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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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ATP13A3
ATPase 13A3
Chromosome 3 Β· 3q29
NCBI Gene: 79572Ensembl: ENSG00000133657.17HGNC: HGNC:24113UniProt: A0A2R8Y635
42PubMed Papers
21Diseases
0Drugs
8Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
membraneearly endosome membranerecycling endosome membraneP-type transmembrane transporter activitypulmonary hypertension, primary, 5pulmonary arterial hypertensionheritable pulmonary arterial hypertensiontympanic membrane disease
✦AI Summary

ATP13A3 is a P-type ATPase functioning as a polyamine transporter localized to recycling endosomes 1. It uses ATP energy to mediate polyamine uptake, particularly of putrescine, spermidine, and spermine, from endosomal compartments into the cytosol 12. In vascular endothelial cells, ATP13A3 maintains polyamine homeostasis critical for cell proliferation, survival under stress, and barrier function 1. Loss-of-function variants in ATP13A3 cause pulmonary arterial hypertension (PAH) with definitive evidence for gene-disease causality 3. PAH-associated variants impair polyamine transport, reducing endothelial polyamine content and causing EC dysfunction including reduced proliferation, increased apoptosis, and enhanced permeability 1. Heterozygous mice carrying disease-associated Atp13a3 variants spontaneously develop PAH with elevated pulmonary pressures and vascular remodeling 1. Beyond PAH, ATP13A3 regulates polyamine uptake in neuroblastoma cells, where high expression associates with poor survival and DFMO-induced polyamine uptake 4. High ATP13A3 expression in pancreatic cancer correlates with metastatic potential and decreased overall survival 2. These findings establish ATP13A3 as a critical regulator of cellular polyamine homeostasis with therapeutic implications for vascular and neoplastic diseases.

Sources cited
1
ATP13A3 localizes to recycling endosomes, transports polyamines, and loss-of-function variants cause PAH through endothelial dysfunction
PMID: 38626311
2
ATP13A3 has definitive evidence for PAH gene-disease causality per expert consensus classification
PMID: 37422716
3
ATP13A3 functions as a polyamine transporter in cancer cells and high expression correlates with poor survival
PMID: 35260637
4
ATP13A3 mediates basal and drug-induced polyamine uptake in neuroblastoma cells and is a therapeutic target
PMID: 39981745
5
Rare variants in ATP13A3 are significantly overrepresented in PAH patients
PMID: 29650961
6
ATP13A3 variants with loss of function explain approximately 2.7% of PAH cases
PMID: 35204766
7
Loss of ATP13A3 (polyamine transporter) improves survival in cells with combined FA pathway and metabolic deficiency
PMID: 40540243
Disease Associationsβ“˜21
pulmonary hypertension, primary, 5Open Targets
0.69Moderate
pulmonary arterial hypertensionOpen Targets
0.60Moderate
heritable pulmonary arterial hypertensionOpen Targets
0.37Weak
tympanic membrane diseaseOpen Targets
0.29Weak
aortic stenosisOpen Targets
0.15Weak
multinodular goiterOpen Targets
0.13Weak
aortic valve calcificationOpen Targets
0.11Weak
neuroblastomaOpen Targets
0.08Suggestive
hypertrophic cardiomyopathyOpen Targets
0.07Suggestive
Rare familial disorder with hypertrophic cardiomyopathyOpen Targets
0.07Suggestive
left ventricular noncompactionOpen Targets
0.07Suggestive
congenital heart diseaseOpen Targets
0.06Suggestive
dilated cardiomyopathyOpen Targets
0.06Suggestive
pulmonary hypertension, primary, 1Open Targets
0.05Suggestive
left ventricular noncompaction 10Open Targets
0.05Suggestive
Abnormal blistering of the skinOpen Targets
0.05Suggestive
hypertrophic cardiomyopathy 15Open Targets
0.05Suggestive
atrial heart septal defectOpen Targets
0.05Suggestive
pulmonary venoocclusive diseaseOpen Targets
0.05Suggestive
Congenitally uncorrected transposition of the great arteriesOpen Targets
0.05Suggestive
Pulmonary hypertension, primary, 5UniProt
Pathogenic Variants8
NM_001367549.1(ATP13A3):c.2227C>T (p.Arg743Cys)Likely pathogenic
Pulmonary arterial hypertension|Pulmonary hypertension, primary, 5
β˜…β˜…β˜†β˜†2022β†’ Residue 743
NM_001367549.1(ATP13A3):c.2549dup (p.Met850fs)Pathogenic
Pulmonary arterial hypertension|Pulmonary hypertension, primary, 5
β˜…β˜…β˜†β˜†2022β†’ Residue 850
NM_001367549.1(ATP13A3):c.3402+1G>TPathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001367549.1(ATP13A3):c.3341dup (p.Leu1114fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1114
NM_001367549.1(ATP13A3):c.2367G>A (p.Trp789Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 789
NM_001367549.1(ATP13A3):c.3328dup (p.Ser1110fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 1110
NM_001367549.1(ATP13A3):c.2563G>A (p.Val855Met)Likely pathogenic
Pulmonary arterial hypertension|Pulmonary hypertension, primary, 5
β˜…β˜†β˜†β˜†2021β†’ Residue 855
NM_001367549.1(ATP13A3):c.3079dup (p.Trp1027fs)Pathogenic
Pulmonary arterial hypertension|Pulmonary hypertension, primary, 5
β˜…β˜†β˜†β˜†2021β†’ Residue 1027
View on ClinVar β†—
Related Genes
ATP7AProtein interaction83%ATP7BProtein interaction83%ATP13A5Shared pathway60%ATP13A4Shared pathway60%SLC45A4Shared pathway33%ATP13A1Shared pathway33%
Tissue Expression6 tissues
Heart
100%
Bone Marrow
90%
Liver
74%
Lung
49%
Brain
27%
Ovary
23%
Gene Interaction Network
Click a node to explore
ATP13A3ATP7AATP7BATP13A5ATP13A4SLC45A4ATP13A1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9H7F0
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.43Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.33 [0.26–0.43]
RankingsWhere ATP13A3 stands among ~20K protein-coding genes
  • #9,837of 20,598
    Most Researched42
  • #3,103of 5,498
    Most Pathogenic Variants8
  • #2,296of 17,882
    Most Constrained (LOEUF)0.43 Β· top quartile
Genes detectedATP13A3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Identification of rare sequence variation underlying heritable pulmonary arterial hypertension.
PMID: 29650961
Nat Commun Β· 2018
1.00
2
Defining the clinical validity of genes reported to cause pulmonary arterial hypertension.
PMID: 37422716
Genet Med Β· 2023
0.90
3
ATP13A3 variants promote pulmonary arterial hypertension by disrupting polyamine transport.
PMID: 38626311
Cardiovasc Res Β· 2024
0.80
4
The polyamine transporter ATP13A3 mediates difluoromethylornithine-induced polyamine uptake in neuroblastoma.
PMID: 39981745
Mol Oncol Β· 2025
0.70
5
Channelopathy Genes in Pulmonary Arterial Hypertension.
PMID: 35204766
Biomolecules Β· 2022
0.60