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Aliases for NPHP4 Gene

Aliases for NPHP4 Gene

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

Epigenetics Products

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

Genomic Location for NPHP4 Gene

5,862,808 bp from pter
5,992,505 bp from pter
129,698 bases
Minus strand

Genomic View for NPHP4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q8IWC0

    Protein attributes for NPHP4 Gene

    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


neXtProt entry for NPHP4 Gene

Proteomics data for NPHP4 Gene at MOPED

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


Suggested Antigen Peptide Sequences for NPHP4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NPHP4 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

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

Jensen Localization Image for NPHP4 Gene COMPARTMENTS Subcellular localization image for NPHP4 gene
Compartment Confidence
cytoskeleton 5
cytosol 4

Gene Ontology (GO) - Cellular Components for NPHP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm --
GO:0005813 centrosome IDA 21399614
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton --
GO:0005911 cell-cell junction IDA 21565611
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:0006996 organelle organization TAS --
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
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:

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

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

Relevant External Links for NPHP4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

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, MOPED, and MaxQB for NPHP4 Gene

SOURCE GeneReport for Unigene cluster for NPHP4 Gene Hs.462348

mRNA Expression by UniProt/SwissProt for NPHP4 Gene

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

Protein tissue co-expression partners for NPHP4 Gene

- Elite partner

Primer Products

In Situ Assay 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
(Bos Taurus)
Mammalia NPHP4 35
  • 80.47 (n)
  • 78.53 (a)
NPHP4 36
  • 78 (a)
(Canis familiaris)
Mammalia NPHP4 35
  • 81.72 (n)
  • 79.07 (a)
NPHP4 36
  • 74 (a)
(Mus musculus)
Mammalia Nphp4 35
  • 80.07 (n)
  • 78.73 (a)
Nphp4 16
Nphp4 36
  • 78 (a)
(Pan troglodytes)
Mammalia NPHP4 35
  • 96.01 (n)
  • 94.64 (a)
(Rattus norvegicus)
Mammalia Nphp4 35
  • 79.83 (n)
  • 78.11 (a)
(Monodelphis domestica)
Mammalia NPHP4 36
  • 66 (a)
(Ornithorhynchus anatinus)
Mammalia NPHP4 36
  • 61 (a)
(Gallus gallus)
Aves NPHP4 35
  • 64.16 (n)
  • 56.31 (a)
NPHP4 36
  • 54 (a)
(Anolis carolinensis)
Reptilia NPHP4 36
  • 59 (a)
(Danio rerio)
Actinopterygii Dr.15520 35
nphp4 35
  • 55.39 (n)
  • 47.77 (a)
nphp4 36
  • 45 (a)
(Caenorhabditis elegans)
Secernentea nphp-4 35
  • 38.66 (n)
  • 27.77 (a)
nphp-4 36
  • 23 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 36 (a)
Species with no ortholog for NPHP4:
  • 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

Gene Tree for NPHP4 (if available)
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 MAF
rs472651 -- 5,872,457(-) TTAAC(A/G)CTTTT intron-variant
rs485942 -- 5,976,155(+) GGTGG(A/T)GCCGT intron-variant
rs487654 -- 5,889,592(-) GAGCC(A/G)GGTCC intron-variant
rs489933 -- 5,865,741(-) TGACT(A/G)TGAAG intron-variant
rs490953 -- 5,923,573(-) accag(C/G)cccta intron-variant

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

Variant ID Type Subtype PubMed ID
nsv508723 CNV Insertion 20534489
nsv871294 CNV Loss 21882294
nsv831203 CNV Loss 17160897
nsv871389 CNV Loss 21882294
nsv871082 CNV Loss 21882294
nsv871579 CNV Loss 21882294
esv2737584 CNV Deletion 23290073
esv2737695 CNV Deletion 23290073
esv2737806 CNV Deletion 23290073
nsv825586 CNV Loss 20364138
esv267940 CNV Insertion 20981092
esv274438 CNV Insertion 20981092
esv2737917 CNV Deletion 23290073
nsv831314 CNV Loss 17160897
nsv743 CNV Loss 18451855
nsv870809 CNV Loss 21882294
nsv506919 CNV Insertion 20534489
esv33437 CNV Gain 17666407
nsv520207 CNV Loss 19592680
nsv871226 CNV Loss 21882294

Variation tolerance for NPHP4 Gene

Residual Variation Intolerance Score: 99.78% 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

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

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

Disorders for NPHP4 Gene

MalaCards: The human disease database

(22) 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
cogan syndrome
  • diffuse interstitual keratitis
  • medullary cystic kidney disease 1
senior-loken syndrome-1
  • senior-loken syndrome
- elite association
Search NPHP4 in MalaCards View complete list of genes associated with diseases


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

No data available for Genatlas for NPHP4 Gene

Publications for NPHP4 Gene

  1. 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 23 67
  2. Normal ciliogenesis requires synergy between the cystic kidney disease genes MKS-3 and NPHP-4. (PMID: 20150540) Williams C.L. … Yoder B.K. (J. Am. Soc. Nephrol. 2010) 23 67
  3. Nephrocystin-1 and nephrocystin-4 are required for epithelial morphogenesis and associate with PALS1/PATJ and Par6. (PMID: 19755384) Delous M. … Saunier S. (Hum. Mol. Genet. 2009) 23 67
  4. Mutation analysis in nephronophthisis using a combined approach of homozygosity mapping, CEL I endonuclease cleavage, and direct sequencing. (PMID: 18076122) Otto E.A. … Hildebrandt F. (Hum. Mutat. 2008) 23 67
  5. Functional redundancy of the B9 proteins and nephrocystins in Caenorhabditis elegans ciliogenesis. (PMID: 18337471) Williams C.L. … Yoder B.K. (Mol. Biol. Cell 2008) 23 67

Products for NPHP4 Gene

Sources for NPHP4 Gene

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