Aliases for ATP9A Gene

Aliases for ATP9A Gene

  • ATPase Phospholipid Transporting 9A (Putative) 2 3 5
  • ATPIIA 2 3 4
  • Probable Phospholipid-Transporting ATPase IIA 3 4
  • ATPase, Class II, Type 9A 2 3
  • KIAA0611 2 4
  • ATPase Type IV, Phospholipid-Transporting (P-Type),(Putative) 3
  • Phospholipid-Transporting ATPase IIA 3
  • ATPase Class II Type 9A 4
  • EC 51
  • EC 4
  • EC 3.6.3 51
  • ATP9A 5

External Ids for ATP9A Gene

Previous GeneCards Identifiers for ATP9A Gene

  • GC20M049936
  • GC20M050851
  • GC20M050898
  • GC20M049646
  • GC20M050213
  • GC20M046960

Summaries for ATP9A Gene

GeneCards Summary for ATP9A Gene

ATP9A (ATPase Phospholipid Transporting 9A (Putative)) is a Protein Coding gene. Diseases associated with ATP9A include Cholestasis, Benign Recurrent Intrahepatic, 1 and Robinow Syndrome, Autosomal Dominant 2. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Ion channel transport. Gene Ontology (GO) annotations related to this gene include nucleotide binding and cation-transporting ATPase activity. An important paralog of this gene is ATP9B.

Additional gene information for ATP9A Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATP9A Gene

Genomics for ATP9A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATP9A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J051765 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 618.9 +0.8 817 3.3 HNRNPL CREB1 CTCF ZBTB33 YBX1 PRDM10 ZNF692 TARDBP ZHX2 FOXA1 ATP9A lnc-MOCS3-6 NFATC2
GH20J051749 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +17.1 17089 5.8 HNRNPL CREB1 GATAD2A ZBTB33 ARID3A PRDM10 ZNF629 TFE3 SOX13 NFKBIZ ADNP PSMD10P1 ZFP64 ATP9A LOC100419570 lnc-MOCS3-6 NFATC2
GH20J051797 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 6.1 -31.8 -31780 6.2 HNRNPL CREB1 GATAD2A CTCF ARID3A TEAD4 TFE3 NFKBIZ ZNF692 TARDBP SALL4 lnc-ATP9A-1 ADNP DPM1 ZFP64 PSMD10P1 RNU7-6P MOCS3 ATP9A piR-43105-389
GH20J051594 Enhancer 1 ENCODE 14.5 +173.3 173272 1.1 GATAD2A CTCF TFE3 IKZF1 NFKBIZ ZNF692 TARDBP ZHX2 JUND ZNF143 ADNP ATP9A PSMD10P1 NFATC2 ZFP64 piR-61101-414
GH20J051741 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.5 +24.5 24489 5.8 CREB1 GATAD2A ZBTB33 YBX1 REST TFE3 SOX13 NFKBIZ KDM1A RCOR2 ATP9A SALL4 LOC100419570 lnc-MOCS3-6 NFATC2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP9A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP9A

Top Transcription factor binding sites by QIAGEN in the ATP9A gene promoter:
  • aMEF-2
  • HOXA9
  • HOXA9B
  • MEF-2
  • MEF-2A
  • Meis-1
  • Meis-1a
  • STAT1alpha
  • STAT1beta
  • STAT3

Genomic Locations for ATP9A Gene

Genomic Locations for ATP9A Gene
171,877 bases
Minus strand
172,121 bases
Minus strand

Genomic View for ATP9A Gene

Genes around ATP9A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP9A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP9A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP9A Gene

Proteins for ATP9A Gene

  • Protein details for ATP9A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable phospholipid-transporting ATPase IIA
    Protein Accession:
    Secondary Accessions:
    • E1P5Y3
    • E1P5Y4
    • Q5TFW5
    • Q5TFW6
    • Q5TFW9
    • Q6ZMF3
    • Q9NQK6
    • Q9NQK7

    Protein attributes for ATP9A Gene

    1047 amino acids
    Molecular mass:
    118583 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAD18775.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for ATP9A Gene


neXtProt entry for ATP9A Gene

Selected DME Specific Peptides for ATP9A Gene


Post-translational modifications for ATP9A Gene

  • Ubiquitination at Lys48, Lys765, and Lys822
  • Modification sites at PhosphoSitePlus

Other Protein References for ATP9A Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for ATP9A Gene

Gene Families for ATP9A Gene

Suggested Antigen Peptide Sequences for ATP9A Gene

GenScript: Design optimal peptide antigens:
  • ATPase class II type 9A (ATP9A_HUMAN)
  • ATP9A protein (Q2NLD0_HUMAN)
  • ATP9A protein (Q96B35_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IV subfamily.
  • Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IV subfamily.
genes like me logo Genes that share domains with ATP9A: view

Function for ATP9A Gene

Molecular function for ATP9A Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H(2)O + phospholipid(Side 1) = ADP + phosphate + phospholipid(Side 2).; EC=;.

Enzyme Numbers (IUBMB) for ATP9A Gene

Phenotypes From GWAS Catalog for ATP9A Gene

Gene Ontology (GO) - Molecular Function for ATP9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0000287 magnesium ion binding IEA --
GO:0002020 protease binding IPI 26094765
GO:0005524 ATP binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ATP9A: view
genes like me logo Genes that share phenotypes with ATP9A: view

Animal Models for ATP9A Gene

MGI Knock Outs for ATP9A:
  • Atp9a Atp9a<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for ATP9A

CRISPR Products

miRNA for ATP9A Gene

miRTarBase miRNAs that target ATP9A

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP9A

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ATP9A Gene

Localization for ATP9A Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP9A Gene

Early endosome membrane. Multi-pass membrane protein. Recycling endosome. Golgi apparatus, trans-Golgi network membrane. Note=Efficient exit from the endoplasmic reticulum does not require TMEM30A, nor TMEM30B.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATP9A gene
Compartment Confidence
endosome 5
golgi apparatus 5
plasma membrane 4
nucleus 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for ATP9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IBA 21873635
GO:0005769 early endosome IDA 21914794
GO:0005794 Golgi apparatus IEA --
GO:0005802 trans-Golgi network IBA,IDA 21914794
GO:0005886 plasma membrane IBA 21873635
genes like me logo Genes that share ontologies with ATP9A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ATP9A Gene

Pathways & Interactions for ATP9A Gene

genes like me logo Genes that share pathways with ATP9A: view

Pathways by source for ATP9A Gene

Gene Ontology (GO) - Biological Process for ATP9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER IBA 21873635
GO:0006897 endocytosis IBA 21873635
GO:0015914 phospholipid transport IEA --
GO:0045332 phospholipid translocation IBA,NAS 21914794
genes like me logo Genes that share ontologies with ATP9A: view

No data available for SIGNOR curated interactions for ATP9A Gene

Drugs & Compounds for ATP9A Gene

(3) Drugs for ATP9A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
PE(16:0/16:0) Experimental Pharma 0
ATP Investigational Nutra Agonist, Activator, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

(401) Additional Compounds for ATP9A Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Agonist, Full agonist, Partial agonist, Gating inhibitor, Antagonist 58-64-0
  • 1,2-Dipalmitoyl-3-sn-phosphatidic acid
  • 1,2-Dipalmitoyl-sn-glycerol-3-phosphate
  • 1,2-Dipalmitoyl-sn-glycerol-3-phosphoric acid
  • Dipalmitoyl phosphatidic acid
  • PA(32:0)
  • 1-Hexadecanoyl-2-(11Z-octadecenoyl)-sn-phosphatidic acid
  • 1-Palmitoyl-2-vaccenoyl-sn-glycero-3-phosphate
  • PA(16:0/18:1)
  • PA(16:0/18:1N7)
  • PA(16:0/18:1W7)
  • (2R)-1-(Palmitoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol 3-phosphate
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-phosphatidic acid
  • PA(16:0/18:1)
  • 1-16:0-2-18:2-Phosphatidic acid
  • 1-Palmitoyl-2-linoleoyl-sn-glycero-3-phosphate
  • 16:0-18:2-PA
  • 2-Linoleoyl-1-palmitoyl-sn-glycero-3-phosphate
  • PA(16:0/18:2)
genes like me logo Genes that share compounds with ATP9A: view

Transcripts for ATP9A Gene

mRNA/cDNA for ATP9A Gene

14 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP9A

Alternative Splicing Database (ASD) splice patterns (SP) for ATP9A Gene

No ASD Table

Relevant External Links for ATP9A Gene

GeneLoc Exon Structure for

Expression for ATP9A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATP9A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ATP9A Gene

This gene is overexpressed in Nasal epithelium (45.0) and Frontal cortex (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATP9A Gene

Protein tissue co-expression partners for ATP9A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP9A

SOURCE GeneReport for Unigene cluster for ATP9A Gene:


Evidence on tissue expression from TISSUES for ATP9A Gene

  • Nervous system(4.9)
  • Intestine(2.6)
genes like me logo Genes that share expression patterns with ATP9A: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP9A Gene

Orthologs for ATP9A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ATP9A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ATP9A 30 31
  • 99.54 (n)
(Ornithorhynchus anatinus)
Mammalia ATP9A 31
  • 97 (a)
(Monodelphis domestica)
Mammalia ATP9A 31
  • 96 (a)
(Canis familiaris)
Mammalia ATP9A 30 31
  • 91.76 (n)
(Bos Taurus)
Mammalia ATP9A 30 31
  • 89.8 (n)
(Mus musculus)
Mammalia Atp9a 30 17 31
  • 88.54 (n)
(Rattus norvegicus)
Mammalia Atp9a 30
  • 88.12 (n)
(Gallus gallus)
Aves ATP9A 30 31
  • 83.04 (n)
(Anolis carolinensis)
Reptilia -- 31
  • 99 (a)
-- 31
  • 87 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atp9a 30
  • 77.99 (n)
MGC76068 30
(Danio rerio)
Actinopterygii ATP9A 31
  • 88 (a)
Dr.15835 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG31729 31
  • 52 (a)
(Caenorhabditis elegans)
Secernentea tat-5 31
  • 55 (a)
F02C9.3 32
  • 55 (a)
tat-6 31
  • 52 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NEO1 31
  • 43 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 54 (a)
Species where no ortholog for ATP9A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ATP9A Gene

Gene Tree for ATP9A (if available)
Gene Tree for ATP9A (if available)
Evolutionary constrained regions (ECRs) for ATP9A: view image

Paralogs for ATP9A Gene

(13) SIMAP similar genes for ATP9A Gene using alignment to 3 proteins:

  • Q96B35_HUMAN
genes like me logo Genes that share paralogs with ATP9A: view

Variants for ATP9A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP9A Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
770302 Benign: not provided 51,604,848(-) G/A SYNONYMOUS_VARIANT
774966 Benign: not provided 51,729,952(-) C/A MISSENSE_VARIANT
777584 Benign: not provided 51,694,020(-) G/A SYNONYMOUS_VARIANT
784411 Benign: not provided 51,656,992(-) G/A SYNONYMOUS_VARIANT
785657 Benign: not provided 51,608,617(-) T/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for ATP9A Gene

Structural Variations from Database of Genomic Variants (DGV) for ATP9A Gene

Variant ID Type Subtype PubMed ID
dgv703n67 CNV gain 20364138
esv1250125 CNV insertion 17803354
esv2501264 CNV insertion 19546169
esv2668584 CNV deletion 23128226
esv2751917 CNV gain 17911159
esv2758800 CNV loss 17122850
esv3395647 CNV insertion 20981092
esv3410408 CNV insertion 20981092
esv3425228 CNV insertion 20981092
esv3646065 CNV loss 21293372
esv3646067 CNV gain 21293372
esv3646068 CNV gain 21293372
esv3646069 CNV gain 21293372
esv3646070 CNV gain 21293372
nsv1114224 CNV deletion 24896259
nsv1114225 CNV deletion 24896259
nsv1123494 CNV deletion 24896259
nsv1136329 CNV deletion 24896259
nsv473453 CNV novel sequence insertion 20440878
nsv513549 CNV insertion 21212237
nsv527764 CNV loss 19592680
nsv834004 CNV loss 17160897
nsv9816 CNV gain 18304495

Variation tolerance for ATP9A Gene

Residual Variation Intolerance Score: 1.98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.92; 35.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP9A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP9A Gene

Disorders for ATP9A Gene

MalaCards: The human disease database

(6) MalaCards diseases for ATP9A Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search ATP9A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ATP9A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with ATP9A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATP9A Gene

Publications for ATP9A Gene

  1. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4
  2. ATP9B, a P4-ATPase (a putative aminophospholipid translocase), localizes to the trans-Golgi network in a CDC50 protein-independent manner. (PMID: 21914794) Takatsu H … Shin HW (The Journal of biological chemistry 2011) 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Molecular genetics of successful smoking cessation: convergent genome-wide association study results. (PMID: 18519826) Uhl GR … Lerman C (Archives of general psychiatry 2008) 3 41
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for ATP9A Gene

Sources for ATP9A Gene