Human Gene ATP2C1 (ENST00000510168.6_10) from GENCODE V47lift37
  Description: ATPase secretory pathway Ca2+ transporting 1, transcript variant 16 (from RefSeq NM_001378687.1)
Gencode Transcript: ENST00000510168.6_10
Gencode Gene: ENSG00000017260.20_17
Transcript (Including UTRs)
   Position: hg19 chr3:130,612,928-130,721,994 Size: 109,067 Total Exon Count: 28 Strand: +
Coding Region
   Position: hg19 chr3:130,613,614-130,720,194 Size: 106,581 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:130,612,928-130,721,994)mRNA (may differ from genome)Protein (919 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AT2C1_HUMAN
DESCRIPTION: RecName: Full=Calcium-transporting ATPase type 2C member 1; Short=ATPase 2C1; EC=3.6.3.8; AltName: Full=ATP-dependent Ca(2+) pump PMR1;
FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of the calcium.
CATALYTIC ACTIVITY: ATP + H(2)O + Ca(2+)(Side 1) = ADP + phosphate + Ca(2+)(Side 2).
SUBCELLULAR LOCATION: Golgi apparatus membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Found in most tissues except colon, thymus, spleen and leukocytes. Most abundant in keratinocytes and kidney.
DISEASE: Defects in ATP2C1 are the cause of Hailey-Hailey disease (HHD) [MIM:169600]; also known as benign familial pemphigus. HHD is an autosomal dominant disorder characterized by persistent blisters and suprabasal cell separation (acantholysis) of the epidermis, due to impaired keratinocyte adhesion. Patients lacking all isoforms except isoform 2 have HHD.
SIMILARITY: Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIA subfamily.
SEQUENCE CAUTION: Sequence=BAA92585.1; Type=Frameshift; Positions=8; Sequence=BAC11142.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ATP2C1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ATP2C1
Diseases sorted by gene-association score: hailey-hailey disease* (1738), darier disease (26), pemphigus (13), bullous skin disease (7), skin disease (3), cardiomyopathy, familial hypertrophic (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 26.33 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 661.88 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -192.20434-0.443 Picture PostScript Text
3' UTR -392.401800-0.218 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR023306 - ATPase_cation_domN
IPR008250 - ATPase_P-typ_ATPase-assoc-dom
IPR006413 - ATPase_P-typ_Ca-transp_PMR1
IPR006068 - ATPase_P-typ_cation-transptr_C
IPR004014 - ATPase_P-typ_cation-transptr_N
IPR023300 - ATPase_P-typ_cyto_domA
IPR023299 - ATPase_P-typ_cyto_domN
IPR000695 - ATPase_P-typ_H-transp
IPR001757 - ATPase_P-typ_ion-transptr
IPR018303 - ATPase_P-typ_P_site
IPR023298 - ATPase_P-typ_TM_dom
IPR005834 - Dehalogen-like_hydro
IPR023214 - HAD-like_dom

Pfam Domains:
PF00122 - E1-E2 ATPase
PF00689 - Cation transporting ATPase, C-terminus
PF00690 - Cation transporter/ATPase, N-terminus
PF00702 - haloacid dehalogenase-like hydrolase
PF13246 - Cation transport ATPase (P-type)

SCOP Domains:
81653 - Calcium ATPase, transduction domain A
56784 - HAD-like
81660 - Metal cation-transporting ATPase, ATP-binding domain N
81665 - Calcium ATPase, transmembrane domain M

ModBase Predicted Comparative 3D Structure on P98194
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005388 calcium-transporting ATPase activity
GO:0005509 calcium ion binding
GO:0005524 ATP binding
GO:0015410 manganese-transporting ATPase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0006828 manganese ion transport
GO:0006874 cellular calcium ion homeostasis
GO:0008544 epidermis development
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0030026 cellular manganese ion homeostasis
GO:0031532 actin cytoskeleton reorganization
GO:0032468 Golgi calcium ion homeostasis
GO:0032472 Golgi calcium ion transport
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0070588 calcium ion transmembrane transport
GO:0071421 manganese ion transmembrane transport
GO:0099132 ATP hydrolysis coupled cation transmembrane transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK296470 - Homo sapiens cDNA FLJ56454 complete cds, highly similar to Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8).
AK299945 - Homo sapiens cDNA FLJ55632 complete cds, highly similar to Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8).
AK304374 - Homo sapiens cDNA FLJ55630 complete cds, highly similar to Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8).
AB037768 - Homo sapiens mRNA for KIAA1347 protein, partial cds.
AF189723 - Homo sapiens calcium transport ATPase ATP2C1 (ATP2C1A) mRNA, complete cds.
AF225981 - Homo sapiens calcium transport ATPase ATP2C1 (ATP2C1) mRNA, complete cds.
AK304175 - Homo sapiens cDNA FLJ53274 complete cds, highly similar to Calcium-transporting ATPase type 2C member 1(EC 3.6.3.8).
BC028139 - Homo sapiens ATPase, Ca++ transporting, type 2C, member 1, mRNA (cDNA clone MGC:39950 IMAGE:5215224), complete cds.
AF181120 - Homo sapiens chromosome 3 ATP-dependent Ca2+ pump PMR1 (ATP2C1) mRNA, complete cds.
AF181121 - Homo sapiens chromosome 3 ATP-dependent Ca2+ pump PMR1 (ATP2C1) mRNA, alternatively spliced, complete cds.
AK314342 - Homo sapiens cDNA, FLJ95103, highly similar to Homo sapiens ATPase, Ca++ transporting, type 2C, member 1 (ATP2C1),mRNA.
AY268374 - Homo sapiens secretory pathway Ca2+/Mn2+ transport ATPase SPCA1b protein (ATP2C1) mRNA, complete cds, alternatively spliced.
AY268375 - Homo sapiens secretory pathway Ca2+/Mn2+ transport ATPase SPCA1d protein (ATP2C1) mRNA, complete cds, alternatively spliced.
KJ904720 - Synthetic construct Homo sapiens clone ccsbBroadEn_14114 ATP2C1 gene, encodes complete protein.
EU176250 - Synthetic construct Homo sapiens clone IMAGE:100006363; FLH169109.01X; RZPDo839G08250D ATPase, Ca++ transporting, type 2C, member 1 (ATP2C1) gene, encodes complete protein.
AK074692 - Homo sapiens cDNA FLJ90211 fis, clone MAMMA1002095, highly similar to Calcium-transporting ATPase type 2C, member 1 (EC 3.6.3.8).
JD459040 - Sequence 440064 from Patent EP1572962.
JD153976 - Sequence 135000 from Patent EP1572962.
JD432752 - Sequence 413776 from Patent EP1572962.
AB209265 - Homo sapiens mRNA for calcium-transporting ATPase 2C1 isoform 1d variant protein.
AK001684 - Homo sapiens cDNA FLJ10822 fis, clone NT2RP4001079, weakly similar to CALCIUM-TRANSPORTING ATPASE 1 (EC 3.6.1.38).
AJ010953 - Homo sapiens mRNA for putative Ca2+-transporting ATPase, partial.
JD037271 - Sequence 18295 from Patent EP1572962.
JD251855 - Sequence 232879 from Patent EP1572962.
JD551461 - Sequence 532485 from Patent EP1572962.
JD044651 - Sequence 25675 from Patent EP1572962.
JD360027 - Sequence 341051 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P98194 (Reactome details) participates in the following event(s):

R-HSA-936883 ATP2C1/2:Mg2+ transport cytosolic Ca2+ to Golgi lumen
R-HSA-936837 Ion transport by P-type ATPases
R-HSA-983712 Ion channel transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: AT2C1_HUMAN, ATP2C1 , B2RAT7, B4DSW3, B7Z3X9, ENST00000510168.1, ENST00000510168.2, ENST00000510168.3, ENST00000510168.4, ENST00000510168.5, G3XAH8, G8JLN9, HUSSY-28, KIAA1347, NM_001378687, O76005, P98194, PMR1L, Q86V72, Q86V73, Q8N6V1, Q8NCJ7, uc323fyi.1, uc323fyi.2
UCSC ID: ENST00000510168.6_10
RefSeq Accession: NM_001378687.1
Protein: P98194 (aka AT2C1_HUMAN or ATC1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.