Details for: NPHP3

Gene ID: 27031

Symbol: NPHP3

Ensembl ID: ENSG00000113971

Description: nephrocystin 3

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: polychromatophilic erythroblast (CL0000550)
    Fold Change: 190.0412
    Cell Significance Index: -29.5600
  • Cell Name: hematopoietic oligopotent progenitor cell (CL0002032)
    Fold Change: 112.6779
    Cell Significance Index: -28.5800
  • Cell Name: smooth muscle fiber of ileum (CL1000278)
    Fold Change: 67.6943
    Cell Significance Index: -31.9600
  • Cell Name: mucosal type mast cell (CL0000485)
    Fold Change: 61.4389
    Cell Significance Index: -24.9600
  • Cell Name: peripheral blood mononuclear cell (CL2000001)
    Fold Change: 57.0195
    Cell Significance Index: -29.3300
  • Cell Name: ciliated cell of the bronchus (CL0002332)
    Fold Change: 26.2112
    Cell Significance Index: -25.0300
  • Cell Name: orthochromatic erythroblast (CL0000552)
    Fold Change: 24.4129
    Cell Significance Index: -30.1000
  • Cell Name: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell (CL0000796)
    Fold Change: 11.4489
    Cell Significance Index: -30.6700
  • Cell Name: CD8-positive, alpha-beta regulatory T cell (CL0000795)
    Fold Change: 8.5204
    Cell Significance Index: -26.1700
  • Cell Name: stromal cell of bone marrow (CL0010001)
    Fold Change: 7.6545
    Cell Significance Index: -30.2100
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: 1.3734
    Cell Significance Index: 395.1800
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: 1.2795
    Cell Significance Index: 256.6700
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: 1.1615
    Cell Significance Index: 89.1300
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: 1.1476
    Cell Significance Index: 30.7500
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 1.0432
    Cell Significance Index: 103.2000
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: 0.7003
    Cell Significance Index: 35.3900
  • Cell Name: epithelial cell of stomach (CL0002178)
    Fold Change: 0.6977
    Cell Significance Index: 81.3100
  • Cell Name: leptomeningeal cell (CL0000708)
    Fold Change: 0.6770
    Cell Significance Index: 14.4700
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: 0.5749
    Cell Significance Index: 32.2600
  • Cell Name: BEST4+ enteroycte (CL4030026)
    Fold Change: 0.5481
    Cell Significance Index: 8.2600
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.5352
    Cell Significance Index: 24.2600
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.5236
    Cell Significance Index: 56.9500
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.5199
    Cell Significance Index: 84.5600
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: 0.5001
    Cell Significance Index: 179.3800
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: 0.4798
    Cell Significance Index: 59.0000
  • Cell Name: gut absorptive cell (CL0000677)
    Fold Change: 0.4727
    Cell Significance Index: 28.3800
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: 0.4143
    Cell Significance Index: 56.9000
  • Cell Name: fibroblast of mammary gland (CL0002555)
    Fold Change: 0.3959
    Cell Significance Index: 11.3500
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.3905
    Cell Significance Index: 8.4600
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: 0.3435
    Cell Significance Index: 61.9200
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.3414
    Cell Significance Index: 9.8400
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: 0.3204
    Cell Significance Index: 221.5700
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: 0.3052
    Cell Significance Index: 13.5000
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 0.3000
    Cell Significance Index: 7.5000
  • Cell Name: odontoblast (CL0000060)
    Fold Change: 0.2749
    Cell Significance Index: 35.2400
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 0.2623
    Cell Significance Index: 18.1400
  • Cell Name: astrocyte of the cerebral cortex (CL0002605)
    Fold Change: 0.2218
    Cell Significance Index: 3.8400
  • Cell Name: lung endothelial cell (CL1001567)
    Fold Change: 0.2100
    Cell Significance Index: 10.9400
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 0.2029
    Cell Significance Index: 110.8200
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.1971
    Cell Significance Index: 37.5000
  • Cell Name: forebrain neuroblast (CL1000042)
    Fold Change: 0.1965
    Cell Significance Index: 12.0800
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: 0.1936
    Cell Significance Index: 7.3300
  • Cell Name: hair follicular keratinocyte (CL2000092)
    Fold Change: 0.1889
    Cell Significance Index: 83.5300
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.1821
    Cell Significance Index: 164.3800
  • Cell Name: basal cell of prostate epithelium (CL0002341)
    Fold Change: 0.1308
    Cell Significance Index: 3.5600
  • Cell Name: decidual cell (CL2000002)
    Fold Change: 0.1272
    Cell Significance Index: 2.0400
  • Cell Name: preadipocyte (CL0002334)
    Fold Change: 0.1050
    Cell Significance Index: 2.0500
  • Cell Name: regular ventricular cardiac myocyte (CL0002131)
    Fold Change: 0.0717
    Cell Significance Index: 0.9200
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: 0.0666
    Cell Significance Index: 4.2000
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: 0.0145
    Cell Significance Index: 2.4800
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0108
    Cell Significance Index: 0.3800
  • Cell Name: early pro-B cell (CL0002046)
    Fold Change: 0.0045
    Cell Significance Index: 0.2900
  • Cell Name: peg cell (CL4033014)
    Fold Change: -0.0130
    Cell Significance Index: -0.3000
  • Cell Name: kidney loop of Henle cortical thick ascending limb epithelial cell (CL1001109)
    Fold Change: -0.0156
    Cell Significance Index: -11.4500
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: -0.0157
    Cell Significance Index: -29.5700
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: -0.0195
    Cell Significance Index: -35.9400
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: -0.0202
    Cell Significance Index: -0.5400
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: -0.0227
    Cell Significance Index: -35.0100
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: -0.0269
    Cell Significance Index: -36.5900
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.0309
    Cell Significance Index: -22.8700
  • Cell Name: pulmonary alveolar epithelial cell (CL0000322)
    Fold Change: -0.0337
    Cell Significance Index: -25.5200
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: -0.0402
    Cell Significance Index: -25.5100
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.0472
    Cell Significance Index: -2.2200
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.0522
    Cell Significance Index: -29.4400
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: -0.0569
    Cell Significance Index: -2.6600
  • Cell Name: pancreatic PP cell (CL0002275)
    Fold Change: -0.0576
    Cell Significance Index: -35.9700
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.0581
    Cell Significance Index: -6.6600
  • Cell Name: cardiac endothelial cell (CL0010008)
    Fold Change: -0.0640
    Cell Significance Index: -0.9200
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0666
    Cell Significance Index: -30.2400
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.0763
    Cell Significance Index: -7.7900
  • Cell Name: sebum secreting cell (CL0000317)
    Fold Change: -0.0813
    Cell Significance Index: -5.7500
  • Cell Name: retinal rod cell (CL0000604)
    Fold Change: -0.0814
    Cell Significance Index: -0.9700
  • Cell Name: lactocyte (CL0002325)
    Fold Change: -0.1314
    Cell Significance Index: -16.9700
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: -0.1475
    Cell Significance Index: -7.6600
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: -0.1494
    Cell Significance Index: -2.5000
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.1605
    Cell Significance Index: -33.8100
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: -0.1704
    Cell Significance Index: -12.7000
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.1960
    Cell Significance Index: -28.4900
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: -0.2043
    Cell Significance Index: -24.0900
  • Cell Name: glycinergic neuron (CL1001509)
    Fold Change: -0.2231
    Cell Significance Index: -11.7200
  • Cell Name: medium spiny neuron (CL1001474)
    Fold Change: -0.2394
    Cell Significance Index: -3.2300
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: -0.2479
    Cell Significance Index: -5.2800
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: -0.2510
    Cell Significance Index: -8.0400
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.2991
    Cell Significance Index: -31.1400
  • Cell Name: kidney loop of Henle descending limb epithelial cell (CL1001021)
    Fold Change: -0.3448
    Cell Significance Index: -27.3100
  • Cell Name: GABAergic amacrine cell (CL4030027)
    Fold Change: -0.3608
    Cell Significance Index: -4.4800
  • Cell Name: endothelial cell of placenta (CL0009092)
    Fold Change: -0.3625
    Cell Significance Index: -2.1900
  • Cell Name: umbrella cell of urothelium (CL4030056)
    Fold Change: -0.3714
    Cell Significance Index: -3.4200
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: -0.3767
    Cell Significance Index: -7.8200
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: -0.3828
    Cell Significance Index: -23.4700
  • Cell Name: fibroblast of dermis (CL0002551)
    Fold Change: -0.4572
    Cell Significance Index: -9.5700
  • Cell Name: OFF midget ganglion cell (CL4033047)
    Fold Change: -0.4635
    Cell Significance Index: -5.7800
  • Cell Name: mesonephric nephron tubule epithelial cell (CL1000022)
    Fold Change: -0.4659
    Cell Significance Index: -16.1900
  • Cell Name: keratocyte (CL0002363)
    Fold Change: -0.4961
    Cell Significance Index: -7.8700
  • Cell Name: conjunctival epithelial cell (CL1000432)
    Fold Change: -0.5460
    Cell Significance Index: -7.4500
  • Cell Name: cortical interneuron (CL0008031)
    Fold Change: -0.5667
    Cell Significance Index: -13.5900
  • Cell Name: ON midget ganglion cell (CL4033046)
    Fold Change: -0.6156
    Cell Significance Index: -7.7700
  • Cell Name: fibroblast of cardiac tissue (CL0002548)
    Fold Change: -0.6219
    Cell Significance Index: -8.9300
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: -0.6716
    Cell Significance Index: -17.6600
  • Cell Name: CD4-positive, alpha-beta memory T cell, CD45RO-positive (CL0001204)
    Fold Change: -0.6834
    Cell Significance Index: -20.0700

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** 1. **Cilia-related functions:** NPHP3 is crucial for the assembly and maintenance of cilia, particularly non-motile cilia, which are essential for various cellular processes, including cell polarity, epithelial function, and signaling pathways. 2. **Cargo trafficking:** NPHP3 is involved in the trafficking of myristoylated proteins to the cilium, suggesting its role in regulating the transport of proteins to specific cellular compartments. 3. **Cell polarity and asymmetry:** NPHP3 contributes to the establishment and maintenance of cell polarity, which is critical for the determination of left-right asymmetry in various organs, including the kidneys, liver, and pancreas. 4. **Wnt signaling pathway regulation:** NPHP3 negatively regulates the Wnt signaling pathway, which is involved in cell proliferation, differentiation, and survival. **Pathways and Functions:** NPHP3's functions are intricately linked to various signaling pathways, including: 1. **Atrial septum development:** NPHP3 is involved in the development of the atrial septum, a critical structure in the heart. 2. **Ciliary base and cilium assembly:** NPHP3 regulates the assembly and maintenance of cilia, which are essential for various cellular processes. 3. **Cargo trafficking to the periciliary membrane:** NPHP3 is involved in the trafficking of myristoylated proteins to the periciliary membrane, which is critical for cilia function. 4. **Convergent extension and gastrulation:** NPHP3 contributes to the regulation of convergent extension and gastrulation, which are critical processes in embryonic development. 5. **Determination of left/right asymmetry:** NPHP3 is involved in the determination of left/right asymmetry in various organs, including the kidneys, liver, and pancreas. **Clinical Significance:** NPHP3 mutations have been associated with autosomal recessive polycystic kidney disease (ARPKD), a condition characterized by the formation of cysts in the kidneys, leading to renal failure. Other NPHP3-related disorders include nephronophthisis, a rare genetic disorder affecting the kidneys and liver, and primary ciliary dyskinesia, a condition characterized by impaired cilia function. In conclusion, NPHP3 plays a critical role in various cellular processes, including cilia-related functions, cell polarity, and Wnt signaling pathway regulation. Its dysregulation has been implicated in several human diseases, highlighting the importance of NPHP3 in maintaining normal cellular function and development.

Genular Protein ID: 517832130

Symbol: NPHP3_HUMAN

Name: Nephrocystin-3

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 12872122

Title: Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis.

PubMed ID: 12872122

DOI: 10.1038/ng1216

PubMed ID: 12056414

Title: Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method.

PubMed ID: 12056414

DOI: 10.1093/dnares/9.2.47

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 20462968

Title: Nephrocystin-3 is required for ciliary function in zebrafish embryos.

PubMed ID: 20462968

DOI: 10.1152/ajprenal.00043.2010

PubMed ID: 22085962

Title: An ARL3-UNC119-RP2 GTPase cycle targets myristoylated NPHP3 to the primary cilium.

PubMed ID: 22085962

DOI: 10.1101/gad.173443.111

PubMed ID: 22863007

Title: Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling.

PubMed ID: 22863007

DOI: 10.1016/j.cell.2012.06.028

PubMed ID: 23418306

Title: Mutations in NEK8 link multiple organ dysplasia with altered Hippo signalling and increased c-MYC expression.

PubMed ID: 23418306

DOI: 10.1093/hmg/ddt070

PubMed ID: 23793029

Title: ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3.

PubMed ID: 23793029

DOI: 10.1038/ng.2681

PubMed ID: 18371931

Title: Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.

PubMed ID: 18371931

DOI: 10.1016/j.ajhg.2008.02.017

Sequence Information:

  • Length: 1330
  • Mass: 150864
  • Checksum: 99C1F17C9A5117F8
  • Sequence:
  • MGTASSLVSP AGGEVIEDTY GAGGGEACEI PVEVKPKARL LRNSFRRGAG AAAGAGPGSL 
    PRGVGAGGLL GASFKSTGSS VPELEYAAAE YERLRKEYEI FRVSKNQELL SMGRREAKLD 
    TENKRLRAEL QALQKTYQKI LREKESALEA KYQAMERAAT FEHDRDKVKR QFKIFRETKE 
    NEIQDLLRAK RELESKLQRL QAQGIQVFDP GESDSDDNCT DVTAAGTQCE YWTGGALGSE 
    PSIGSMIQLQ QSFRGPEFAH SSIDVEGPFA NVNRDDWDIA VASLLQVTPL FSHSLWSNTV 
    RCYLIYTDET QPEMDLFLKD YSPKLKRMCE TMGYFFHAVY FPIDVENQYL TVRKWEIEKS 
    SLVILFIHLT LPSLLLEDCE EAFLKNPEGK PRLIFHRLED GKVSSDSVQQ LIDQVSNLNK 
    TSKAKIIDHS GDPAEGVYKT YICVEKIIKQ DILGFENTDL ETKDLGSEDS IPEEDDFGDV 
    LWDIHDEQEQ METFQQASNS AHELGFEKYY QRLNDLVAAP APIPPLLVSG GPGSGKSLLL 
    SKWIQLQQKN SPNTLILSHF VGRPMSTSSE SSLIIKRLTL KLMQHSWSVS ALTLDPAKLL 
    EEFPRWLEKL SARHQGSIII VIDSIDQVQQ VEKHMKWLID PLPVNVRVIV SVNVETCPPA 
    WRLWPTLHLD PLSPKDAKSI IIAECHSVDI KLSKEQEKKL ERHCRSATTC NALYVTLFGK 
    MIARAGRAGN LDKILHQCFQ CQDTLSLYRL VLHSIRESMA NDVDKELMKQ ILCLVNVSHN 
    GVSESELMEL YPEMSWTFLT SLIHSLYKMC LLTYGCGLLR FQHLQAWETV RLEYLEGPTV 
    TSSYRQKLIN YFTLQLSQDR VTWRSADELP WLFQQQGSKQ KLHDCLLNLF VSQNLYKRGH 
    FAELLSYWQF VGKDKSAMAT EYFDSLKQYE KNCEGEDNMS CLADLYETLG RFLKDLGLLS 
    QAIVPLQRSL EIRETALDPD HPRVAQSLHQ LASVYVQWKK FGNAEQLYKQ ALEISENAYG 
    ADHPYTAREL EALATLYQKQ NKYEQAEHFR KKSFKIHQKA IKKKGNLYGF ALLRRRALQL 
    EELTLGKDTP DNARTLNELG VLYYLQNNLE TADQFLKRSL EMRERVLGPD HPDCAQSLNN 
    LAALCNEKKQ YDKAEELYER ALDIRRRALA PDHPSLAYTV KHLAILYKKM GKLDKAVPLY 
    ELAVEIRQKS FGPKHPSVAT ALVNLAVLYS QMKKHVEALP LYERALKIYE DSLGRMHPRV 
    GETLKNLAVL SYEGGDFEKA AELYKRAMEI KEAETSLLGG KAPSRHSSSG DTFSLKTAHS 
    PNVFLQQGQR

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.