ATP9A Gene

HGNC Family	ATPases
Name	ATPase, class II, type 9A
Description	Enables protease binding activity. Involved in negative regulation of exosomal secretion; regulation of endocytic recycling; and regulation of retrograde transport, endosome to Golgi. Located in several cellular components, including endosome; perinuclear region of cytoplasm; and trans-Golgi network membrane. Implicated in neurodevelopmental disorder with poor growth and behavioral abnormalities. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n ATP9A is a member of the type IV P‐type ATPase family that appears to function as a putative aminophospholipid flippase with unique characteristics compared to other family members. Unlike many P4‐ATPases that require CDC50 subunits for proper endoplasmic reticulum exit, ATP9A localizes to both endosomal compartments and the plasma membrane. Its activity contributes to the regulation of membrane lipid asymmetry, which in turn influences several cellular processes. For example, ATP9A participates in the SNX3–retromer–mediated trafficking pathway, where it associates with conserved membrane‐remodeling factors (including MON2 and DOPEY2) to control the recycling and sorting of cargo proteins such as Wntless, thereby impacting Wnt morphogen secretion."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In addition, ATP9A plays an inhibitory role in the release of extracellular vesicles (EVs). Knockdown or knockout of ATP9A in human cells has been shown to significantly increase EV release and alter the lipid composition of exosomes, indicating that ATP9A helps maintain proper vesicular trafficking and exosome homeostasis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In pancreatic beta cells, ATP9A is concentrated at the plasma membrane, and silencing studies have implicated it in the regulation of insulin exocytosis, suggesting a critical role in secretory processes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": " Moreover, ATP9A has emerged as a candidate involved in cellular stress responses; its altered expression has been associated with responses to heat stress in pigs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n Notably, genetic studies have linked recessive splicing variants in ATP9A with neurodevelopmental disorders characterized by intellectual disability, motor impairment, and behavioral anomalies, highlighting its importance in proper neuronal development and function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": " Furthermore, epigenome‐wide analyses have identified methylation changes at the ATP9A locus in cord blood associated with in utero maternal smoking exposure, suggesting that modulation of ATP9A expression may have long‐term developmental consequences."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, ATP9A functions primarily by modulating phospholipid distribution across membranes, thereby governing key aspects of endosomal recycling, protein cargo sorting, extracellular vesicle release, and regulated exocytosis. Its proper activity is essential for maintaining cellular homeostasis, and disruptions in its function are linked to impaired secretion, stress responses, and neurodevelopmental disorders.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Ian J McGough, Reinoud E A de Groot, Adam P Jellett, et al. "}, {"type": "b", "children": [{"type": "t", "text": "SNX3-retromer requires an evolutionary conserved MON2:DOPEY2:ATP9A complex to mediate Wntless sorting and Wnt secretion."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-018-06114-3"}], "href": "https://doi.org/10.1038/s41467-018-06114-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30213940"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30213940"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Jyoti Naik, Chi M Hau, Lysbeth Ten Bloemendaal, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The P4-ATPase ATP9A is a novel determinant of exosome release."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0213069"}], "href": "https://doi.org/10.1371/journal.pone.0213069"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30947313"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30947313"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Xiao Xu, Limei Xu, Peng Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Effects of ATP9A on Extracellular Vesicle Release and Exosomal Lipid Composition."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oxid Med Cell Longev (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1155/2020/8865499"}], "href": "https://doi.org/10.1155/2020/8865499"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33178388"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33178388"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Israr-ul H Ansari, Melissa J Longacre, Coen C Paulusma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of P4 ATPase Phospholipid Translocases (Flippases) in Human and Rat Pancreatic Beta Cells: THEIR GENE SILENCING INHIBITS INSULIN SECRETION."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M115.655027"}], "href": "https://doi.org/10.1074/jbc.M115.655027"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26240149"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26240149"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Xuecong Wang, Yogesh Srivastava, Aleksander Jankowski, et al. "}, {"type": "b", "children": [{"type": "t", "text": "DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gky259"}], "href": "https://doi.org/10.1093/nar/gky259"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29669022"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29669022"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Francesca Mattioli, Hossein Darvish, Sohail Aziz Paracha, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Biallelic truncation variants in ATP9A are associated with a novel autosomal recessive neurodevelopmental disorder."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "NPJ Genom Med (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41525-021-00255-z"}], "href": "https://doi.org/10.1038/s41525-021-00255-z"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34764295"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34764295"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Christina A Markunas, Zongli Xu, Sophia Harlid, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Environ Health Perspect (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1289/ehp.1307892"}], "href": "https://doi.org/10.1289/ehp.1307892"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24906187"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24906187"}]}]}]}
Synonyms	ATPIIA
Proteins	ATP9A_HUMAN
NCBI Gene ID	10079
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

ATP9A has 11,317 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 118 datasets.

Click the + buttons to view associations for ATP9A from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

ATP9A Gene

Functional Associations

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

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ATP9A 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 ATP9A 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 ATP9A 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 RNA-seq	tissue samples with high or low expression of ATP9A 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 ATP9A 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 ATP9A 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 ATP9A 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 ATP9A 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 ATP9A gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of ATP9A 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 ATP9A gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with ATP9A protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with ATP9A 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 ATP9A gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of ATP9A 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 ATP9A 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 ATP9A gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing ATP9A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing ATP9A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing ATP9A protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing ATP9A protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with ATP9A 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 ATP9A 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 ATP9A gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with ATP9A gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with ATP9A gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with ATP9A gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of ATP9A 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 ATP9A gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with ATP9A 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 ATP9A 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 ATP9A 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 ATP9A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with ATP9A 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 ATP9A 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 ATP9A gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of ATP9A 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 ATP9A from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with ATP9A gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with ATP9A gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.