U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

ATP2C2 ATPase secretory pathway Ca2+ transporting 2 [ Homo sapiens (human) ]

Gene ID: 9914, updated on 2-Nov-2024

Summary

Go to the top of the page Help
Official Symbol
ATP2C2provided by HGNC
Official Full Name
ATPase secretory pathway Ca2+ transporting 2provided by HGNC
Primary source
HGNC:HGNC:29103
See related
Ensembl:ENSG00000064270 MIM:613082; AllianceGenome:HGNC:29103
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPCA2
Summary
Enables P-type calcium transporter activity and P-type manganese transporter activity. Predicted to be involved in calcium ion transmembrane transport; intracellular calcium ion homeostasis; and manganese ion transport. Predicted to act upstream of or within mammary gland epithelium development; positive regulation of calcium ion import; and protein localization to plasma membrane. Predicted to be located in trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in colon (RPKM 16.5), skin (RPKM 9.9) and 12 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See ATP2C2 in Genome Data Viewer
Location:
16q24.1
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84368538..84464187)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90434936..90530568)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84402144..84497793)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903734 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:84340158-84341357 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84348057-84348215 Neighboring gene WAP four-disulfide core domain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84353071-84353592 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:84393612-84394811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84492707-84493206 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84494562-84495761 Neighboring gene ATP2C2 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:84512589-84513788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84516869-84517370 Neighboring gene MTOR associated protein, eak-7 homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84537675-84538175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84538296-84539243 Neighboring gene uncharacterized LOC124903736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7783 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84540344-84540580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84540853-84541353

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Secretory pathway Ca(2+)-ATPase SPCA2 regulates mitochondrial respiration and DNA damage response through store-independent calcium entry. Makena MR, et al. Redox Biol, 2022 Apr. PMID 35063802, Free PMC Article
  2. The secretory pathway Ca2+/Mn2+-ATPase 2 is a Golgi-localized pump with high affinity for Ca2+ ions. Vanoevelen J, et al. J Biol Chem, 2005 Jun 17. PMID 15831496
  3. Deletion of 16q24.1 supports a role for the ATP2C2 gene in specific language impairment. Smith AW, et al. J Child Neurol, 2015 Mar. PMID 25296922
  4. Identification of novel inhibitors of human SPCA2. Yamamoto S, et al. Biochem Biophys Res Commun, 2016 Aug 19. PMID 27297103
  5. The Ca2+/Mn2+-transporting SPCA2 pump is regulated by oxygen and cell density in colon cancer cells. Jenkins J, et al. Biochem J, 2016 Aug 15. PMID 27316461

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures.
    Title: A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures.
  2. Secretory pathway Ca(2+)-ATPase SPCA2 regulates mitochondrial respiration and DNA damage response through store-independent calcium entry.
    Title: Secretory pathway Ca(2+)-ATPase SPCA2 regulates mitochondrial respiration and DNA damage response through store-independent calcium entry.
  3. ATP2C2 Has Potential to Define Tumor Microenvironment in Breast Cancer.
    Title: ATP2C2 Has Potential to Define Tumor Microenvironment in Breast Cancer.
  4. Original association of ion transporters mediates the ECM-induced breast cancer cell survival: Kv10.1-Orai1-SPCA2 partnership.
    Title: Original association of ion transporters mediates the ECM-induced breast cancer cell survival: Kv10.1-Orai1-SPCA2 partnership.
  5. SPCA2C influences Ca(2+) homeostasis through multiple mechanisms, some of which are independent of Orai1, suggesting novel and possibly cell-specific Ca(2+) regulation.
    Title: The pancreas-specific form of secretory pathway calcium ATPase 2 regulates multiple pathways involved in calcium homeostasis.
  6. Low SPCA2 expression is associated with Epithelial-Mesenchymal Transition in Breast Cancer.
    Title: A Ca(2+)-ATPase Regulates E-cadherin Biogenesis and Epithelial-Mesenchymal Transition in Breast Cancer Cells.
  7. The genome-wide association meta-analysis identified five single nucleotide polymorphisms (SNPs) on chromosome 16 within ATP2C2 that associated with age of first cannabis use.
    Title: Genome-wide association meta-analysis of age at first cannabis use.
  8. In total, four independent SNPs within DYX1C1 and ATP2C2 were found to be associated with MMR stronger than expected from multiple testing. To explore potential pathomechanisms, we annotated these variants with functional data including tissue-specific expression analysis and eQTLs.
    Title: ATP2C2 and DYX1C1 are putative modulators of dyslexia-related MMR.
  9. The Secretory Pathway Ca(2+) -ATPases SPCA1 and SPCA2 are strongly induced under osteogenic conditions that elicit microcalcifications. SPCA gene expression is significantly elevated in breast cancer subtypes that are associated with microcalcifications.
    Title: Secretory pathway Ca(2+) -ATPases promote in vitro microcalcifications in breast cancer cells.
  10. The extract was found to comprise mainly primary fatty acid amides (PFAAs) by NMR analysis. Individual PFAAs, especially oleamide and linoleamide, almost completely inhibited hSPCA2 activity with IC50 values of 7.5 muM and 3.8 muM, respectively.
    Title: Identification of novel inhibitors of human SPCA2.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-09-17)

ClinGen Genome Curation Page
Haploinsufficency

No evidence available (Last evaluated 2018-09-17)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association analysis of blood biomarkers in chronic obstructive pulmonary disease.
EBI GWAS Catalog
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • KIAA0703, DKFZp686H22230

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables P-type calcium transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables P-type calcium transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables P-type manganese transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in calcium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mammary gland epithelium development IEA
Inferred from Electronic Annotation
more info
  
involved_in manganese ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in manganese ion transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of calcium ion import IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to plasma membrane IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in basolateral plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic side of plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in trans-Golgi network membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

Go to the top of the page Help
Preferred Names
calcium-transporting ATPase type 2C member 2
Names
ATPase 2C2
ATPase, Ca++ transporting, type 2C, member 2
Ca(2+)/Mn(2+)-ATPase 2C2
secretory pathway Ca(2+)-ATPase 2
secretory pathway Ca(2+)-transporting ATPase type 2
secretory pathway calcium ATPase 2
NP_001273456.2
NP_001278383.1
NP_055676.3
XP_011521788.1
XP_011521789.1
XP_047290950.1
XP_054170532.1
XP_054170533.1
XP_054170534.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001286527.3 → NP_001273456.2  calcium-transporting ATPase type 2C member 2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC022165, AY791884, BX648333
    Consensus CDS
    CCDS67088.1
    UniProtKB/TrEMBL
    B7ZA13
    Related
    ENSP00000397925.2, ENST00000416219.6
    Conserved Domains (6) summary
    TIGR01522
    Location:55 → 960
    ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase
    COG4087
    Location:625 → 709
    COG4087; Soluble P-type ATPase [General function prediction only]
    pfam00122
    Location:149 → 368
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:756 → 957
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:63 → 125
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam13246
    Location:441 → 523
    Cation_ATPase; Cation transport ATPase (P-type)

  2. NM_001291454.2 → NP_001278383.1  calcium-transporting ATPase type 2C member 2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, contains multiple differences in the coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The resulting isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK091051, AY791884, BX648333
    UniProtKB/TrEMBL
    B3KR57
    Related
    ENST00000420010.6
    Conserved Domains (5) summary
    COG4087
    Location:474 → 558
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01116
    Location:23 → 777
    ATPase-IIA1_Ca; sarco/endoplasmic reticulum calcium-translocating P-type ATPase
    pfam00122
    Location:23 → 217
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:605 → 777
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam13246
    Location:290 → 372
    Cation_ATPase; Cation transport ATPase (P-type)

  3. NM_014861.4 → NP_055676.3  calcium-transporting ATPase type 2C member 2 isoform 2

    See identical proteins and their annotated locations for NP_055676.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AY791884, BX648333
    Consensus CDS
    CCDS42207.1
    UniProtKB/Swiss-Prot
    B4DU76, E7ES94, O75185, Q5HYC3, Q5S053, Q68CQ2
    UniProtKB/TrEMBL
    B7ZA13
    Related
    ENSP00000262429.4, ENST00000262429.9
    Conserved Domains (1) summary
    cd02085
    Location:85 → 927
    P-type_ATPase_SPCA; golgi-associated secretory pathway Ca(2+) transport ATPases, similar to human ATPase secretory pathway Ca(2+) transporting 1/hSPCA1 and Saccharomyces cerevisiae Ca(2+)/Mn(2+)-transporting P-type ATPase, Pmr1p

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    84368538..84464187
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011523486.3 → XP_011521788.1  calcium-transporting ATPase type 2C member 2 isoform X1

    UniProtKB/TrEMBL
    B7ZA13
    Conserved Domains (6) summary
    TIGR01522
    Location:32 → 937
    ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase
    COG4087
    Location:602 → 686
    COG4087; Soluble P-type ATPase [General function prediction only]
    pfam00122
    Location:126 → 345
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:733 → 934
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:40 → 102
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam13246
    Location:418 → 500
    Cation_ATPase; Cation transport ATPase (P-type)

  2. XM_047434994.1 → XP_047290950.1  calcium-transporting ATPase type 2C member 2 isoform X2

  3. XM_011523487.3 → XP_011521789.1  calcium-transporting ATPase type 2C member 2 isoform X3

    Conserved Domains (3) summary
    COG4087
    Location:282 → 366
    COG4087; Soluble P-type ATPase [General function prediction only]
    pfam00689
    Location:413 → 614
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam13246
    Location:98 → 180
    Cation_ATPase; Cation transport ATPase (P-type)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90434936..90530568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314557.1 → XP_054170532.1  calcium-transporting ATPase type 2C member 2 isoform X1

  2. XM_054314558.1 → XP_054170533.1  calcium-transporting ATPase type 2C member 2 isoform X2

  3. XM_054314559.1 → XP_054170534.1  calcium-transporting ATPase type 2C member 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75185.3 GenPept UniProtKB/Swiss-Prot:O75185

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous