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Nphp4 nephronophthisis 4 (juvenile) homolog (human) [ Mus musculus (house mouse) ]

Gene ID: 260305, updated on 2-Nov-2024

Summary

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Official Symbol
Nphp4provided by MGI
Official Full Name
nephronophthisis 4 (juvenile) homolog (human)provided by MGI
Primary source
MGI:MGI:2384210
See related
Ensembl:ENSMUSG00000039577 AllianceGenome:MGI:2384210
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
nmf192; 4930564O18Rik
Summary
Acts upstream of or within several processes, including flagellated sperm motility; photoreceptor cell maintenance; and photoreceptor cell outer segment organization. Located in several cellular components, including centriole; ciliary base; and photoreceptor distal connecting cilium. Used to study nephronophthisis 4. Human ortholog(s) of this gene implicated in Joubert syndrome 4; Senior-Loken syndrome; congenital heart disease; nephronophthisis; and nephronophthisis 4. Orthologous to human NPHP4 (nephrocystin 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis adult (RPKM 3.8), cortex adult (RPKM 2.4) and 21 other tissues See more
Orthologs
human all
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Genomic context

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See Nphp4 in Genome Data Viewer
Location:
4 E2; 4 83.14 cM
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (152561163..152647641)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (152476706..152563184)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene chromodomain helicase DNA binding protein 5 Neighboring gene potassium voltage-gated channel, shaker-related subfamily, beta member 2 Neighboring gene predicted gene 16333 Neighboring gene predicted gene, 30734 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes. Keller LC, et al. Curr Biol, 2005 Jun 21. PMID 15964273
  2. NPHP4 is necessary for normal photoreceptor ribbon synapse maintenance and outer segment formation, and for sperm development. Won J, et al. Hum Mol Genet, 2011 Feb 1. PMID 21078623, Free PMC Article
  3. The gene mutated in juvenile nephronophthisis type 4 encodes a novel protein that interacts with nephrocystin. Mollet G, et al. Nat Genet, 2002 Oct. PMID 12244321
  4. A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution. Otto E, et al. Am J Hum Genet, 2002 Nov. PMID 12205563, Free PMC Article
  5. Characterization of the nephrocystin/nephrocystin-4 complex and subcellular localization of nephrocystin-4 to primary cilia and centrosomes. Mollet G, et al. Hum Mol Genet, 2005 Mar 1. PMID 15661758

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A mutation in NPHP4 in mice does not result in renal defects which are observed in human patients with mutations in NPHP4, but they do develop severe photoreceptor degeneration and extinguished rod and cone ERG responses.
    Title: NPHP4 is necessary for normal photoreceptor ribbon synapse maintenance and outer segment formation, and for sperm development.
  2. retinitis pigmentosa GTPase regulator interacting protein 1 and nephrocystin-4 interact strongly in vitro and in vivo, and that they colocalize in the retina
    Title: Interaction of nephrocystin-4 and RPGRIP1 is disrupted by nephronophthisis or Leber congenital amaurosis-associated mutations.
  3. Recessive mutations in the NPHP4 gene, encoding the protein nephroretinin, in humans cause nephronophthisis type 4 and Senior-Loken. There is evolutionary conservation of the NPHP4 gene, with an orhtolog in C. elegans.
    Title: A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (3) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within flagellated sperm motility IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of canonical Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within photoreceptor cell outer segment organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of bicellular tight junction assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of bicellular tight junction assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to ciliary transition zone IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in bicellular tight junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell-cell junction ISO
Inferred from Sequence Orthology
more info
  
located_in cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in centriole IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
located_in centrosome ISO
Inferred from Sequence Orthology
more info
  
is_active_in ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary basal body IEA
Inferred from Electronic Annotation
more info
  
located_in ciliary basal body ISO
Inferred from Sequence Orthology
more info
  
is_active_in ciliary base IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary base IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in ciliary transition zone IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary transition zone IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
is_active_in non-motile cilium IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear body IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in photoreceptor distal connecting cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ribbon synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
nephrocystin-4
Names
nephroretinin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001355738.1 → NP_001342667.1  nephrocystin-4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AF537131, AK038879, AL611970, AL611985, BP753185, CO430221, CV783895
    Consensus CDS
    CCDS38985.1
    UniProtKB/Swiss-Prot
    B1AS30, P59240
    UniProtKB/TrEMBL
    Q8CGY9
    Related
    ENSMUSP00000049920.6, ENSMUST00000056567.6
    Conserved Domains (2) summary
    PHA03247
    Location:447 → 629
    PHA03247; large tegument protein UL36; Provisional
    cd22239
    Location:55 → 1417
    NPHP4; Nephrocystin-4

  2. NM_001355739.1 → NP_001342668.1  nephrocystin-4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AF537131, AK038879, BP753185, CJ108378, CO430221, CV783895
    Consensus CDS
    CCDS38985.1
    UniProtKB/Swiss-Prot
    B1AS30, P59240
    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (2) summary
    PHA03247
    Location:447 → 629
    PHA03247; large tegument protein UL36; Provisional
    cd22239
    Location:55 → 1417
    NPHP4; Nephrocystin-4

  3. NM_153424.2 → NP_700473.2  nephrocystin-4

    See identical proteins and their annotated locations for NP_700473.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1-3 encode the same protein.
    Source sequence(s)
    AK084539, BP753185
    Consensus CDS
    CCDS38985.1
    UniProtKB/Swiss-Prot
    B1AS30, P59240
    UniProtKB/TrEMBL
    Q8CGY9
    Related
    ENSMUSP00000080128.4, ENSMUST00000081393.10
    Conserved Domains (2) summary
    PHA03247
    Location:447 → 629
    PHA03247; large tegument protein UL36; Provisional
    cd22239
    Location:55 → 1417
    NPHP4; Nephrocystin-4

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    152561163..152647641
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006538871.5 → XP_006538934.1  nephrocystin-4 isoform X1

    See identical proteins and their annotated locations for XP_006538934.1

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:477 → 645
    TALPID3; Hedgehog signalling target

  2. XM_006538867.3 → XP_006538930.1  nephrocystin-4 isoform X1

    See identical proteins and their annotated locations for XP_006538930.1

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:477 → 645
    TALPID3; Hedgehog signalling target

  3. XM_006538875.2 → XP_006538938.1  nephrocystin-4 isoform X2

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:187 → 355
    TALPID3; Hedgehog signalling target

  4. XM_006538869.2 → XP_006538932.1  nephrocystin-4 isoform X1

    See identical proteins and their annotated locations for XP_006538932.1

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:477 → 645
    TALPID3; Hedgehog signalling target

  5. XM_006538868.5 → XP_006538931.1  nephrocystin-4 isoform X1

    See identical proteins and their annotated locations for XP_006538931.1

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:477 → 645
    TALPID3; Hedgehog signalling target

  6. XM_006538870.5 → XP_006538933.1  nephrocystin-4 isoform X1

    See identical proteins and their annotated locations for XP_006538933.1

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:477 → 645
    TALPID3; Hedgehog signalling target

  7. XM_011250257.4 → XP_011248559.1  nephrocystin-4 isoform X1

    See identical proteins and their annotated locations for XP_011248559.1

    UniProtKB/TrEMBL
    Q8CGY9
    Conserved Domains (1) summary
    pfam15324
    Location:477 → 645
    TALPID3; Hedgehog signalling target

  8. XM_036164135.1 → XP_036020028.1  nephrocystin-4 isoform X3

    Conserved Domains (1) summary
    cd22239
    Location:188 → 724
    NPHP4; Nephrocystin-4

RNA

  1. XR_001784146.2 RNA Sequence

  2. XR_004941906.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P59240.2 GenPept UniProtKB/Swiss-Prot:P59240

Gene LinkOut

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