Nphp3 nephronophthisis 3 (adolescent) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nphp3provided by MGI
Official Full Name: nephronophthisis 3 (adolescent)provided by MGI
Primary source: MGI:MGI:1921275
See related: Ensembl:ENSMUSG00000032558 AllianceGenome:MGI:1921275
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: pcy; C230078J01; 3632410F03Rik; D330020E01Rik
Summary: Involved in several processes, including cilium assembly; determination of left/right symmetry; and maintenance of animal organ identity. Acts upstream of or within several processes, including establishment or maintenance of cell polarity; extracellular matrix organization; and non-motile cilium assembly. Located in ciliary base and ciliary inversin compartment. Is expressed in embryo and secondary heart field. Used to study autosomal dominant polycystic kidney disease and nephronophthisis 3. Human ortholog(s) of this gene implicated in Meckel syndrome 7; hypertension; nephronophthisis; nephronophthisis 3; and renal-hepatic-pancreatic dysplasia. Orthologous to human NPHP3 (nephrocystin 3). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Ubiquitous expression in limb E14.5 (RPKM 5.9), bladder adult (RPKM 3.2) and 28 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 9 F1; 9 56.11 cM

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (103879743..103921010)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (104002544..104043811)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia.
Title: Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia.
The pcy mutation generates a hypomorphic Nphp3 allele that is responsible for the cystic kidney disease phenotype, whereas complete loss of Nphp3 function results in situs inversus, congenital heart defects, and embryonic lethality in mice.
Title: Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.
a homozygous missense mutation in Nphp3 is probably responsible for the polycystic kidney disease (pcy) mouse phenotype
Title: Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis.

Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

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

Chemically induced (ENU) (1)
Endonuclease-mediated (2)
Spontaneous (1) 1 citation
Targeted (2) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

AI550417 (e-PCR)
- UniSTS:164415

14.MMHAP63FLE2.seq (e-PCR)
- UniSTS:123224

D9Mgc30 (e-PCR), detects polymorphism
- UniSTS:142771

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in atrial septum development	IEA Inferred from Electronic Annotation more info
involved_in atrial septum development	ISO Inferred from Sequence Orthology more info
involved_in cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in convergent extension	IBA Inferred from Biological aspect of Ancestor more info
involved_in convergent extension involved in gastrulation	IEA Inferred from Electronic Annotation more info
involved_in convergent extension involved in gastrulation	ISO Inferred from Sequence Orthology more info
involved_in determination of intestine left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of intestine left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of left/right symmetry	IBA Inferred from Biological aspect of Ancestor more info
involved_in determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of left/right symmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of liver left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of liver left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of pancreatic left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of pancreatic left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of stomach left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of stomach left/right asymmetry	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment or maintenance of cell polarity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within extracellular matrix organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart looping	IEA Inferred from Electronic Annotation more info
involved_in heart looping	ISO Inferred from Sequence Orthology more info
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within kidney morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lung development	IEA Inferred from Electronic Annotation more info
involved_in lung development	ISO Inferred from Sequence Orthology more info
involved_in maintenance of animal organ identity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maintenance of animal organ identity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within non-motile cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of protein binding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of Wnt signaling pathway, planar cell polarity pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of Wnt signaling pathway, planar cell polarity pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureter development	IEA Inferred from Electronic Annotation more info
involved_in ureter development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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 inversin compartment	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary inversin compartment	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info

General protein information

Go to the top of the page Help

Preferred Names: nephrocystin-3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_028721.3 → NP_082997.3 nephrocystin-3 isoform a

See identical proteins and their annotated locations for NP_082997.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform a).

Source sequence(s)

AK133217, AK173327, BM219539

Consensus CDS

CCDS40749.1

UniProtKB/Swiss-Prot

D6RHB4, E9Q5X1, E9QN29, Q69Z39, Q7TNH6, Q8C798, Q8C7Z3, Q9D6D1

UniProtKB/TrEMBL

H9KV07

Related

ENSMUSP00000035167.9, ENSMUST00000035167.15

Conserved Domains (7) summary

sd00006
Location:1130 → 1158

TPR; TPR repeat [structural motif]

pfam03938
Location:120 → 202

OmpH; Outer membrane protein (OmpH-like)

pfam04871
Location:113 → 199

Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region

pfam12711
Location:76 → 145

Kinesin-relat_1; Kinesin motor

pfam13374
Location:1130 → 1169

TPR_10; Tetratricopeptide repeat

pfam13424
Location:1085 → 1162

TPR_12; Tetratricopeptide repeat

cl21455
Location:502 → 570

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_172460.1 → NP_766048.1 nephrocystin-3 isoform b

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses a different splice site in the 5' CDS and lacks all of the downstream CDS, compared to variant 1. The resulting protein (isoform b) is much shorter and has a distinct C-terminus when it is compared to isoform a.

Source sequence(s)

AK052281, AK133217

UniProtKB/Swiss-Prot

Q7TNH6

Related

ENSMUST00000191919.2

Conserved Domains (3) summary

pfam03938
Location:120 → 202

OmpH; Outer membrane protein (OmpH-like)

pfam04871
Location:113 → 199

Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region

pfam12711
Location:76 → 145

Kinesin-relat_1; Kinesin motor