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Protein

Polycystin-2

Gene

PKD2

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

Functioni

Functions as a cation channel involved in fluid-flow mechanosensation by the primary cilium in renal epithelium (PubMed:18695040). Functions as outward-rectifying K+ channel, but is also permeable to Ca2+, and to a much lesser degree also to Na+ (PubMed:11854751, PubMed:15692563, PubMed:27071085, PubMed:27991905). May contribute to the release of Ca2+ stores from the endoplasmic reticulum (PubMed:11854751, PubMed:20881056). Together with TRPV4, forms mechano- and thermosensitive channels in cilium (PubMed:18695040). PKD1 and PKD2 may function through a common signaling pathway that is necessary to maintain the normal, differentiated state of renal tubule cells. Acts as a regulator of cilium length, together with PKD1. The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling. Also involved in left-right axis specification via its role in sensing nodal flow; forms a complex with PKD1L1 in cilia to facilitate flow detection in left-right patterning. Detection of asymmetric nodal flow gives rise to a Ca2+ signal that is required for normal, asymmetric expression of genes involved in the specification of body left-right laterality (By similarity).By similarityCurated6 Publications

Miscellaneous

The mechanisms that govern channel opening are complex and still under debate; heterologous expression of PKD2 by itself or together with PKD1 gives rise to very low or undetectable spontaneous ion channel activity, in spite of its presence at the cell membrane.2 Publications

Activity regulationi

Channnel activity is regulated by phosphorylation (PubMed:16551655, PubMed:20881056, PubMed:26269590). Channnel activity is regulated by intracellular Ca2+ (PubMed:11854751).4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi763CalciumCombined sources1 Publication1
Metal bindingi765CalciumCombined sources1 Publication1
Metal bindingi767CalciumCombined sources1 Publication1
Metal bindingi769Calcium; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi774CalciumCombined sources1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Calcium bindingi763 – 774PROSITE-ProRule annotationCombined sources2 PublicationsAdd BLAST12

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionCalcium channel, Ion channel, Potassium channel, Voltage-gated channel
Biological processCalcium transport, Ion transport, Potassium transport, Transport
LigandCalcium, Metal-binding, Potassium

Enzyme and pathway databases

ReactomeiR-HSA-5620916 VxPx cargo-targeting to cilium
SIGNORiQ13563

Protein family/group databases

TCDBi1.A.5.2.1 the polycystin cation channel (pcc) family

Names & Taxonomyi

Protein namesi
Recommended name:
Polycystin-2
Short name:
PC21 Publication
Alternative name(s):
Autosomal dominant polycystic kidney disease type II protein
Polycystic kidney disease 2 protein
Polycystwin1 Publication
R48321
Transient receptor potential cation channel subfamily P member 21 PublicationImported
Gene namesi
Name:PKD2Imported
Synonyms:TRPP21 PublicationImported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

EuPathDBiHostDB:ENSG00000118762.7
HGNCiHGNC:9009 PKD2
MIMi173910 gene
neXtProtiNX_Q13563

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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 219Cytoplasmic3 PublicationsAdd BLAST219
Transmembranei220 – 241Helical; Name=S13 PublicationsAdd BLAST22
Topological domaini242 – 468Extracellular3 PublicationsAdd BLAST227
Transmembranei469 – 489Helical; Name=S23 PublicationsAdd BLAST21
Topological domaini490 – 505Cytoplasmic3 PublicationsAdd BLAST16
Transmembranei506 – 526Helical; Name=S33 PublicationsAdd BLAST21
Topological domaini527 – 552Extracellular3 PublicationsAdd BLAST26
Transmembranei553 – 573Helical; Name=S43 PublicationsAdd BLAST21
Topological domaini574 – 597Cytoplasmic3 PublicationsAdd BLAST24
Transmembranei598 – 619Helical; Name=53 PublicationsAdd BLAST22
Topological domaini620 – 631Extracellular3 PublicationsAdd BLAST12
Intramembranei632 – 646Pore-forming3 PublicationsAdd BLAST15
Topological domaini647 – 654Extracellular3 Publications8
Transmembranei655 – 675Helical; Name=S63 PublicationsAdd BLAST21
Topological domaini676 – 968Cytoplasmic3 PublicationsAdd BLAST293

Keywords - Cellular componenti

Cell membrane, Cell projection, Cilium, Cytoplasmic vesicle, Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Polycystic kidney disease 2 with or without polycystic liver disease (PKD2)11 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal dominant disorder characterized by progressive formation and enlargement of cysts in both kidneys, typically leading to end-stage renal disease in adult life. Cysts also occurs in the liver and other organs. It represents approximately 15% of the cases of autosomal dominant polycystic kidney disease. PKD2 is clinically milder than PKD1 but it has a deleterious impact on overall life expectancy.
See also OMIM:613095
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_058822306R → Q in PKD2. 1 PublicationCorresponds to variant dbSNP:rs990932947Ensembl.1
Natural variantiVAR_058823322R → Q in PKD2. 1 PublicationCorresponds to variant dbSNP:rs145877597Ensembl.1
Natural variantiVAR_058824322R → W in PKD2. 1 Publication1
Natural variantiVAR_011073356A → P in PKD2. 2 Publications1
Natural variantiVAR_064394384A → P in PKD2. 1 Publication1
Natural variantiVAR_009195414W → G in PKD2; affects channel activity as it is able to abolish channel currents induced by the gain-of-function artificial mutant P-604. 3 Publications1
Natural variantiVAR_058825420R → G in PKD2; affects channel activity as it is able to abolish channel currents induced by the gain-of-function artificial mutant P-604. 2 Publications1
Natural variantiVAR_011074479Missing in PKD2; somatic mutation. 1 Publication1
Natural variantiVAR_011075504 – 512Missing in PKD2; somatic mutation. 1 Publication9
Natural variantiVAR_058827511D → V in PKD2; loss of function in the release of Ca(2+) stores from the endoplasmic reticulum; no effect on location at the endoplasmic reticulum; affects channel activity as it is able to abolish channel currents induced by the gain-of-function artificial mutant P-604. 3 PublicationsCorresponds to variant dbSNP:rs121918043EnsemblClinVar.1
Natural variantiVAR_058828632C → R in PKD2. 1 Publication1
Natural variantiVAR_011076684Missing in PKD2; somatic mutation. 1 Publication1
Natural variantiVAR_058830807R → Q in PKD2. 1 PublicationCorresponds to variant dbSNP:rs147654263EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi76S → A: Abolishes phosphorylation of the N-terminal domain. Abolishes the ability to complement a pkd2-deficient zebrafish mutant; when associated with A-80. 1 Publication1
Mutagenesisi80S → A: Decreases phosphorylation of the N-terminal domain. Abolishes the ability to complement a pkd2-deficient zebrafish mutant; when associated with A-76. 1 Publication1
Mutagenesisi604F → A or I: No effect on channel activation. 1 Publication1
Mutagenesisi604F → P: Gain-of-function mutation resulting in increased channel activity. Absence of gain of function; when associated with F-605 DEL; when associated with V-511; when associated with G-414; when associated with G-420. Increased channel activity; when associated with 736-L-N-737 DEL. 1 Publication1
Mutagenesisi605Missing : Abolishes increased channel activity due to a gain of function mutation; when associated with P-604. 1 Publication1
Mutagenesisi721T → A: Decreases phosphorylation; when associated with A-801; A-812; A-831 and A-943. 1 Publication1
Mutagenesisi736 – 737Missing : Increased channel activity; when associated with P-604. 1 Publication2
Mutagenesisi768Q → G: Strongly increases calcium binding affinity. 1 Publication1
Mutagenesisi771T → A: Loss of calcium-binding site; when associated with A-774. 1 Publication1
Mutagenesisi774E → A: Loss of calcium-binding site; when associated with A-771. 1 Publication1
Mutagenesisi774E → Q: Abolishes calcium binding via the EF-hand. 1 Publication1
Mutagenesisi801S → A: Decreases phosphorylation; when associated with A-721; A-812; A-831 and A-943. 1 Publication1
Mutagenesisi801S → D: Phosphomimetic mutant. No effect on release of Ca(2+) stores from the endoplasmic reticulum. 1 Publication1
Mutagenesisi801S → G: Loss of phosphorylation at this site. Impairs release of Ca(2+) stores from the endoplasmic reticulum. 1 Publication1
Mutagenesisi804S → N: Loss of phosphorylation at Ser-801. 1 Publication1
Mutagenesisi812S → A: Decreases interaction with PACS1 and enhances expression at the cell membrane. Decreases phosphorylation; when associated with A-721; A-801; A-831 and A-943. 2 Publications1
Mutagenesisi812S → D: No effect on interaction with PACS1. 1 Publication1
Mutagenesisi815 – 817DDD → AAA: Strongly decreases interaction with PACS1 and enhances expression at the cell membrane. 1 Publication3
Mutagenesisi829S → A: Abolishes increased channel opening in response to cAMP and phosphorylation by PKA. 1 Publication1
Mutagenesisi831S → A: Decreases phosphorylation; when associated with A-721; A-801; A-812 and A-943. 1 Publication1
Mutagenesisi842L → A: Abolishes oligomerization and interaction with PKD1; when associated with A-846; A-849; A-860; A-863 and A-867. 1 Publication1
Mutagenesisi842L → P: Loss of protein solubility. 1 Publication1
Mutagenesisi846V → A: Abolishes oligomerization and interaction with PKD1; when associated with A-842; A-849; A-860; A-863 and A-867. 1 Publication1
Mutagenesisi846V → E: Loss of protein solubility. 1 Publication1
Mutagenesisi849M → A: Abolishes oligomerization and interaction with PKD1; when associated with A-842; A-846; A-860; A-863 and A-867. 1 Publication1
Mutagenesisi849M → K: Loss of protein solubility. 1 Publication1
Mutagenesisi853I → P: Loss of protein solubility. 1 Publication1
Mutagenesisi856I → K: Loss of protein solubility. 1 Publication1
Mutagenesisi860I → A: Abolishes oligomerization and interaction with PKD1; when associated with A-842; A-846; A-849; A-863 and A-867. 1 Publication1
Mutagenesisi863V → A: Abolishes oligomerization and interaction with PKD1; when associated with A-842; A-846; A-849; A-860 and A-867. 1 Publication1
Mutagenesisi863V → E: Loss of protein solubility; when associated with K-849. 1 Publication1
Mutagenesisi867L → A: Abolishes oligomerization and interaction with PKD1; when associated with A-842; A-846; A-849; A-860 and A-863. 1 Publication1
Mutagenesisi943S → A: Decreases phosphorylation; when associated with A-721; A-801; A-812 and A-831. 1 Publication1

Keywords - Diseasei

Ciliopathy, Disease mutation

Organism-specific databases

DisGeNETi5311
GeneReviewsiPKD2
MalaCardsiPKD2
MIMi613095 phenotype
OpenTargetsiENSG00000118762
Orphaneti730 Autosomal dominant polycystic kidney disease
PharmGKBiPA33343

Chemistry databases

GuidetoPHARMACOLOGYi504

Polymorphism and mutation databases

BioMutaiPKD2
DMDMi116242717

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001643561 – 968Polycystin-2Add BLAST968

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei76Phosphoserine1 Publication1
Modified residuei80Phosphoserine1 Publication1
Modified residuei137Omega-N-methylarginineBy similarity1
Glycosylationi299N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi305N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi328N-linked (GlcNAc...) (complex) asparagine4 Publications1
Disulfide bondi331 ↔ 344Combined sources2 Publications
Glycosylationi362N-linked (GlcNAc...) asparagine3 Publications1
Glycosylationi375N-linked (GlcNAc...) asparagine3 Publications1
Modified residuei801Phosphoserine1 Publication1 Publication1
Modified residuei808PhosphoserineBy similarity1
Modified residuei812PhosphoserineCombined sources2 Publications1
Modified residuei829Phosphoserine1 Publication1

Post-translational modificationi

Phosphorylated. Phosphorylation is important for protein function; a mutant that lacks the N-terminal phosphorylation sites cannot complement a zebrafish pkd2-deficient mutant (PubMed:16551655). PKD-mediated phosphorylation at the C-terminus regulates its function in the release of Ca2+ stores from the endoplasmic reticulum (PubMed:20881056). PKA-mediated phosphorylation at a C-terminal site strongly increases the open probability of the channel, but does not increase single channel conductance (PubMed:26269590).3 Publications
N-glycosylated. The four subunits in a tetramer probably differ in the extent of glycosylation; simultaneous glycosylation of all experimentally validated sites would probably create steric hindrance. Thus, glycosylation at Asn-305 is not compatible with glycosylation at Asn-328; only one of these two residues is glycosylated at a given time.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein, Methylation, Phosphoprotein

Proteomic databases

EPDiQ13563
MaxQBiQ13563
PaxDbiQ13563
PeptideAtlasiQ13563
PRIDEiQ13563
ProteomicsDBi59562
59563 [Q13563-2]
59564 [Q13563-3]
59565 [Q13563-4]
59566 [Q13563-5]

PTM databases

iPTMnetiQ13563
PhosphoSitePlusiQ13563

Expressioni

Tissue specificityi

Detected in fetal and adult kidney (PubMed:10770959). Detected at the thick ascending limb of the loop of Henle, at distal tubules, including the distal convoluted tubule and cortical collecting tubules, with weak staining of the collecting duct (PubMed:10770959). Detected on placenta syncytiotrophoblasts (at protein level) (PubMed:26269590). Strongly expressed in ovary, fetal and adult kidney, testis, and small intestine. Not detected in peripheral leukocytes.3 Publications

Gene expression databases

BgeeiENSG00000118762 Expressed in 235 organ(s), highest expression level in thoracic aorta
CleanExiHS_PKD2
ExpressionAtlasiQ13563 baseline and differential
GenevisibleiQ13563 HS

Organism-specific databases

HPAiCAB004544
HPA015794

Interactioni

Subunit structurei

Homotetramer (PubMed:20881056, PubMed:27768895, PubMed:27991905, PubMed:28092368). Interacts with PKD1, giving rise to a complex formed by one PKD1 chain and a PKD2 homooligomer (PubMed:20881056, PubMed:19556541). In vitro results suggest assembly of a complex composed of one PKD1 chain and a PKD2 trimer; the physiological significance of this is uncertain (PubMed:19556541). Isoform 1 interacts with PKD1 while isoform 3 does not (By similarity). Interacts with PKD1L1. PKD1 requires the presence of PKD2 for stable expression (By similarity). Interacts with CD2AP (PubMed:10913159). Interacts with HAX1 (PubMed:10760273). Interacts with NEK8 (By similarity). Part of a complex containing AKAP5, ADCY5, ADCY6 and PDE4C (By similarity). Interacts (via C-terminus) with TRPV4 (via C-terminus) (PubMed:18695040). Interacts (via C-terminal acidic region) with PACS1 and PACS2; these interactions retain the protein in the endoplasmic reticulum and prevent trafficking to the cell membrane (PubMed:15692563).By similarity9 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111328, 46 interactors
CORUMiQ13563
DIPiDIP-47455N
ELMiQ13563
IntActiQ13563, 25 interactors
MINTiQ13563
STRINGi9606.ENSP00000237596

Chemistry databases

BindingDBiQ13563

Structurei

Secondary structure

1968
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ13563
SMRiQ13563
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13563

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini750 – 785EF-handPROSITE-ProRule annotation2 PublicationsAdd BLAST36

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni803 – 822Linker1 PublicationAdd BLAST20
Regioni810 – 821Important for interaction with PACS1 and PACS21 PublicationAdd BLAST12

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili833 – 8721 Publication1 PublicationAdd BLAST40

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi641 – 643Selectivity filter1 Publication3

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi95 – 107Poly-GluAdd BLAST13
Compositional biasi153 – 157Poly-Arg5

Domaini

The C-terminal coiled-coil domain is involved in oligomerization and the interaction with PKD1 (PubMed:18694932, PubMed:19556541). The isolated coiled-coil domain forms a homotrimer in vitro; the homotrimer interacts with a single PKD1 chain (PubMed:19556541). The coiled-coil domain binds calcium and undergoes a calcium-induced conformation change (in vitro) (PubMed:18694932).2 Publications

Sequence similaritiesi

Belongs to the polycystin family.Curated

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3599 Eukaryota
ENOG410XTGE LUCA
GeneTreeiENSGT00700000104221
HOGENOMiHOG000230858
HOVERGENiHBG014945
InParanoidiQ13563
KOiK04986
OMAiGVIPSWQ
OrthoDBiEOG091G034F
PhylomeDBiQ13563
TreeFamiTF316484

Family and domain databases

Gene3Di1.20.120.350, 1 hit
InterProiView protein in InterPro
IPR011992 EF-hand-dom_pair
IPR002048 EF_hand_dom
IPR013122 PKD1_2_channel
IPR003915 PKD_2
IPR027359 Volt_channel_dom_sf
PfamiView protein in Pfam
PF08016 PKD_channel, 1 hit
PRINTSiPR01433 POLYCYSTIN2
SUPFAMiSSF47473 SSF47473, 1 hit
PROSITEiView protein in PROSITE
PS50222 EF_HAND_2, 1 hit

Sequences (5+)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q13563-1) [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
MVNSSRVQPQ QPGDAKRPPA PRAPDPGRLM AGCAAVGASL AAPGGLCEQR
60 70 80 90 100
GLEIEMQRIR QAAARDPPAG AAASPSPPLS SCSRQAWSRD NPGFEAEEEE
110 120 130 140 150
EEVEGEEGGM VVEMDVEWRP GSRRSAASSA VSSVGARSRG LGGYHGAGHP
160 170 180 190 200
SGRRRRREDQ GPPCPSPVGG GDPLHRHLPL EGQPPRVAWA ERLVRGLRGL
210 220 230 240 250
WGTRLMEESS TNREKYLKSV LRELVTYLLF LIVLCILTYG MMSSNVYYYT
260 270 280 290 300
RMMSQLFLDT PVSKTEKTNF KTLSSMEDFW KFTEGSLLDG LYWKMQPSNQ
310 320 330 340 350
TEADNRSFIF YENLLLGVPR IRQLRVRNGS CSIPQDLRDE IKECYDVYSV
360 370 380 390 400
SSEDRAPFGP RNGTAWIYTS EKDLNGSSHW GIIATYSGAG YYLDLSRTRE
410 420 430 440 450
ETAAQVASLK KNVWLDRGTR ATFIDFSVYN ANINLFCVVR LLVEFPATGG
460 470 480 490 500
VIPSWQFQPL KLIRYVTTFD FFLAACEIIF CFFIFYYVVE EILEIRIHKL
510 520 530 540 550
HYFRSFWNCL DVVIVVLSVV AIGINIYRTS NVEVLLQFLE DQNTFPNFEH
560 570 580 590 600
LAYWQIQFNN IAAVTVFFVW IKLFKFINFN RTMSQLSTTM SRCAKDLFGF
610 620 630 640 650
AIMFFIIFLA YAQLAYLVFG TQVDDFSTFQ ECIFTQFRII LGDINFAEIE
660 670 680 690 700
EANRVLGPIY FTTFVFFMFF ILLNMFLAII NDTYSEVKSD LAQQKAEMEL
710 720 730 740 750
SDLIRKGYHK ALVKLKLKKN TVDDISESLR QGGGKLNFDE LRQDLKGKGH
760 770 780 790 800
TDAEIEAIFT KYDQDGDQEL TEHEHQQMRD DLEKEREDLD LDHSSLPRPM
810 820 830 840 850
SSRSFPRSLD DSEEDDDEDS GHSSRRRGSI SSGVSYEEFQ VLVRRVDRME
860 870 880 890 900
HSIGSIVSKI DAVIVKLEIM ERAKLKRREV LGRLLDGVAE DERLGRDSEI
910 920 930 940 950
HREQMERLVR EELERWESDD AASQISHGLG TPVGLNGQPR PRSSRPSSSQ
960
STEGMEGAGG NGSSNVHV
Length:968
Mass (Da):109,691
Last modified:October 17, 2006 - v3
Checksum:iF8D2E760EBEA8B47
GO
Isoform 2 (identifier: Q13563-2) [UniParc]FASTAAdd to basket
Also known as: delta6

The sequence of this isoform differs from the canonical sequence as follows:
     476-483: CEIIFCFF → FICSSYGD
     484-968: Missing.

Show »
Length:483
Mass (Da):53,686
Checksum:i6F4CC2DD18EEF56F
GO
Isoform 3 (identifier: Q13563-3) [UniParc]FASTAAdd to basket
Also known as: delta7

The sequence of this isoform differs from the canonical sequence as follows:
     517-572: Missing.

Show »
Length:912
Mass (Da):103,134
Checksum:iEDD0DB1BD7750772
GO
Isoform 4 (identifier: Q13563-4) [UniParc]FASTAAdd to basket
Also known as: delta9

The sequence of this isoform differs from the canonical sequence as follows:
     633-646: IFTQFRIILGDINF → IICSWRSSMIRTLK
     647-968: Missing.

Show »
Length:646
Mass (Da):73,171
Checksum:iC3773DAF9FFDB249
GO
Isoform 5 (identifier: Q13563-5) [UniParc]FASTAAdd to basket
Also known as: delta12/13

The sequence of this isoform differs from the canonical sequence as follows:
     748-841: Missing.

Note: Minor isoform.
Show »
Length:874
Mass (Da):98,838
Checksum:i887260C960F987BE
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B4DFN3B4DFN3_HUMAN
cDNA FLJ50473, highly similar to Po...
PKD2
386Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti45G → R in AAC16004 (PubMed:9286709).Curated1
Sequence conflicti449G → V in AAC50933 (PubMed:8954772).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05882024P → L1 PublicationCorresponds to variant dbSNP:rs1004860210Ensembl.1
Natural variantiVAR_01107228R → P Common polymorphism. 5 PublicationsCorresponds to variant dbSNP:rs1805044EnsemblClinVar.1
Natural variantiVAR_058821190A → T1 PublicationCorresponds to variant dbSNP:rs117078377EnsemblClinVar.1
Natural variantiVAR_058822306R → Q in PKD2. 1 PublicationCorresponds to variant dbSNP:rs990932947Ensembl.1
Natural variantiVAR_058823322R → Q in PKD2. 1 PublicationCorresponds to variant dbSNP:rs145877597Ensembl.1
Natural variantiVAR_058824322R → W in PKD2. 1 Publication1
Natural variantiVAR_011073356A → P in PKD2. 2 Publications1
Natural variantiVAR_064394384A → P in PKD2. 1 Publication1
Natural variantiVAR_009195414W → G in PKD2; affects channel activity as it is able to abolish channel currents induced by the gain-of-function artificial mutant P-604. 3 Publications1
Natural variantiVAR_058825420R → G in PKD2; affects channel activity as it is able to abolish channel currents induced by the gain-of-function artificial mutant P-604. 2 Publications1
Natural variantiVAR_014919452I → V. Corresponds to variant dbSNP:rs1801612EnsemblClinVar.1
Natural variantiVAR_011074479Missing in PKD2; somatic mutation. 1 Publication1
Natural variantiVAR_058826482F → C1 PublicationCorresponds to variant dbSNP:rs75762896EnsemblClinVar.1
Natural variantiVAR_011075504 – 512Missing in PKD2; somatic mutation. 1 Publication9
Natural variantiVAR_058827511D → V in PKD2; loss of function in the release of Ca(2+) stores from the endoplasmic reticulum; no effect on location at the endoplasmic reticulum; affects channel activity as it is able to abolish channel currents induced by the gain-of-function artificial mutant P-604. 3 PublicationsCorresponds to variant dbSNP:rs121918043EnsemblClinVar.1
Natural variantiVAR_058828632C → R in PKD2. 1 Publication1
Natural variantiVAR_011076684Missing in PKD2; somatic mutation. 1 Publication1
Natural variantiVAR_058829800M → L1 PublicationCorresponds to variant dbSNP:rs2234917EnsemblClinVar.1
Natural variantiVAR_058830807R → Q in PKD2. 1 PublicationCorresponds to variant dbSNP:rs147654263EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_042479476 – 483CEIIFCFF → FICSSYGD in isoform 2. Curated8
Alternative sequenceiVSP_042480484 – 968Missing in isoform 2. CuratedAdd BLAST485
Alternative sequenceiVSP_042481517 – 572Missing in isoform 3. CuratedAdd BLAST56
Alternative sequenceiVSP_042482633 – 646IFTQF…GDINF → IICSWRSSMIRTLK in isoform 4. CuratedAdd BLAST14
Alternative sequenceiVSP_042483647 – 968Missing in isoform 4. CuratedAdd BLAST322
Alternative sequenceiVSP_042484748 – 841Missing in isoform 5. CuratedAdd BLAST94

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50928 mRNA Translation: AAC50520.1
AF004873
, AF004859, AF004860, AF004861, AF004862, AF004863, AF004864, AF004865, AF004866, AF004867, AF004868, AF004869, AF004870, AF004871, AF004872 Genomic DNA Translation: AAC16004.1
BC112261 mRNA Translation: AAI12262.1
BC112263 mRNA Translation: AAI12264.1
U56813 mRNA Translation: AAC50933.1
CCDSiCCDS3627.1 [Q13563-1]
PIRiG02640
RefSeqiNP_000288.1, NM_000297.3 [Q13563-1]
UniGeneiHs.181272

Genome annotation databases

EnsembliENST00000237596; ENSP00000237596; ENSG00000118762 [Q13563-1]
GeneIDi5311
KEGGihsa:5311
UCSCiuc003hre.4 human [Q13563-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

Polycystin 2 - Not a C-type lectin

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50928 mRNA Translation: AAC50520.1
AF004873
, AF004859, AF004860, AF004861, AF004862, AF004863, AF004864, AF004865, AF004866, AF004867, AF004868, AF004869, AF004870, AF004871, AF004872 Genomic DNA Translation: AAC16004.1
BC112261 mRNA Translation: AAI12262.1
BC112263 mRNA Translation: AAI12264.1
U56813 mRNA Translation: AAC50933.1
CCDSiCCDS3627.1 [Q13563-1]
PIRiG02640
RefSeqiNP_000288.1, NM_000297.3 [Q13563-1]
UniGeneiHs.181272

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KLDNMR-A680-796[»]
2KLENMR-A680-796[»]
2KQ6NMR-A720-797[»]
2Y4QNMR-A717-792[»]
3HRNX-ray1.90A833-895[»]
3HROX-ray1.90A833-872[»]
5K47electron microscopy4.20A/B/C/D185-723[»]
5MKEelectron microscopy4.30A/B/C/D1-968[»]
5MKFelectron microscopy4.20A/B/C/D1-968[»]
5T4Delectron microscopy3.00A/B/C/D198-702[»]
6A70electron microscopy3.60A/F/G185-723[»]
6D1Welectron microscopy3.54A/B/C/D53-792[»]
ProteinModelPortaliQ13563
SMRiQ13563
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111328, 46 interactors
CORUMiQ13563
DIPiDIP-47455N
ELMiQ13563
IntActiQ13563, 25 interactors
MINTiQ13563
STRINGi9606.ENSP00000237596

Chemistry databases

BindingDBiQ13563
GuidetoPHARMACOLOGYi504

Protein family/group databases

TCDBi1.A.5.2.1 the polycystin cation channel (pcc) family

PTM databases

iPTMnetiQ13563
PhosphoSitePlusiQ13563

Polymorphism and mutation databases

BioMutaiPKD2
DMDMi116242717

Proteomic databases

EPDiQ13563
MaxQBiQ13563
PaxDbiQ13563
PeptideAtlasiQ13563
PRIDEiQ13563
ProteomicsDBi59562
59563 [Q13563-2]
59564 [Q13563-3]
59565 [Q13563-4]
59566 [Q13563-5]

Protocols and materials databases

DNASUi5311
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000237596; ENSP00000237596; ENSG00000118762 [Q13563-1]
GeneIDi5311
KEGGihsa:5311
UCSCiuc003hre.4 human [Q13563-1]

Organism-specific databases

CTDi5311
DisGeNETi5311
EuPathDBiHostDB:ENSG00000118762.7
GeneCardsiPKD2
GeneReviewsiPKD2
HGNCiHGNC:9009 PKD2
HPAiCAB004544
HPA015794
MalaCardsiPKD2
MIMi173910 gene
613095 phenotype
neXtProtiNX_Q13563
OpenTargetsiENSG00000118762
Orphaneti730 Autosomal dominant polycystic kidney disease
PharmGKBiPA33343
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3599 Eukaryota
ENOG410XTGE LUCA
GeneTreeiENSGT00700000104221
HOGENOMiHOG000230858
HOVERGENiHBG014945
InParanoidiQ13563
KOiK04986
OMAiGVIPSWQ
OrthoDBiEOG091G034F
PhylomeDBiQ13563
TreeFamiTF316484

Enzyme and pathway databases

ReactomeiR-HSA-5620916 VxPx cargo-targeting to cilium
SIGNORiQ13563

Miscellaneous databases

ChiTaRSiPKD2 human
EvolutionaryTraceiQ13563
GeneWikiiPolycystic_kidney_disease_2
GenomeRNAii5311
PROiPR:Q13563
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000118762 Expressed in 235 organ(s), highest expression level in thoracic aorta
CleanExiHS_PKD2
ExpressionAtlasiQ13563 baseline and differential
GenevisibleiQ13563 HS

Family and domain databases

Gene3Di1.20.120.350, 1 hit
InterProiView protein in InterPro
IPR011992 EF-hand-dom_pair
IPR002048 EF_hand_dom
IPR013122 PKD1_2_channel
IPR003915 PKD_2
IPR027359 Volt_channel_dom_sf
PfamiView protein in Pfam
PF08016 PKD_channel, 1 hit
PRINTSiPR01433 POLYCYSTIN2
SUPFAMiSSF47473 SSF47473, 1 hit
PROSITEiView protein in PROSITE
PS50222 EF_HAND_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPKD2_HUMAN
AccessioniPrimary (citable) accession number: Q13563
Secondary accession number(s): O60441
, Q15764, Q2M1Q3, Q2M1Q5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: October 17, 2006
Last modified: November 7, 2018
This is version 193 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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