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Protein

Nephrocystin-3

Gene

NPHP3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.1 Publication

GO - Biological processi

  • atrial septum development Source: BHF-UCL
  • cilium assembly Source: UniProtKB
  • convergent extension involved in gastrulation Source: BHF-UCL
  • determination of intestine left/right asymmetry Source: BHF-UCL
  • determination of left/right symmetry Source: BHF-UCL
  • determination of liver left/right asymmetry Source: BHF-UCL
  • determination of pancreatic left/right asymmetry Source: BHF-UCL
  • determination of stomach left/right asymmetry Source: BHF-UCL
  • epithelial cilium movement involved in determination of left/right asymmetry Source: BHF-UCL
  • heart looping Source: BHF-UCL
  • kidney development Source: BHF-UCL
  • kidney morphogenesis Source: BHF-UCL
  • lung development Source: BHF-UCL
  • maintenance of animal organ identity Source: HGNC
  • negative regulation of canonical Wnt signaling pathway Source: UniProtKB
  • photoreceptor cell maintenance Source: HGNC
  • regulation of planar cell polarity pathway involved in neural tube closure Source: BHF-UCL
  • regulation of Wnt signaling pathway, planar cell polarity pathway Source: UniProtKB
  • ureter development Source: BHF-UCL
  • Wnt signaling pathway Source: UniProtKB-KW

Keywordsi

Biological processWnt signaling pathway

Enzyme and pathway databases

ReactomeiR-HSA-5624138 Trafficking of myristoylated proteins to the cilium

Names & Taxonomyi

Protein namesi
Recommended name:
Nephrocystin-3
Gene namesi
Name:NPHP3
Synonyms:KIAA2000
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000113971.18
HGNCiHGNC:7907 NPHP3
MIMi608002 gene
neXtProtiNX_Q7Z494

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell projection, Cilium

Pathology & Biotechi

Involvement in diseasei

Nephronophthisis 3 (NPHP3)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn 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.
See also OMIM:604387
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_022815360S → T in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs119456960EnsemblClinVar.1
Natural variantiVAR_022816386N → S in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs142021049EnsemblClinVar.1
Natural variantiVAR_022817397R → H in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs755094682Ensembl.1
Natural variantiVAR_0228181141L → P in NPHP3. 1 Publication1
Natural variantiVAR_0228191221A → V in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs202048210EnsemblClinVar.1
Natural variantiVAR_0228201252S → R in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs143451766EnsemblClinVar.1
Natural variantiVAR_0228211314S → T in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs75316802EnsemblClinVar.1
Renal-hepatic-pancreatic dysplasia 1 (RHPD1)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:208540
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_044121973R → Q in RHPD1. 1 PublicationCorresponds to variant dbSNP:rs119456963EnsemblClinVar.1
Meckel syndrome 7 (MKS7)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:267010

Keywords - Diseasei

Ciliopathy, Disease mutation, Meckel syndrome, Nephronophthisis

Organism-specific databases

DisGeNETi27031
MalaCardsiNPHP3
MIMi208540 phenotype
267010 phenotype
604387 phenotype
OpenTargetsiENSG00000113971
ENSG00000274810
Orphaneti93589 Late-onset nephronophthisis
3032 NPHP3-related Meckel-like syndrome
294415 Renal-hepatic-pancreatic dysplasia
3156 Senior-Loken syndrome
PharmGKBiPA31708

Polymorphism and mutation databases

BioMutaiNPHP3
DMDMi68565783

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001063012 – 1330Nephrocystin-3Add BLAST1329

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine1 Publication1

Keywords - PTMi

Lipoprotein, Myristate

Proteomic databases

EPDiQ7Z494
MaxQBiQ7Z494
PaxDbiQ7Z494
PeptideAtlasiQ7Z494
PRIDEiQ7Z494

PTM databases

CarbonylDBiQ7Z494
iPTMnetiQ7Z494
PhosphoSitePlusiQ7Z494

Expressioni

Tissue specificityi

Widely expressed at low level. Expressed in heart, placenta, liver, skeletal muscle, kidney and pancreas. Expressed at very low level in brain and lung.1 Publication

Gene expression databases

BgeeiENSG00000113971
ExpressionAtlasiQ7Z494 baseline and differential
GenevisibleiQ7Z494 HS

Organism-specific databases

HPAiHPA009150

Interactioni

Subunit structurei

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.6 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi117962, 30 interactors
CORUMiQ7Z494
IntActiQ7Z494, 9 interactors
MINTiQ7Z494
STRINGi9606.ENSP00000338766

Structurei

Secondary structure

11330
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 6Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5L7KX-ray2.10B2-7[»]
ProteinModelPortaliQ7Z494
SMRiQ7Z494
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati471 – 504TPR 1Add BLAST34
Repeati885 – 918TPR 2Add BLAST34
Repeati920 – 942TPR 3Add BLAST23
Repeati943 – 976TPR 4Add BLAST34
Repeati985 – 1018TPR 5Add BLAST34
Repeati1027 – 1060TPR 6Add BLAST34
Repeati1093 – 1126TPR 7Add BLAST34
Repeati1135 – 1168TPR 8Add BLAST34
Repeati1177 – 1210TPR 9Add BLAST34
Repeati1219 – 1252TPR 10Add BLAST34
Repeati1261 – 1294TPR 11Add BLAST34

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili83 – 207Sequence analysisAdd BLAST125

Keywords - Domaini

Coiled coil, Repeat, TPR repeat

Phylogenomic databases

eggNOGiKOG1840 Eukaryota
COG0457 LUCA
GeneTreeiENSGT00390000006393
HOVERGENiHBG079457
InParanoidiQ7Z494
KOiK19360
OMAiSMAAEYF
OrthoDBiEOG091G00M2
PhylomeDBiQ7Z494
TreeFamiTF314010

Family and domain databases

Gene3Di1.25.40.10, 3 hits
InterProiView protein in InterPro
IPR027417 P-loop_NTPase
IPR013026 TPR-contain_dom
IPR011990 TPR-like_helical_dom_sf
IPR019734 TPR_repeat
PfamiView protein in Pfam
PF13176 TPR_7, 1 hit
SMARTiView protein in SMART
SM00028 TPR, 8 hits
SUPFAMiSSF48452 SSF48452, 2 hits
SSF52540 SSF52540, 1 hit
PROSITEiView protein in PROSITE
PS50005 TPR, 8 hits
PS50293 TPR_REGION, 1 hit

Sequences (7)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 7 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q7Z494-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGTASSLVSP AGGEVIEDTY GAGGGEACEI PVEVKPKARL LRNSFRRGAG
60 70 80 90 100
AAAGAGPGSL PRGVGAGGLL GASFKSTGSS VPELEYAAAE YERLRKEYEI
110 120 130 140 150
FRVSKNQELL SMGRREAKLD TENKRLRAEL QALQKTYQKI LREKESALEA
160 170 180 190 200
KYQAMERAAT FEHDRDKVKR QFKIFRETKE NEIQDLLRAK RELESKLQRL
210 220 230 240 250
QAQGIQVFDP GESDSDDNCT DVTAAGTQCE YWTGGALGSE PSIGSMIQLQ
260 270 280 290 300
QSFRGPEFAH SSIDVEGPFA NVNRDDWDIA VASLLQVTPL FSHSLWSNTV
310 320 330 340 350
RCYLIYTDET QPEMDLFLKD YSPKLKRMCE TMGYFFHAVY FPIDVENQYL
360 370 380 390 400
TVRKWEIEKS SLVILFIHLT LPSLLLEDCE EAFLKNPEGK PRLIFHRLED
410 420 430 440 450
GKVSSDSVQQ LIDQVSNLNK TSKAKIIDHS GDPAEGVYKT YICVEKIIKQ
460 470 480 490 500
DILGFENTDL ETKDLGSEDS IPEEDDFGDV LWDIHDEQEQ METFQQASNS
510 520 530 540 550
AHELGFEKYY QRLNDLVAAP APIPPLLVSG GPGSGKSLLL SKWIQLQQKN
560 570 580 590 600
SPNTLILSHF VGRPMSTSSE SSLIIKRLTL KLMQHSWSVS ALTLDPAKLL
610 620 630 640 650
EEFPRWLEKL SARHQGSIII VIDSIDQVQQ VEKHMKWLID PLPVNVRVIV
660 670 680 690 700
SVNVETCPPA WRLWPTLHLD PLSPKDAKSI IIAECHSVDI KLSKEQEKKL
710 720 730 740 750
ERHCRSATTC NALYVTLFGK MIARAGRAGN LDKILHQCFQ CQDTLSLYRL
760 770 780 790 800
VLHSIRESMA NDVDKELMKQ ILCLVNVSHN GVSESELMEL YPEMSWTFLT
810 820 830 840 850
SLIHSLYKMC LLTYGCGLLR FQHLQAWETV RLEYLEGPTV TSSYRQKLIN
860 870 880 890 900
YFTLQLSQDR VTWRSADELP WLFQQQGSKQ KLHDCLLNLF VSQNLYKRGH
910 920 930 940 950
FAELLSYWQF VGKDKSAMAT EYFDSLKQYE KNCEGEDNMS CLADLYETLG
960 970 980 990 1000
RFLKDLGLLS QAIVPLQRSL EIRETALDPD HPRVAQSLHQ LASVYVQWKK
1010 1020 1030 1040 1050
FGNAEQLYKQ ALEISENAYG ADHPYTAREL EALATLYQKQ NKYEQAEHFR
1060 1070 1080 1090 1100
KKSFKIHQKA IKKKGNLYGF ALLRRRALQL EELTLGKDTP DNARTLNELG
1110 1120 1130 1140 1150
VLYYLQNNLE TADQFLKRSL EMRERVLGPD HPDCAQSLNN LAALCNEKKQ
1160 1170 1180 1190 1200
YDKAEELYER ALDIRRRALA PDHPSLAYTV KHLAILYKKM GKLDKAVPLY
1210 1220 1230 1240 1250
ELAVEIRQKS FGPKHPSVAT ALVNLAVLYS QMKKHVEALP LYERALKIYE
1260 1270 1280 1290 1300
DSLGRMHPRV GETLKNLAVL SYEGGDFEKA AELYKRAMEI KEAETSLLGG
1310 1320 1330
KAPSRHSSSG DTFSLKTAHS PNVFLQQGQR
Length:1,330
Mass (Da):150,864
Last modified:October 1, 2003 - v1
Checksum:i99C1F17C9A5117F8
GO
Isoform 2 (identifier: Q7Z494-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-720: Missing.
     1330-1330: R → RKVQSNLLSPEGLSNICAQEKTTRFTSS

Note: No experimental confirmation available.
Show »
Length:637
Mass (Da):73,014
Checksum:iB12632DACE1A9058
GO
Isoform 3 (identifier: Q7Z494-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     630-636: QVEKHMK → VVAYTSS
     637-1330: Missing.

Show »
Length:636
Mass (Da):71,101
Checksum:i8960364D3DFD50EA
GO
Isoform 4 (identifier: Q7Z494-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     132-181: ALQKTYQKIL...FKIFRETKEN → VTPGWAATPG...HILFESEMIP
     182-1330: Missing.

Note: No experimental confirmation available.
Show »
Length:181
Mass (Da):19,138
Checksum:iF5B40DF9324E1D1E
GO
Isoform 5 (identifier: Q7Z494-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     224-239: AAGTQCEYWTGGALGS → VSLESDQHPGIFIANF
     240-1330: Missing.

Note: No experimental confirmation available.
Show »
Length:239
Mass (Da):26,342
Checksum:i05AFCF865C45DC45
GO
Isoform 6 (identifier: Q7Z494-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     697-704: EKKLERHC → CWESRQFR
     705-1330: Missing.

Show »
Length:704
Mass (Da):79,132
Checksum:i6C99314707B4ED2C
GO
Isoform 7 (identifier: Q7Z494-7) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     132-150: ALQKTYQKILREKESALEA → GLAAVARSRLTATWNSWAQ
     151-1330: Missing.

Note: No experimental confirmation available.
Show »
Length:150
Mass (Da):15,798
Checksum:i10593BB409D181B0
GO

Sequence cautioni

The sequence BAB70891 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAC02709 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAC04268 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti223T → TT in CAI46202 (PubMed:17974005).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_022815360S → T in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs119456960EnsemblClinVar.1
Natural variantiVAR_022816386N → S in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs142021049EnsemblClinVar.1
Natural variantiVAR_022817397R → H in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs755094682Ensembl.1
Natural variantiVAR_044121973R → Q in RHPD1. 1 PublicationCorresponds to variant dbSNP:rs119456963EnsemblClinVar.1
Natural variantiVAR_0228181141L → P in NPHP3. 1 Publication1
Natural variantiVAR_0228191221A → V in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs202048210EnsemblClinVar.1
Natural variantiVAR_0228201252S → R in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs143451766EnsemblClinVar.1
Natural variantiVAR_0441221305R → C. Corresponds to variant dbSNP:rs35485382EnsemblClinVar.1
Natural variantiVAR_0228211314S → T in NPHP3. 1 PublicationCorresponds to variant dbSNP:rs75316802EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0144801 – 720Missing in isoform 2. 1 PublicationAdd BLAST720
Alternative sequenceiVSP_014482132 – 181ALQKT…ETKEN → VTPGWAATPGDPWEARPSCS LSKPSGFESSAETAHFNLRG HILFESEMIP in isoform 4. 1 PublicationAdd BLAST50
Alternative sequenceiVSP_014484132 – 150ALQKT…SALEA → GLAAVARSRLTATWNSWAQ in isoform 7. 1 PublicationAdd BLAST19
Alternative sequenceiVSP_014485151 – 1330Missing in isoform 7. 1 PublicationAdd BLAST1180
Alternative sequenceiVSP_014483182 – 1330Missing in isoform 4. 1 PublicationAdd BLAST1149
Alternative sequenceiVSP_014486224 – 239AAGTQ…GALGS → VSLESDQHPGIFIANF in isoform 5. 1 PublicationAdd BLAST16
Alternative sequenceiVSP_014487240 – 1330Missing in isoform 5. 1 PublicationAdd BLAST1091
Alternative sequenceiVSP_014488630 – 636QVEKHMK → VVAYTSS in isoform 3. 2 Publications7
Alternative sequenceiVSP_014489637 – 1330Missing in isoform 3. 2 PublicationsAdd BLAST694
Alternative sequenceiVSP_014490697 – 704EKKLERHC → CWESRQFR in isoform 6. 1 Publication8
Alternative sequenceiVSP_014491705 – 1330Missing in isoform 6. 1 PublicationAdd BLAST626
Alternative sequenceiVSP_0144811330R → RKVQSNLLSPEGLSNICAQE KTTRFTSS in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY257864 mRNA Translation: AAP83423.1
AY257865 mRNA Translation: AAP83424.1
AY257866 mRNA Translation: AAP83425.1
AB082531 mRNA Translation: BAC02709.1 Different initiation.
AK055253 mRNA Translation: BAB70891.1 Different initiation.
AK055893 mRNA Translation: BAB71038.1
AK094015 mRNA Translation: BAC04268.1 Different initiation.
AL832863 mRNA Translation: CAI46200.2
AL832877 Transcribed RNA Translation: CAI46202.1
CR749498 mRNA Translation: CAH18321.1
BC068082 mRNA Translation: AAH68082.1
CCDSiCCDS3078.1 [Q7Z494-1]
RefSeqiNP_694972.3, NM_153240.4 [Q7Z494-1]
UniGeneiHs.511991

Genome annotation databases

EnsembliENST00000337331; ENSP00000338766; ENSG00000113971 [Q7Z494-1]
ENST00000383282; ENSP00000372769; ENSG00000113971 [Q7Z494-7]
GeneIDi27031
KEGGihsa:27031
UCSCiuc003epe.3 human [Q7Z494-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiNPHP3_HUMAN
AccessioniPrimary (citable) accession number: Q7Z494
Secondary accession number(s): Q5JPE3
, Q5JPE6, Q68D99, Q6NVH3, Q7Z492, Q7Z493, Q8N9R2, Q8NCM5, Q96N70, Q96NK2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: October 1, 2003
Last modified: May 23, 2018
This is version 140 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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