PKD1

polycystin 1, transient receptor potential channel interacting | PBP, Pc-1, TRPP1

This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]

Developmental clusters: GC6

Biological processes 104 terms

Golgi apparatus (GO:0005794)Golgi apparatus (GO:0005794)Golgi membrane (GO:0000139)Golgi-associated vesicle membrane (GO:0030660)Wnt receptor activity (GO:0042813)Wnt signaling pathway (GO:0016055)anatomical structure morphogenesis (GO:0009653)animal organ morphogenesis (GO:0009887)basolateral plasma membrane (GO:0016323)branching morphogenesis of an epithelial tube (GO:0048754)branching morphogenesis of an epithelial tube (GO:0048754)calcium channel activity (GO:0005262)calcium channel activity (GO:0005262)calcium channel activity (GO:0005262)calcium channel complex (GO:0034704)calcium ion transmembrane transport (GO:0070588)calcium ion transmembrane transport (GO:0070588)calcium ion transport (GO:0006816)calcium ion transport (GO:0006816)calcium ion transport (GO:0006816)calcium-independent cell-matrix adhesion (GO:0007161)cartilage development (GO:0051216)cartilage development (GO:0051216)cation channel complex (GO:0034703)cell surface (GO:0009986)cell surface receptor signaling pathway (GO:0007166)cell surface receptor signaling pathway (GO:0007166)cell surface receptor signaling pathway via JAK-STAT (GO:0007259)cell-cell adhesion (GO:0098609)cell-matrix adhesion (GO:0007160)chordate embryonic development (GO:0043009)ciliary membrane (GO:0060170)ciliary membrane (GO:0060170)cilium (GO:0005929)cilium (GO:0005929)cilium (GO:0005929)cytoplasm (GO:0005737)cytoplasm (GO:0005737)detection of mechanical stimulus (GO:0050982)digestive tract development (GO:0048565)embryonic placenta development (GO:0001892)embryonic placenta development (GO:0001892)endoplasmic reticulum (GO:0005783)endoplasmic reticulum (GO:0005783)extracellular exosome (GO:0070062)extracellular exosome (GO:0070062)extracellular region (GO:0005576)genitalia development (GO:0048806)heart development (GO:0007507)heart development (GO:0007507)homophilic cell-cell adhesion (GO:0007156)in utero embryonic development (GO:0001701)kidney development (GO:0001822)kidney development (GO:0001822)lateral plasma membrane (GO:0016328)lung epithelium development (GO:0060428)membrane (GO:0016020)membrane (GO:0016020)membrane (GO:0016020)mesonephric duct development (GO:0072177)mesonephric tubule development (GO:0072164)metanephric ascending thin limb development (GO:0072218)metanephric collecting duct development (GO:0072205)metanephric distal tubule morphogenesis (GO:0072287)metanephric proximal tubule development (GO:0072237)migrasome (GO:0140494)mitochondria-associated endoplasmic reticulum membrane contact site (GO:0044233)mitochondrion organization (GO:0007005)mitocytosis (GO:0160040)monoatomic cation channel activity (GO:0005261)monoatomic cation channel activity (GO:0005261)motile cilium (GO:0031514)motile cilium (GO:0031514)neural tube development (GO:0021915)nucleus (GO:0005634)nucleus (GO:0005634)placenta blood vessel development (GO:0060674)placenta blood vessel development (GO:0060674)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)polycystin complex (GO:0002133)polycystin complex (GO:0002133)positive regulation of cytosolic calcium ion concentration (GO:0007204)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein domain specific binding (GO:0019904)protein export from nucleus (GO:0006611)protein export from nucleus (GO:0006611)protein heterotetramerization (GO:0051290)protein kinase binding (GO:0019901)regulation of G1/S transition of mitotic cell cycle (GO:2000045)regulation of cell cycle (GO:0051726)regulation of cell cycle process (GO:0010564)regulation of gene expression (GO:0010468)regulation of proteasomal protein catabolic process (GO:0061136)regulation of proteasomal protein catabolic process (GO:0061136)skin development (GO:0043588)spinal cord development (GO:0021510)transcription regulator inhibitor activity (GO:0140416)transcription regulator inhibitor activity (GO:0140416)transmembrane transporter binding (GO:0044325)vesicle (GO:0031982)

Expression (TPM)

TFs regulating PKD1 0 TFs

Transcription factors with Perturb-seq knockdown data for PKD1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = PKD1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to PKD1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PKD1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr16:1,826,102–1,827,535	263.9 kb	Distal (>10kb) Multiome	1006
chr16:1,918,171–1,918,773	172.4 kb	Distal (>10kb) Multiome	129
chr16:1,929,283–1,930,271	161.0 kb	Distal (>10kb) Multiome	780
chr16:1,942,671–1,943,761	147.5 kb	Distal (>10kb) Multiome	750
chr16:1,958,923–1,960,140	131.4 kb	Distal (>10kb) Multiome	826
chr16:1,964,300–1,965,434	125.9 kb	Distal (>10kb) Multiome	933
chr16:1,971,481–1,972,435	118.9 kb	Distal (>10kb) Multiome HiCAR	1010
chr16:1,979,111–1,980,324	111.4 kb	Distal (>10kb) Multiome HiCAR	296
chr16:1,983,450–1,984,851	106.9 kb	Distal (>10kb) Multiome	917
chr16:1,989,307–1,993,568	98.5 kb	Distal (>10kb) Multiome	706
chr16:2,003,882–2,004,348	86.8 kb	Distal (>10kb) Multiome HiCAR	619
chr16:2,009,742–2,010,504	81.0 kb	Distal (>10kb) Multiome HiCAR	752
chr16:2,022,700–2,023,923	67.6 kb	Distal (>10kb) Multiome HiCAR	682
chr16:2,026,629–2,027,149	64.0 kb	Distal (>10kb) Multiome HiCAR	249
chr16:2,047,366–2,048,252	43.0 kb	Distal (>10kb) Multiome	875
chr16:2,090,476–2,092,232	467 bp	At TSS Multiome	344
chr16:2,128,331–2,128,834	7.1 kb	Proximal (<10kb)	119
chr16:2,135,536–2,136,505	45.3 kb	Distal (>10kb) Multiome	263
chr16:2,147,864–2,149,260	57.7 kb	Distal (>10kb) Multiome	679
chr16:2,149,550–2,152,180	60.2 kb	Distal (>10kb) Multiome	618
chr16:2,152,861–2,153,999	62.8 kb	Distal (>10kb) Multiome	734
chr16:2,154,834–2,156,329	64.7 kb	Distal (>10kb) Multiome	932
chr16:2,178,140–2,179,722	88.0 kb	Distal (>10kb) Multiome	318
chr16:2,205,129–2,206,297	114.7 kb	Distal (>10kb) Multiome	887
chr16:2,214,212–2,215,803	124.2 kb	Distal (>10kb) Multiome	953
chr16:2,223,095–2,224,285	132.6 kb	Distal (>10kb) Multiome	918
chr16:2,251,044–2,252,460	160.8 kb	Distal (>10kb) Multiome	996
chr16:2,267,625–2,269,111	177.4 kb	Distal (>10kb) Multiome	1044
chr16:2,339,631–2,342,283	250.0 kb	Distal (>10kb) Multiome	1129
chr16:2,428,282–2,429,948	338.4 kb	Distal (>10kb) Multiome	827

Genome Browser

Genomic view of the PKD1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.