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

Summary

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

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_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (1)
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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)

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
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
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