isoforms for NPHP4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NPHP4 Gene

Post-translational modifications for NPHP4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NPHP4 Gene

No data available for DME Specific Peptides for NPHP4 Gene

Domains & Families for NPHP4 Gene

Protein Domains for NPHP4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NPHP4 Gene

Graphical View of Domain Structure for InterPro Entry

O75161

UniProtKB/Swiss-Prot:

NPHP4_HUMAN :
  • Belongs to the NPHP4 family.
Family:
  • Belongs to the NPHP4 family.
genes like me logo Genes that share domains with NPHP4: view

No data available for Gene Families for NPHP4 Gene

Function for NPHP4 Gene

Molecular function for NPHP4 Gene

UniProtKB/Swiss-Prot Function:
Involved in the organization of apical junctions in kidney cells together with NPHP1 and RPGRIP1L/NPHP8. Does not seem to be strictly required for ciliogenesis.

Gene Ontology (GO) - Molecular Function for NPHP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity NAS 12006559
GO:0005515 protein binding IPI 12244321
genes like me logo Genes that share ontologies with NPHP4: view
genes like me logo Genes that share phenotypes with NPHP4: view

Human Phenotype Ontology for NPHP4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for NPHP4 Gene

Localization for NPHP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPHP4 Gene

Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cell junction, tight junction. Note=In cultured renal cells, it localizes diffusely in the cytoplasm but, as cells approach confluence, it accumulates to basolateral tight junctions.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NPHP4 Gene COMPARTMENTS Subcellular localization image for NPHP4 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 3

Gene Ontology (GO) - Cellular Components for NPHP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 21399614
GO:0005829 cytosol TAS --
GO:0005911 cell-cell junction IDA 21565611
GO:0005923 bicellular tight junction IEA --
genes like me logo Genes that share ontologies with NPHP4: view

Pathways & Interactions for NPHP4 Gene

genes like me logo Genes that share pathways with NPHP4: view

Gene Ontology (GO) - Biological Process for NPHP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction NAS 12244321
GO:0007632 visual behavior NAS 12205563
GO:0016337 single organismal cell-cell adhesion NAS 12006559
GO:0030036 actin cytoskeleton organization NAS 12006559
GO:0030317 sperm motility IEA --
genes like me logo Genes that share ontologies with NPHP4: view

No data available for SIGNOR curated interactions for NPHP4 Gene

Drugs & Compounds for NPHP4 Gene

No Compound Related Data Available

Transcripts for NPHP4 Gene

Unigene Clusters for NPHP4 Gene

Nephronophthisis 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPHP4 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b
SP1: -
SP2: -
SP3:

Relevant External Links for NPHP4 Gene

GeneLoc Exon Structure for
NPHP4
ECgene alternative splicing isoforms for
NPHP4

Expression for NPHP4 Gene

mRNA expression in normal human tissues for NPHP4 Gene

Protein differential expression in normal tissues from HIPED for NPHP4 Gene

This gene is overexpressed in Heart (55.4) and Adipocyte (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NPHP4 Gene



Protein tissue co-expression partners for NPHP4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NPHP4 Gene:

NPHP4

SOURCE GeneReport for Unigene cluster for NPHP4 Gene:

Hs.462348

mRNA Expression by UniProt/SwissProt for NPHP4 Gene:

O75161-NPHP4_HUMAN
Tissue specificity: Expressed in kidney, skeletal muscle, heart and liver, and to a lesser extent in brain and lung.
genes like me logo Genes that share expression patterns with NPHP4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for NPHP4 Gene

Orthologs for NPHP4 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPHP4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia NPHP4 34
  • 80.47 (n)
  • 78.53 (a)
NPHP4 35
  • 78 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NPHP4 34
  • 81.72 (n)
  • 79.07 (a)
NPHP4 35
  • 74 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nphp4 34
  • 80.07 (n)
  • 78.73 (a)
Nphp4 16
Nphp4 35
  • 78 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia NPHP4 34
  • 96.01 (n)
  • 94.64 (a)
rat
(Rattus norvegicus)
Mammalia Nphp4 34
  • 79.83 (n)
  • 78.11 (a)
oppossum
(Monodelphis domestica)
Mammalia NPHP4 35
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NPHP4 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPHP4 34
  • 64.16 (n)
  • 56.31 (a)
NPHP4 35
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPHP4 35
  • 59 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii Dr.15520 34
nphp4 34
  • 55.39 (n)
  • 47.77 (a)
nphp4 35
  • 45 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea nphp-4 34
  • 38.66 (n)
  • 27.77 (a)
nphp-4 35
  • 23 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 36 (a)
OneToOne
Species where no ortholog for NPHP4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for NPHP4 Gene

ENSEMBL:
Gene Tree for NPHP4 (if available)
TreeFam:
Gene Tree for NPHP4 (if available)

Paralogs for NPHP4 Gene

(1) SIMAP similar genes for NPHP4 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with NPHP4: view

No data available for Paralogs for NPHP4 Gene

Variants for NPHP4 Gene

Sequence variations from dbSNP and Humsavar for NPHP4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs28940891 Nephronophthisis 4 (NPHP4) 5,874,946(-) GTTCT(C/T)TGAGT nc-transcript-variant, reference, missense
rs373962831 Nephronophthisis 4 (NPHP4) 5,890,912(+) GTCTC(C/T)GTCCC intron-variant, nc-transcript-variant, reference, missense
rs17472401 - 5,880,183(+) GACCC(A/G)AGATC nc-transcript-variant, reference, missense
rs145078518 Senior-Loken syndrome 4 (SLSN4) 5,986,283(+) CCAGT(A/C/T)GTTCA intron-variant, nc-transcript-variant, reference, missense, utr-variant-5-prime
rs12142270 - 5,986,204(+) ATGCC(A/G)TGGAT intron-variant, nc-transcript-variant, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for NPHP4 Gene

Variant ID Type Subtype PubMed ID
dgv9e212 CNV loss 25503493
esv2737584 CNV deletion 23290073
esv2737695 CNV deletion 23290073
esv2737806 CNV deletion 23290073
esv2737917 CNV deletion 23290073
esv2763437 CNV loss 21179565
esv3303661 CNV mobile element insertion 20981092
esv3310166 CNV mobile element insertion 20981092
esv3339145 CNV insertion 20981092
esv33437 CNV gain 17666407
esv3373910 CNV duplication 20981092
esv3395207 CNV duplication 20981092
esv3427069 CNV insertion 20981092
esv3585100 CNV loss 21293372
nsv1008071 CNV loss 25217958
nsv506919 OTHER sequence alteration 20534489
nsv508723 CNV insertion 20534489
nsv520207 CNV loss 19592680
nsv545173 CNV gain 21841781
nsv545174 CNV loss 21841781
nsv545175 CNV loss 21841781
nsv743 CNV deletion 18451855
nsv825586 CNV loss 20364138
nsv831203 CNV loss 17160897
nsv831314 CNV loss 17160897

Variation tolerance for NPHP4 Gene

Residual Variation Intolerance Score: 99.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.41; 77.14% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NPHP4 Gene

Human Gene Mutation Database (HGMD)
NPHP4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPHP4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPHP4 Gene

Disorders for NPHP4 Gene

MalaCards: The human disease database

(20) MalaCards diseases for NPHP4 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
nephronophthisis 4
  • juvenile nephronophthisis
senior-loken syndrome 4
  • slsn4
senior-loken syndrome-1
  • senior-loken syndrome
nephronophthisis
  • medullary cystic disease
ciliopathy
- elite association - COSMIC cancer census association via MalaCards
Search NPHP4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NPHP4_HUMAN
  • Nephronophthisis 4 (NPHP4) [MIM:606966]: An autosomal recessive inherited disease resulting in end-stage renal disease at age ranging between 6 and 35 years. It is a progressive tubulo-interstitial kidney disorder characterized by polydipsia, polyuria, anemia and growth retardation. The most prominent histological features are modifications of the tubules with thickening of the basement membrane, interstitial fibrosis and, in the advanced stages, medullary cysts. {ECO:0000269 PubMed:12205563, ECO:0000269 PubMed:12244321, ECO:0000269 PubMed:15776426}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Ciliary dysfunction leads to a broad spectrum of disorders, collectively termed ciliopathies. Overlapping clinical features include retinal degeneration, renal cystic disease, skeletal abnormalities, fibrosis of various organ, and a complex range of anatomical and functional defects of the central and peripheral nervous system. The ciliopathy range of diseases includes Meckel-Gruber syndrome, Bardet-Biedl syndrome, Joubert syndrome, nephronophtisis, Senior-Loken syndrome, and Jeune asphyxiating thoracic dystrophy among others. Single-locus allelism is insufficient to explain the variable penetrance and expressivity of such disorders, leading to the suggestion that variations across multiple sites of the ciliary proteome, including NPHP4, influence the clinical outcome (PubMed:21258341). {ECO:0000269 PubMed:21258341}.
  • Senior-Loken syndrome 4 (SLSN4) [MIM:606996]: 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:12244321, ECO:0000269 PubMed:15776426}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NPHP4

Genetic Association Database (GAD)
NPHP4
Human Genome Epidemiology (HuGE) Navigator
NPHP4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NPHP4
genes like me logo Genes that share disorders with NPHP4: view

No data available for Genatlas for NPHP4 Gene

Publications for NPHP4 Gene

  1. Mutational analysis of the NPHP4 gene in 250 patients with nephronophthisis. (PMID: 15776426) Hoefele J. … Hildebrandt F. (Hum. Mutat. 2005) 3 4 22 46 65
  2. A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution. (PMID: 12205563) Otto E. … Hildebrandt F. (Am. J. Hum. Genet. 2002) 2 3 4 22 65
  3. Mutations in the gene encoding the basal body protein RPGRIP1L, a nephrocystin-4 interactor, cause Joubert syndrome. (PMID: 17558407) Arts H.H. … Roepman R. (Nat. Genet. 2007) 3 4 22 65
  4. The gene mutated in juvenile nephronophthisis type 4 encodes a novel protein that interacts with nephrocystin. (PMID: 12244321) Mollet G. … Saunier S. (Nat. Genet. 2002) 3 4 22 65
  5. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. (PMID: 22863007) Chaki M. … Hildebrandt F. (Cell 2012) 3 4 65

Products for NPHP4 Gene

Sources for NPHP4 Gene

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