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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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ATP9A
ATPase phospholipid transporting 9A
Chromosome 20 Β· 20q13.2
NCBI Gene: 10079Ensembl: ENSG00000054793.15HGNC: HGNC:13540UniProt: B4DR18
50PubMed Papers
21Diseases
0Drugs
12Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
regulation of retrograde transport, endosome to Golgiregulation of endocytic recyclinglate endosometrans-Golgi networkneurodevelopmental disorder with poor growth and behavioral abnormalitiesAbnormality of the skeletal systemFailure to thriveSecondary microcephaly
✦AI Summary

ATP9A is a Class II P4-ATPase lipid flippase primarily localized to endosomal compartments and the trans-Golgi network 1, functioning as a CDC50-independent monomer with unique gating mechanisms 2. Its primary role involves regulating endosomal cargo recycling through modulation of RAB5 and RAB11 small GTPase activities 1, directing recycling endosome-to-plasma membrane trafficking and retrograde endosome-to-trans-Golgi transport. ATP9A works with MON2 and DOP1B to regulate SNX3 retromer-mediated sorting, preventing Wnt transporter WLS from lysosomal degradation 3. The protein also participates in exocytic Golgi-to-plasma membrane transport via phospholipid substrate recognition, preferentially binding negatively charged phospholipids including phosphatidylserine and phosphoinositides 2. ATP9A negatively regulates extracellular vesicle/exosome release and modulates exosomal lipid composition 4. Biallelic loss-of-function variants cause autosomal recessive neurodevelopmental disorders characterized by intellectual disability, ADHD, hypotonia, and impaired synaptic transmission 1, while de novo heterozygous missense variants also cause intellectual disability with dendritic spine defects 5. ATP9A deficiency in mice recapitulates human neurological phenotypes, including memory deficits and hyperkinetic movement 1. Additionally, ATP9A controls phosphoinositide membrane asymmetry, and its deficiency causes neomycin sensitivity 6.

Sources cited
1
ATP9A deficiency causes ADHD, intellectual disability, and hypotonia via impaired RAB5/RAB11-dependent endosomal recycling and neurite morphology defects
PMID: 36604604
2
ATP9A is a monomeric P4-ATPase flippase with unique TM6-10 helix-driven gating mechanism, preferentially binding negatively charged phospholipids
PMID: 40876594
3
ATP9A and ATP9B form homo/heteromeric complexes and regulate exocytic Golgi-to-plasma membrane transport
PMID: 40234049
4
De novo heterozygous ATP9A missense variants cause intellectual disability with dendritic spine and neuronal arborization defects
PMID: 40226306
5
ATP9A negatively regulates extracellular vesicle release and modulates exosomal ceramide and sphingosine composition
PMID: 33178388
6
ATP9A controls phosphoinositide membrane asymmetry by flipping PI4P; deficiency causes phosphoinositide exposure and neomycin sensitivity
PMID: 40646185
Disease Associationsβ“˜21
neurodevelopmental disorder with poor growth and behavioral abnormalitiesOpen Targets
0.71Strong
Abnormality of the skeletal systemOpen Targets
0.44Moderate
Failure to thriveOpen Targets
0.42Moderate
Secondary microcephalyOpen Targets
0.42Moderate
Intellectual disabilityOpen Targets
0.37Weak
Global developmental delayOpen Targets
0.37Weak
Abnormal abdomen morphologyOpen Targets
0.37Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
osteoarthritis, kneeOpen Targets
0.37Weak
alcohol drinkingOpen Targets
0.34Weak
nutritional deficiency diseaseOpen Targets
0.32Weak
deep vein thrombosisOpen Targets
0.31Weak
thrombophiliaOpen Targets
0.31Weak
medical procedureOpen Targets
0.27Weak
vascular diseaseOpen Targets
0.24Weak
glaucomaOpen Targets
0.23Weak
open-angle glaucomaOpen Targets
0.22Weak
genetic disorderOpen Targets
0.19Weak
Neurodevelopmental disorderOpen Targets
0.19Weak
Neurodevelopmental delayOpen Targets
0.19Weak
Neurodevelopmental disorder with poor growth and behavioral abnormalitiesUniProt
Pathogenic Variants12
NM_006045.3(ATP9A):c.2701G>T (p.Glu901Ter)Pathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜…β˜†β˜†β˜†2025β†’ Residue 901
NM_006045.3(ATP9A):c.307dup (p.Tyr103fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 103
NM_006045.3(ATP9A):c.2031_2032del (p.Asp679fs)Likely pathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜…β˜†β˜†β˜†2024β†’ Residue 679
NM_006045.3(ATP9A):c.1777C>T (p.Arg593Ter)Likely pathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜…β˜†β˜†β˜†2024β†’ Residue 593
NM_006045.3(ATP9A):c.1164dup (p.Leu389fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 389
NM_006045.3(ATP9A):c.868C>T (p.Arg290Ter)Pathogenic
not specified|Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜…β˜†β˜†β˜†2022β†’ Residue 290
NM_006045.3(ATP9A):c.799+1G>TPathogenic
See cases|Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜…β˜†β˜†β˜†2021
NM_006045.3(ATP9A):c.327+1G>TPathogenic
See cases
β˜…β˜†β˜†β˜†2021
NM_006045.3(ATP9A):c.983G>A (p.Trp328Ter)Pathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜†β˜†β˜†β˜†2023β†’ Residue 328
NM_006045.3(ATP9A):c.433C>T (p.Arg145Ter)Pathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜†β˜†β˜†β˜†2023β†’ Residue 145
NM_006045.3(ATP9A):c.642+1G>APathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜†β˜†β˜†β˜†2023
NM_006045.3(ATP9A):c.658C>T (p.Arg220Ter)Pathogenic
Neurodevelopmental disorder with poor growth and behavioral abnormalities
β˜†β˜†β˜†β˜†2023β†’ Residue 220
View on ClinVar β†—
Related Genes
ATP9BShared pathway38%ATP8B3Shared pathway22%ATP8B4Shared pathway22%ATP10BShared pathway22%ATP11CShared pathway20%ATP10DShared pathway20%
Tissue Expression6 tissues
Brain
100%
Heart
24%
Ovary
19%
Liver
10%
Lung
8%
Bone Marrow
6%
Gene Interaction Network
Click a node to explore
ATP9AATP9BATP8B3ATP8B4ATP10BATP11CATP10D
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt O75110
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.46Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.36 [0.28–0.46]
RankingsWhere ATP9A stands among ~20K protein-coding genes
  • #8,775of 20,598
    Most Researched50
  • #2,692of 5,498
    Most Pathogenic Variants12
  • #2,555of 17,882
    Most Constrained (LOEUF)0.46 Β· top quartile
Genes detectedATP9A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
ATP9A deficiency causes ADHD and aberrant endosomal recycling via modulating RAB5 and RAB11 activity.
PMID: 36604604
Mol Psychiatry Β· 2023
1.00
2
Lipid flippases ATP9A and ATP9B form a complex and contribute to the exocytic pathway from the Golgi.
PMID: 40234049
Life Sci Alliance Β· 2025
0.90
3
Heterozygous Missense Variants in the ATPase Phospholipid Transporting 9A Gene,
PMID: 40226306
Hum Mutat Β· 2025
0.80
4
Circular RNA circATP9A promotes non-small cell lung cancer progression by interacting with HuR and by promoting extracellular vesicles-mediated macrophage M2 polarization.
PMID: 38049814
J Exp Clin Cancer Res Β· 2023
0.70
5
P4-ATPases control phosphoinositide membrane asymmetry and neomycin resistance.
PMID: 40646185
Nat Cell Biol Β· 2025
0.60