NPHP3 nephrocystin 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPHP3provided by HGNC
Official Full Name: nephrocystin 3provided by HGNC
Primary source: HGNC:HGNC:7907
See related: Ensembl:ENSG00000113971 MIM:608002; AllianceGenome:HGNC:7907
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: MKS7; NPH3; RHPD; RHPD1; SLSN3; CFAP31
Summary: This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]
Expression: Ubiquitous expression in ovary (RPKM 12.5), endometrium (RPKM 10.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q22.1

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (132680609..132722409, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (135425099..135466912, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (132399453..132441253, complement)

Chromosome 3 - NC_000003.12 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?

Vinblastine Resistance Is Associated with Nephronophthisis 3-Mediated Primary Cilia via Intraflagellar Transport Protein 88 and Apoptosis-Antagonizing Transcription Factor.
Title: Vinblastine Resistance Is Associated with Nephronophthisis 3-Mediated Primary Cilia via Intraflagellar Transport Protein 88 and Apoptosis-Antagonizing Transcription Factor.
HeLa Cervical Cancer Cells Are Maintained by Nephronophthisis 3-Associated Primary Cilium Formation via ROS-Induced ERK and HIF-1alpha Activation under Serum-Deprived Normoxic Condition.
Title: HeLa Cervical Cancer Cells Are Maintained by Nephronophthisis 3-Associated Primary Cilium Formation via ROS-Induced ERK and HIF-1α Activation under Serum-Deprived Normoxic Condition.
A discarded synonymous variant in NPHP3 explains nephronophthisis and congenital hepatic fibrosis in several families.
Title: A discarded synonymous variant in NPHP3 explains nephronophthisis and congenital hepatic fibrosis in several families.
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.
Thymosin beta-4 is a novel regulator for primary cilium formation by nephronophthisis 3 in HeLa human cervical cancer cells.
Title: Thymosin β-4 is a novel regulator for primary cilium formation by nephronophthisis 3 in HeLa human cervical cancer cells.
Case Report: NPHP3 related nephronophthisis manifesting in the fetal period.
Title: Homozygous mutation in the NPHP3 gene causing foetal nephronophthisis.
Inherited 3 deleterious mutations in two nephronophthisis genes, NPHP3 and NPHP4 cause unusually severe form of infantile nephronophthisis.
Title: A familial case of severe infantile nephronophthisis explained by oligogenic inheritance.
NPHP3 mutations were prevalent in Chinese infantile nephronophthisis patients. All patients with NPHP3 mutations showed renal-hepatic phenotype.
Title: High mutation rate of NPHP3 in 18 Chinese infantile nephronophthisis patients.
a rare neonatal ciliopathy presentation of NPHP3 mutations leading to severe multiorgan failure in two siblings.
Title: NPHP3 mutations are associated with neonatal onset multiorgan polycystic disease in two siblings.
The known phenotype of NPHP3 mutation caused renal-hepatic-pancreatic dysplasia has been extended to include skeletal and CNS anomalies.
Title: Renal-hepatic-pancreatic dysplasia: a sibship with skeletal and central nervous system anomalies and NPHP3 mutation.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Nephronophthisis 3 MedGen: C1858392 OMIM: 604387 GeneReviews: Nephronophthisis-Related Ciliopathies	Compare labs
NPHP3-related Meckel-like syndrome MedGen: C2673885 OMIM: 267010 GeneReviews: Not available	Compare labs
Renal-hepatic-pancreatic dysplasia 1 MedGen: C3715199 OMIM: 208540 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of nephronophthisis 3 (NPHP3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D10S16 (e-PCR)
- UniSTS:155756

Readthrough NPHP3-ACAD11

Readthrough gene: NPHP3-ACAD11, Included gene: ACAD11

Clone Names

FLJ30691, FLJ36696, KIAA2000, MGC78666, DKFZp667K242, DKFZp781K1312

Gene Ontology Provided by GOA

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	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	IGI Inferred from Genetic Interaction more info	PubMed
involved_in determination of intestine left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
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 liver left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of pancreatic left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of stomach left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial cilium movement involved in determination of left/right asymmetry	IC Inferred by Curator more info
involved_in establishment or maintenance of cell polarity	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IEA Inferred from Electronic Annotation more info
involved_in heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in lung development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maintenance of animal organ identity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in non-motile cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of Wnt signaling pathway, planar cell polarity pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of Wnt signaling pathway, planar cell polarity pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureter development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in ciliary base	IBA Inferred from Biological aspect of Ancestor more info
is_active_in ciliary inversin compartment	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: nephrocystin-3

Names: Meckel syndrome, type 7; cilia and flagella associated protein 31; nephronophthisis 3 (adolescent)

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_008130.2 RefSeqGene

Range

5024..46824

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_153240.5 → NP_694972.3 nephrocystin-3

See identical proteins and their annotated locations for NP_694972.3

Status: REVIEWED

Source sequence(s)

AC055732, AY257864, DB114822, EB387619

Consensus CDS

CCDS3078.1

UniProtKB/Swiss-Prot

Q5JPE3, Q5JPE6, Q68D99, Q6NVH3, Q7Z492, Q7Z493, Q7Z494, Q8N9R2, Q8NCM5, Q96N70, Q96NK2

Related

ENSP00000338766.5, ENST00000337331.10

Conserved Domains (6) summary

sd00006
Location:1135 → 1163

TPR; TPR repeat [structural motif]

pfam03938
Location:124 → 206

OmpH; Outer membrane protein (OmpH-like)

pfam04871
Location:117 → 203

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

pfam12711
Location:80 → 149

Kinesin-relat_1; Kinesin motor

pfam13374
Location:1135 → 1174

TPR_10; Tetratricopeptide repeat

pfam13424
Location:1131 → 1209

TPR_12; Tetratricopeptide repeat