Nphp1 nephronophthisis 1 (juvenile) homolog (human) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nphp1provided by MGI
Official Full Name: nephronophthisis 1 (juvenile) homolog (human)provided by MGI
Primary source: MGI:MGI:1858233
See related: Ensembl:ENSMUSG00000027378 AllianceGenome:MGI:1858233
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
Summary: Involved in several processes, including photoreceptor cell outer segment organization; retina development in camera-type eye; and spermatid differentiation. Located in ciliary base; cytoplasm; and photoreceptor distal connecting cilium. Is expressed in several structures, including central nervous system; genitourinary system; gut; respiratory system; and white fat. Used to study nephronophthisis 1. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome; Joubert syndrome 4; Senior-Loken syndrome; nephronophthisis; and nephronophthisis 1. Orthologous to human NPHP1 (nephrocystin 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in testis adult (RPKM 216.9) and CNS E11.5 (RPKM 14.7) See more
Orthologs: human all
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Genomic context

Location:: 2 F1; 2 62.09 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (127582652..127630833, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (127740732..127788913, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

An Nphp1 knockout mouse model targeting exon 2-20 demonstrates characteristic phenotypes of human nephronophthisis.
Title: An Nphp1 knockout mouse model targeting exon 2-20 demonstrates characteristic phenotypes of human nephronophthisis.
Differential requirement of NPHP1 for compartmentalized protein localization during photoreceptor outer segment development and maintenance.
Title: Differential requirement of NPHP1 for compartmentalized protein localization during photoreceptor outer segment development and maintenance.
PC-1 polyproline motif interacts with the SH3 domain of NPHP1.
Title: Nephrocystin-1 forms a complex with polycystin-1 via a polyproline motif/SH3 domain interaction and regulates the apoptotic response in mammals.
Nphp1 affect the sorting mechanism and transportation efficiency of the traffic machinery between inner and outer segments of photoreceptors.
Title: Essential role of nephrocystin in photoreceptor intraflagellar transport in mouse.
homozygous Nphp1 mutant mice were viable without renal manifestations of nephronophthisis, but males were infertile with oligoteratozoospermia
Title: Targeted disruption of Nphp1 causes male infertility due to defects in the later steps of sperm morphogenesis in mice.
Nphp1 is most abundantly expressed in tissues rich in highly ciliated cells, such as olfactory sensory neurons, and is predicted to be important to cilia.
Title: Tissue expression patterns identify mouse cilia genes.
casein kinase 2 induces PACS-1 binding of nephrocystin and targeting to cilia
Title: Phosphorylation by casein kinase 2 induces PACS-1 binding of nephrocystin and targeting to cilia.

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Variation

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Alleles

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

Endonuclease-mediated (2) 1 citation
Targeted (5) 1 citation

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
involved_in cell projection organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell outer segment organization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of bicellular tight junction assembly	ISO Inferred from Sequence Orthology more info
involved_in protein localization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein localization involved in establishment of planar polarity	IBA Inferred from Biological aspect of Ancestor more info
involved_in retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatid differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in adherens junction	IEA Inferred from Electronic Annotation more info
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 ciliary base	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary transition zone	IDA Inferred from Direct Assay more info	PubMed
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in motile cilium	ISO Inferred from Sequence Orthology more info
located_in motile cilium	ISS Inferred from Sequence or Structural Similarity 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

General protein information

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Preferred Names: nephrocystin-1

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_001291012.1 → NP_001277941.1 nephrocystin-1 isoform b

See identical proteins and their annotated locations for NP_001277941.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (b) that is 1 aa shorter than isoform a.

Source sequence(s)

AA107655, AK159627, BY147655

Consensus CDS

CCDS71140.1

UniProtKB/Swiss-Prot

Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2

UniProtKB/TrEMBL

Q3TWM5

Related

ENSMUSP00000105986.2, ENSMUST00000110357.2

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001291013.1 → NP_001277942.1 nephrocystin-1 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses two alternate in-frame splice sites in the central coding region, compared to variant 1, resulting in an isoform (c) that is 2 aa shorter than isoform a.

Source sequence(s)

AA107655, AL844204, BY147655

UniProtKB/TrEMBL

Q0VF70

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001355429.1 → NP_001342358.1 nephrocystin-1 isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (d) that is 1 aa shorter than isoform a.

Source sequence(s)

AL844204

UniProtKB/Swiss-Prot

Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2

UniProtKB/TrEMBL

Q0VF70

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001369236.1 → NP_001356165.1 nephrocystin-1 isoform e

Status: VALIDATED

Source sequence(s)

AL844204

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001421487.1 → NP_001408416.1 nephrocystin-1 isoform f

Status: VALIDATED

Source sequence(s)

AL844204

UniProtKB/Swiss-Prot

Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2
NM_001421488.1 → NP_001408417.1 nephrocystin-1 isoform g

Status: VALIDATED

Source sequence(s)

AL844204
NM_001421489.1 → NP_001408418.1 nephrocystin-1 isoform h

Status: VALIDATED

Source sequence(s)

AL844204
NM_001421490.1 → NP_001408419.1 nephrocystin-1 isoform i

Status: VALIDATED

Source sequence(s)

AL844204
NM_001421491.1 → NP_001408420.1 nephrocystin-1 isoform j

Status: VALIDATED

Source sequence(s)

AL844204
NM_001421492.1 → NP_001408421.1 nephrocystin-1 isoform k

Status: VALIDATED

Source sequence(s)

AL844204

Related

ENSMUST00000144938.2
NM_001421493.1 → NP_001408422.1 nephrocystin-1 isoform l

Status: VALIDATED

Source sequence(s)

AL844204
NM_016902.4 → NP_058598.1 nephrocystin-1 isoform a

See identical proteins and their annotated locations for NP_058598.1

Status: VALIDATED

Description

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

Source sequence(s)

AA107655, AK159627, BY147655, BY353783

Consensus CDS

CCDS16709.1

UniProtKB/Swiss-Prot

Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2

UniProtKB/TrEMBL

A2APS1

Related

ENSMUSP00000028857.8, ENSMUST00000028857.14

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

127582652..127630833 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030251881.1 → XP_030107741.1 nephrocystin-1 isoform X5

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
XM_036162392.1 → XP_036018285.1 nephrocystin-1 isoform X2

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
XM_011239696.2 → XP_011237998.1 nephrocystin-1 isoform X3

Conserved Domains (1) summary

cd11770
Location:160 → 212

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)