NPHP1 nephrocystin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPHP1provided by HGNC
Official Full Name: nephrocystin 1provided by HGNC
Primary source: HGNC:HGNC:7905
See related: Ensembl:ENSG00000144061 MIM:607100; AllianceGenome:HGNC:7905
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NPH1; JBTS4; SLSN1
Summary: This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Biased expression in testis (RPKM 11.1), thyroid (RPKM 3.0) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q13

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (110123348..110205013, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (110588729..110670393)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (110880925..110962590, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[C/EBPbeta mediates expressions of downstream inflammatory factors of the tumor necrosis factor-alpha signaling pathway in renal tubular epithelial cells with NPHP1 knockdown].
Title: [C/EBPβ mediates expressions of downstream inflammatory factors of the tumor necrosis factor-α signaling pathway in renal tubular epithelial cells with NPHP1 knockdown].
Scalp Tumor and Hydroureteronephrosis in Patients with Nephronophthisis and Homozygous NPHP1 Deletion.
Title: Scalp Tumor and Hydroureteronephrosis in Patients with Nephronophthisis and Homozygous NPHP1 Deletion.
Copy-number variation of the NPHP1 gene in patients with juvenile Nephronophthisis.
Title: Copy-number variation of the NPHP1 gene in patients with juvenile Nephronophthisis.
A case report of two Chinese monozygotic twins with NPHP1 gene-associated nephronophthisis undergoing kidney transplantation from a related living-donor.
Title: A case report of two Chinese monozygotic twins with NPHP1 gene-associated nephronophthisis undergoing kidney transplantation from a related living-donor.
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.
SENIOR-LOKEN SYNDROME: A Case Series and Review of the Renoretinal Phenotype and Advances of Molecular Diagnosis.
Title: SENIOR-LØKEN SYNDROME: A Case Series and Review of the Renoretinal Phenotype and Advances of Molecular Diagnosis.
NPHP1 gene-associated nephronophthisis is associated with an occult retinopathy.
Title: NPHP1 gene-associated nephronophthisis is associated with an occult retinopathy.
Clinical and pathological features and varied mutational spectra of pathogenic genes in 55 Chinese patients with nephronophthisis.
Title: Clinical and pathological features and varied mutational spectra of pathogenic genes in 55 Chinese patients with nephronophthisis.
Homozygous full gene deletion of the NPHP1 gene was identified in a Chinese family with NPHP, which was the molecular pathogenic basis of this disorder.
Title: A case report of NPHP1 deletion in Chinese twins with nephronophthisis.
The genetic investigation revealed a novel homozygous nonsense mutation, p. E697X,37 and a novel homozygous missense mutation, p. F691 L, in the NPHP1 gene. His parents and fraternal twin harbored heterozygous mutations of the two loci and had no renal symptoms. His elder sister developed ESRD and died at 23 years of age. CONCLUSIONS: The report indicated that adult NPHP should be taken into consideration for adults with
Title: Two novel homozygous mutations in NPHP1 lead to late onset end-stage renal disease: a case report of an adult nephronophthisis in a Chinese intermarriage family.

Submit: New GeneRIF Correction See all GeneRIFs (41)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Joubert syndrome with renal defect MedGen: C1846790 OMIM: 609583 GeneReviews: Joubert Syndrome	not available
Nephronophthisis 1 MedGen: C1855681 OMIM: 256100 GeneReviews: Nephronophthisis-Related Ciliopathies	not available
Senior-Loken syndrome 1 MedGen: C4551559 OMIM: 266900 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-22078 (e-PCR)
- UniSTS:78629

RH47050 (e-PCR)
- UniSTS:91703

D1S1423 (e-PCR)
- UniSTS:149619

GDB:451658 (e-PCR)
- UniSTS:157338

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	NAS Non-traceable Author Statement more info	PubMed
involved_in cell projection organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of bicellular tight junction assembly	IMP Inferred from Mutant Phenotype 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	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed
involved_in spermatid differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in visual behavior	NAS Non-traceable Author Statement 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	IDA Inferred from Direct Assay more info	PubMed
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	TAS Traceable Author Statement more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in motile cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nephrocystin-1

Names: juvenile nephronophthisis 1 protein; nephronophthisis 1 (juvenile)

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.

Genomic

NG_008287.1 RefSeqGene

Range

5050..86715

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000272.5 → NP_000263.2 nephrocystin-1 isoform 1

See identical proteins and their annotated locations for NP_000263.2

Status: REVIEWED

Description

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

Source sequence(s)

AF023674, BC062574, DB454094

Consensus CDS

CCDS2086.1

UniProtKB/TrEMBL

A0A6Q8PHD4

Related

ENSP00000313169.4, ENST00000316534.8

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001128178.3 → NP_001121650.1 nephrocystin-1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice donor site in the mid-coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.

Source sequence(s)

AJ001815, AK225600, BC062574, DB454094

Consensus CDS

CCDS46386.1

UniProtKB/TrEMBL

A0A6Q8PHD4

Related

ENSP00000389879.3, ENST00000445609.7

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001128179.3 → NP_001121651.1 nephrocystin-1 isoform 4

See identical proteins and their annotated locations for NP_001121651.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame segment in the 5' coding region, and uses two alternate in-frame splice sites in the mid-coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.

Source sequence(s)

AJ001815, BC062574, DB454094

Consensus CDS

CCDS46384.1

UniProtKB/TrEMBL

A0A6Q8PHD4

Related

ENSP00000502475.1, ENST00000676053.1

Conserved Domains (1) summary

cd11770
Location:94 → 147

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001374256.1 → NP_001361185.1 nephrocystin-1 isoform 5

Status: REVIEWED

Source sequence(s)

AC140479, AJ001815, AK299011

UniProtKB/TrEMBL

A0A6Q8PHD4, B4DQY0

Related

ENSP00000502639.1, ENST00000676028.1

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_001374257.1 → NP_001361186.1 nephrocystin-1 isoform 6

Status: REVIEWED

Source sequence(s)

AC013268, AC140479

UniProtKB/TrEMBL

A0A6Q8PGI7

Related

ENSP00000502265.1, ENST00000674677.1

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
NM_207181.4 → NP_997064.2 nephrocystin-1 isoform 2

See identical proteins and their annotated locations for NP_997064.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice acceptor site in the mid-coding region, compared to variant 1, resulting in an isoform (2) that lacks a residue, compared to isoform 1.

Source sequence(s)

AJ001815, BC062574, DB454094

Consensus CDS

CCDS46385.1

UniProtKB/Swiss-Prot

O14837, O15259

UniProtKB/TrEMBL

A0A6Q8PHD4

Related

ENSP00000376953.3, ENST00000393272.7

Conserved Domains (1) summary

cd11770
Location:156 → 209

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

110123348..110205013 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005263677.2 → XP_005263734.1 nephrocystin-1 isoform X4

UniProtKB/TrEMBL

A0A6Q8PHD4, C9JNM7

Related

ENSP00000402176.1, ENST00000417665.5

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
XM_005263676.2 → XP_005263733.1 nephrocystin-1 isoform X3

UniProtKB/TrEMBL

A0A6Q8PHD4

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
XM_006712551.2 → XP_006712614.1 nephrocystin-1 isoform X1

UniProtKB/TrEMBL

A0A6Q8PHD4

Conserved Domains (1) summary

cd11770
Location:156 → 209

SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
XM_011511244.2 → XP_011509546.1 nephrocystin-1 isoform X2

Conserved Domains (2) summary

cd11770
Location:156 → 209

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

cl09111
Location:10 → 105

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
XM_006712552.3 → XP_006712615.1 nephrocystin-1 isoform X5

Conserved Domains (1) summary

cd11770
Location:156 → 209

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