ATP2C2 Gene

HGNC Family	ATPases
Name	ATPase, Ca++ transporting, type 2C, member 2
Description	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, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n ATP2C2 encodes SPCA2, a specialized secretory pathway Ca<sup>2+</sup>/Mn<sup>2+</sup>-ATPase that transports Ca<sup>2+</sup> and Mn<sup2+</sup> into the Golgi lumen, thereby contributing to the regulation of intracellular ion homeostasis. Functional analyses have demonstrated that, in contrast to the ubiquitously expressed SPCA1, SPCA2 exhibits a more restricted tissue distribution (notably in the gastrointestinal and respiratory tracts, brain, and mammary gland) and possesses distinct kinetic properties—including a high apparent affinity for cytosolic Ca<sup>2+</sup> and unique regulatory transitions during its catalytic cycle—which underscore its specialized role in fine‐tuning calcium signalling within the secretory pathway (see."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": " In addition to its physiological function in controlling Golgi ion concentrations, genetic studies have implicated variants in ATP2C2 in neurodevelopmental phenotypes. For example, common and rare variants have been associated with deficits in phonological short‐term memory and specific language impairment, with certain missense mutations altering the ATPase activity of SPCA2 and correlating with lower performance on reading and language measures."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "6"}]}, {"type": "t", "text": " Furthermore, genome-wide association data have linked polymorphisms within ATP2C2 to age at first cannabis use, suggesting that altered Ca<sup>2+</sup> signalling via SPCA2 may extend its influence to broader aspects of neural development and behavior."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Together, these studies highlight the multifaceted role of ATP2C2 in modulating intracellular Ca<sup>2+</sup>/Mn<sup>2+</sup> transport and underscore its potential contribution to the etiology of language-related and other neurobehavioral traits.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Jo Vanoevelen, Leonard Dode, Kurt Van Baelen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The secretory pathway Ca2+/Mn2+-ATPase 2 is a Golgi-localized pump with high affinity for Ca2+ ions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M501026200"}], "href": "https://doi.org/10.1074/jbc.M501026200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15831496"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15831496"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Minghui Xiang, Deepti Mohamalawari, Rajini Rao "}, {"type": "b", "children": [{"type": "t", "text": "A novel isoform of the secretory pathway Ca2+,Mn(2+)-ATPase, hSPCA2, has unusual properties and is expressed in the brain."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M413116200"}], "href": "https://doi.org/10.1074/jbc.M413116200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15677451"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15677451"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Leonard Dode, Jens Peter Andersen, Jo Vanoevelen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Dissection of the functional differences between human secretory pathway Ca2+/Mn2+-ATPase (SPCA) 1 and 2 isoenzymes by steady-state and transient kinetic analyses."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M511547200"}], "href": "https://doi.org/10.1074/jbc.M511547200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16332677"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16332677"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Tom S Scerri, Andrew P Morris, Lyn-Louise Buckingham, et al. "}, {"type": "b", "children": [{"type": "t", "text": "DCDC2, KIAA0319 and CMIP are associated with reading-related traits."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biol Psychiatry (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.biopsych.2011.02.005"}], "href": "https://doi.org/10.1016/j.biopsych.2011.02.005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21457949"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21457949"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Dianne F Newbury, Laura Winchester, Laura Addis, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CMIP and ATP2C2 modulate phonological short-term memory in language impairment."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Hum Genet (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ajhg.2009.07.004"}], "href": "https://doi.org/10.1016/j.ajhg.2009.07.004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19646677"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19646677"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Angela Martinelli, Mabel L Rice, Joel B Talcott, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddab111"}], "href": "https://doi.org/10.1093/hmg/ddab111"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33864365"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33864365"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Camelia C Minică, Karin J H Verweij, Peter J van der Most, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Genome-wide association meta-analysis of age at first cannabis use."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Addiction (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/add.14368"}], "href": "https://doi.org/10.1111/add.14368"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30003630"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30003630"}]}]}]}
Synonyms	SPCA2
Proteins	AT2C2_HUMAN
NCBI Gene ID	9914
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

ATP2C2 has 4,858 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 112 datasets.

Click the + buttons to view associations for ATP2C2 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

ATP2C2 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by ATP2C2 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ATP2C2 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of ATP2C2 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of ATP2C2 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of ATP2C2 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of ATP2C2 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ATP2C2 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of ATP2C2 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of ATP2C2 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of ATP2C2 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of ATP2C2 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of ATP2C2 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of ATP2C2 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with ATP2C2 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of ATP2C2 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of ATP2C2 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of ATP2C2 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ATP2C2 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing ATP2C2 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing ATP2C2 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with ATP2C2 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with ATP2C2 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of ATP2C2 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with ATP2C2 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with ATP2C2 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with ATP2C2 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of ATP2C2 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by ATP2C2 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with ATP2C2 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with ATP2C2 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with ATP2C2 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with ATP2C2 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with ATP2C2 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with ATP2C2 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at ATP2C2 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of ATP2C2 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of ATP2C2 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing ATP2C2 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with ATP2C2 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with ATP2C2 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.