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Aliases for NPHP3 Gene

Aliases for NPHP3 Gene

  • Nephrocystin 3 2 3 5
  • Cilia And Flagella Associated Protein 31 2 3
  • Nephronophthisis 3 (Adolescent) 2 3
  • Meckel Syndrome, Type 7 2 3
  • Nephrocystin-3 3
  • KIAA2000 4
  • CFAP31 3
  • RHPD1 3
  • SLSN3 3
  • MKS7 3
  • NPH3 3
  • RHPD 3

External Ids for NPHP3 Gene

Previous GeneCards Identifiers for NPHP3 Gene

  • GC03U990139
  • GC03M133598
  • GC03M133599
  • GC03M133760
  • GC03M133882
  • GC03M132277
  • GC03M129779

Summaries for NPHP3 Gene

Entrez Gene Summary for NPHP3 Gene

  • 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]

GeneCards Summary for NPHP3 Gene

NPHP3 (Nephrocystin 3) is a Protein Coding gene. Diseases associated with NPHP3 include Meckel Syndrome, Type 7 and Nephronophthisis 3. Among its related pathways are Organelle biogenesis and maintenance and Cargo trafficking to the periciliary membrane. An important paralog of this gene is NPHP3-ACAD11.

UniProtKB/Swiss-Prot for NPHP3 Gene

  • Required for normal ciliary development and function. Inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling which regulates planar cell polarity. Probably acts as a molecular switch between different Wnt signaling pathways. Required for proper convergent extension cell movements.

Gene Wiki entry for NPHP3 Gene

Additional gene information for NPHP3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPHP3 Gene

Genomics for NPHP3 Gene

GeneHancer (GH) Regulatory Elements for NPHP3 Gene

Promoters and enhancers for NPHP3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J132721 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 697.5 -0.1 -83 3.1 HDGF ATF1 ARID4B SIN3A BRCA1 ZNF48 YY1 ETS1 ZNF121 GLIS2 NPHP3 NPHP3-ACAD11 NPHP3-AS1 TOPBP1 LOC105374115
GH03J132681 Promoter 0.5 EPDnew 650.3 +40.4 40435 0.1 NPHP3 ACAD11 UBA5 NPHP3-AS1 NPHP3-ACAD11
GH03J132657 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 29.9 +62.5 62533 4.5 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ACAD11 UBA5 NPHP3 DNAJC13 NPHP3-ACAD11
GH03J133568 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.8 -849.9 -849898 9 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 YBX1 CDV3 NPHP3 RYK TOPBP1 SRPRB TFP1 RAB6B UBA5 GC03P133569
GH03J132415 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 7.2 +304.7 304665 4.1 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 ETS1 GLIS2 ZNF207 ZNF143 DNAJC13 NPHP3 ACKR4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPHP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NPHP3 gene promoter:
  • AREB6
  • STAT1beta
  • STAT1alpha
  • STAT1
  • POU2F1a
  • POU2F1
  • FOXJ2 (long isoform)
  • FOXJ2

Genomic Locations for NPHP3 Gene

Genomic Locations for NPHP3 Gene
chr3:132,680,609-132,722,459
(GRCh38/hg38)
Size:
41,851 bases
Orientation:
Minus strand
chr3:132,276,986-132,441,303
(GRCh37/hg19)
Size:
164,318 bases
Orientation:
Minus strand

Genomic View for NPHP3 Gene

Genes around NPHP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPHP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPHP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPHP3 Gene

Proteins for NPHP3 Gene

  • Protein details for NPHP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z494-NPHP3_HUMAN
    Recommended name:
    Nephrocystin-3
    Protein Accession:
    Q7Z494
    Secondary Accessions:
    • Q5JPE3
    • Q5JPE6
    • Q68D99
    • Q6NVH3
    • Q7Z492
    • Q7Z493
    • Q8N9R2
    • Q8NCM5
    • Q96N70
    • Q96NK2

    Protein attributes for NPHP3 Gene

    Size:
    1330 amino acids
    Molecular mass:
    150864 Da
    Quaternary structure:
    • Interacts with NPHP1 and INVS/NPHP2. Interacts (when myristoylated) with UNC119 and UNC119B; interaction is required for localization to cilium. Interacts with CEP164. Component of a complex containing at least ANKS6, INVS, NEK8 and NPHP3. ANKS6 may organize complex assembly by linking INVS and NPHP3 to NEK8 and INVS may target the complex to the proximal ciliary axoneme.
    SequenceCaution:
    • Sequence=BAB70891.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC02709.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAC04268.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NPHP3 Gene

    Alternative splice isoforms for NPHP3 Gene

neXtProt entry for NPHP3 Gene

Post-translational modifications for NPHP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NPHP3 Gene

No data available for DME Specific Peptides for NPHP3 Gene

Domains & Families for NPHP3 Gene

Gene Families for NPHP3 Gene

Protein Domains for NPHP3 Gene

Suggested Antigen Peptide Sequences for NPHP3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NPHP3: view

No data available for UniProtKB/Swiss-Prot for NPHP3 Gene

Function for NPHP3 Gene

Molecular function for NPHP3 Gene

UniProtKB/Swiss-Prot Function:
Required for normal ciliary development and function. Inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling which regulates planar cell polarity. Probably acts as a molecular switch between different Wnt signaling pathways. Required for proper convergent extension cell movements.

Phenotypes From GWAS Catalog for NPHP3 Gene

Gene Ontology (GO) - Molecular Function for NPHP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12872122
genes like me logo Genes that share ontologies with NPHP3: view
genes like me logo Genes that share phenotypes with NPHP3: view

Human Phenotype Ontology for NPHP3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NPHP3 Gene

MGI Knock Outs for NPHP3:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for NPHP3 Gene

Localization for NPHP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPHP3 Gene

Cell projection, cilium. Note=Localization to cilium is mediated via interaction with UNC119 and UNC119B, which bind to the myristoyl moiety of the N-terminus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NPHP3 gene
Compartment Confidence
cytosol 5
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for NPHP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005929 cilium TAS --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with NPHP3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NPHP3 Gene

Pathways & Interactions for NPHP3 Gene

genes like me logo Genes that share pathways with NPHP3: view

Gene Ontology (GO) - Biological Process for NPHP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001822 kidney development IMP 20007846
GO:0001947 heart looping IMP 18371931
GO:0003283 atrial septum development IMP 18371931
GO:0007368 determination of left/right symmetry IMP 18371931
GO:0016055 Wnt signaling pathway IEA --
genes like me logo Genes that share ontologies with NPHP3: view

No data available for SIGNOR curated interactions for NPHP3 Gene

Drugs & Compounds for NPHP3 Gene

No Compound Related Data Available

Transcripts for NPHP3 Gene

mRNA/cDNA for NPHP3 Gene

Unigene Clusters for NPHP3 Gene

Nephronophthisis 3 (adolescent):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPHP3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
SP1: - -
SP2:
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

ExUns: 25a · 25b ^ 26 ^ 27 ^ 28a · 28b · 28c ^ 29a · 29b ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35a · 35b ^ 36 ^ 37 ^ 38 ^ 39 ^ 40a · 40b ^ 41 ^ 42a · 42b ^ 43 ^
SP1: -
SP2: - -
SP3: - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: - - - - -

ExUns: 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for NPHP3 Gene

GeneLoc Exon Structure for
NPHP3
ECgene alternative splicing isoforms for
NPHP3

Expression for NPHP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NPHP3 Gene

Protein differential expression in normal tissues from HIPED for NPHP3 Gene

This gene is overexpressed in Nasal epithelium (46.1) and Cerebrospinal fluid (16.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NPHP3 Gene



NURSA nuclear receptor signaling pathways regulating expression of NPHP3 Gene:

NPHP3

SOURCE GeneReport for Unigene cluster for NPHP3 Gene:

Hs.511991

mRNA Expression by UniProt/SwissProt for NPHP3 Gene:

Q7Z494-NPHP3_HUMAN
Tissue specificity: Widely expressed at low level. Expressed in heart, placenta, liver, skeletal muscle, kidney and pancreas. Expressed at very low level in brain and lung.

Evidence on tissue expression from TISSUES for NPHP3 Gene

  • Nervous system(4.3)
  • Lymph node(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NPHP3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • mouth
  • pituitary gland
  • salivary gland
  • skull
Thorax:
  • aorta
  • breast
  • esophagus
  • heart
  • heart valve
  • lung
Abdomen:
  • abdominal wall
  • biliary tract
  • duodenum
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
Pelvis:
  • placenta
  • testicle
  • ureter
  • urinary bladder
  • uterus
Limb:
  • digit
  • femur
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • thigh
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with NPHP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for NPHP3 Gene

Orthologs for NPHP3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPHP3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPHP3 34 33
  • 99.47 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NPHP3 34 33
  • 92.65 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NPHP3 34 33
  • 92.08 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nphp3 16 34 33
  • 84.74 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NPHP3 34
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nphp3 33
  • 83.94 (n)
chicken
(Gallus gallus)
Aves NPHP3 34 33
  • 77.89 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPHP3 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nphp3 33
  • 72.27 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19365 33
zebrafish
(Danio rerio)
Actinopterygii nphp3 34 33
  • 66.38 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Klc 34
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea klc-2 34
  • 24 (a)
ManyToMany
klc-1 34
  • 21 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.801 34
  • 37 (a)
OneToOne
Species where no ortholog for NPHP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NPHP3 Gene

ENSEMBL:
Gene Tree for NPHP3 (if available)
TreeFam:
Gene Tree for NPHP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NPHP3: view image

Paralogs for NPHP3 Gene

Paralogs for NPHP3 Gene

(5) SIMAP similar genes for NPHP3 Gene using alignment to 5 proteins:

  • NPHP3_HUMAN
  • F2Z3A8_HUMAN
  • H0YAM4_HUMAN
  • L8E9N9_HUMAN
  • Q7Z491_HUMAN
genes like me logo Genes that share paralogs with NPHP3: view

Variants for NPHP3 Gene

Sequence variations from dbSNP and Humsavar for NPHP3 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1060499938 pathogenic, Adolescent nephronophthisis 132,683,487(-) G/ coding_sequence_variant, frameshift
rs1060503156 uncertain-significance, Nephronophthisis 132,688,797(-) C/T coding_sequence_variant, missense_variant
rs1060503157 uncertain-significance, Nephronophthisis 132,692,732(-) C/G coding_sequence_variant, missense_variant
rs1060504844 likely-benign, Nephronophthisis 132,700,361(-) G/C coding_sequence_variant, synonymous_variant
rs111727307 conflicting-interpretations-of-pathogenicity, likely-benign, not specified, Nephronophthisis 132,684,624(-) C/A/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for NPHP3 Gene

Variant ID Type Subtype PubMed ID
esv3893774 CNV loss 25118596
nsv1073681 CNV deletion 25765185
nsv1133563 CNV deletion 24896259
nsv1144051 CNV deletion 24896259
nsv4014 CNV insertion 18451855
nsv591798 CNV loss 21841781
nsv591799 CNV gain 21841781
nsv998211 CNV loss 25217958

Variation tolerance for NPHP3 Gene

Residual Variation Intolerance Score: 12.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.05; 60.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPHP3 Gene

Human Gene Mutation Database (HGMD)
NPHP3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPHP3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPHP3 Gene

Disorders for NPHP3 Gene

MalaCards: The human disease database

(20) MalaCards diseases for NPHP3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search NPHP3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NPHP3_HUMAN
  • Nephronophthisis 3 (NPHP3) [MIM:604387]: An autosomal recessive disorder resulting in end-stage renal disease. It is characterized by polyuria, polydipsia, anemia. Onset of terminal renal failure occurr significantly later (median age, 19 years) than in juvenile nephronophthisis. Renal pathology is characterized by alterations of tubular basement membranes, tubular atrophy and dilation, sclerosing tubulointerstitial nephropathy, and renal cyst development predominantly at the corticomedullary junction. {ECO:0000269 PubMed:12872122}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Renal-hepatic-pancreatic dysplasia 1 (RHPD1) [MIM:208540]: A disease characterized by cystic malformations of the kidneys, liver, and pancreas. The pathological findings consist of multicystic dysplastic kidneys, dilated and dysgenetic bile ducts, a dysplastic pancreas with dilated ducts, cysts, fibrosis and inflammatory infiltrates. {ECO:0000269 PubMed:18371931}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Meckel syndrome 7 (MKS7) [MIM:267010]: A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269 PubMed:18371931}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NPHP3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NPHP3: view

No data available for Genatlas for NPHP3 Gene

Publications for NPHP3 Gene

  1. Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. (PMID: 12872122) Olbrich H … Omran H (Nature genetics 2003) 2 3 4 22 44 58
  2. Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia. (PMID: 18371931) Bergmann C … Omran H (American journal of human genetics 2008) 3 4 22 58
  3. STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. (PMID: 15381417) Leipe DD … Aravind L (Journal of molecular biology 2004) 2 3 22 58
  4. Mutations in NEK8 link multiple organ dysplasia with altered Hippo signalling and increased c-MYC expression. (PMID: 23418306) Frank V … Bergmann C (Human molecular genetics 2013) 3 4 58
  5. ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3. (PMID: 23793029) Hoff S … Lienkamp SS (Nature genetics 2013) 3 4 58

Products for NPHP3 Gene

Sources for NPHP3 Gene

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