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Aliases for ATP13A2 Gene

Aliases for ATP13A2 Gene

  • ATPase Cation Transporting 13A2 2 3
  • ATPase 13A2 2 3 5
  • ATPase Type 13A2 2 3
  • PARK9 3 4
  • Parkinson Disease (Autosomal Recessive) 9 (Kufor-Rakeb Syndrome) 2
  • Probable Cation-Transporting ATPase 13A2 3
  • Cation-Transporting ATPase 13A2 3
  • EC 3.6.3.- 4
  • HSA9947 3
  • CLN12 3
  • KRPPD 3
  • SPG78 3

External Ids for ATP13A2 Gene

Previous HGNC Symbols for ATP13A2 Gene

  • PARK9

Previous GeneCards Identifiers for ATP13A2 Gene

  • GC01M017058
  • GC01M017185
  • GC01M017312
  • GC01M015556

Summaries for ATP13A2 Gene

Entrez Gene Summary for ATP13A2 Gene

  • This gene encodes a member of the P5 subfamily of ATPases which transports inorganic cations as well as other substrates. Mutations in this gene are associated with Kufor-Rakeb syndrome (KRS), also referred to as Parkinson disease 9. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2008]

GeneCards Summary for ATP13A2 Gene

ATP13A2 (ATPase Cation Transporting 13A2) is a Protein Coding gene. Diseases associated with ATP13A2 include Kufor-Rakeb Syndrome and Spastic Paraplegia 78, Autosomal Recessive. Among its related pathways are Cardiac conduction and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include nucleotide binding and cation-transporting ATPase activity. An important paralog of this gene is ATP13A3.

UniProtKB/Swiss-Prot for ATP13A2 Gene

  • ATPase that plays a role in intracellular cation homeostasis and the maintenance of neuronal integrity (PubMed:22186024). Required for a proper lysosomal and mitochondrial maintenance (PubMed:22296644, PubMed:28137957).

Gene Wiki entry for ATP13A2 Gene

Additional gene information for ATP13A2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATP13A2 Gene

Genomics for ATP13A2 Gene

GeneHancer (GH) Regulatory Elements for ATP13A2 Gene

Promoters and enhancers for ATP13A2 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
GH01J017011 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 -0.5 -522 2.6 ATF1 ZFP64 ARID4B SIN3A ETS1 ZNF766 GLIS2 ZNF213 ZNF143 ZFP91 ATP13A2 MFAP2 ARHGEF19 CROCC CROCCP3 ENSG00000235241 RPL22P3 LINC01772 NBPF1 FBXO42
GH01J016938 Enhancer 0.9 Ensembl ENCODE dbSUPER 11.3 +72.8 72780 2.2 BCOR GLIS2 POLR2A ZNF10 ZFP36 ZMYM3 ZBTB33 SDHB LOC105376805 ATP13A2 PADI2 CROCC TRE-TTC3-1 PIR55831 GC01M016886
GH01J016977 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 5 +31.8 31845 4.7 MXI1 ZIC2 ZNF48 HIC1 ZNF121 ZNF335 POLR2A ZNF143 RCOR1 FOS MFAP2 ENSG00000226526 LOC105376805 PADI3 ATP13A2 CROCCP2 LOC105376806
GH01J016925 Enhancer 0.9 ENCODE dbSUPER 4.6 +85.7 85713 2.4 CTCF MXI1 SIN3A ZIC2 ZKSCAN1 HIC1 ZNF664 ZFHX2 GLIS2 SCRT2 GC01M016886 SDHB ESPNP CROCCP2 ATP13A2 PIR55831 CROCC
GH01J017188 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 1.4 -179.4 -179366 5.2 HDAC1 PKNOX1 ATF1 YBX1 NFXL1 TCF12 GATA2 ATF7 CREM ZBTB11 ENSG00000204362 NECAP2 CROCC PADI3 ATP13A2 ENSG00000282843 GC01M017107 GC01M017106
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ATP13A2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ATP13A2 gene promoter:

Genomic Locations for ATP13A2 Gene

Genomic Locations for ATP13A2 Gene
26,015 bases
Minus strand

Genomic View for ATP13A2 Gene

Genes around ATP13A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP13A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP13A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP13A2 Gene

Proteins for ATP13A2 Gene

  • Protein details for ATP13A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cation-transporting ATPase 13A2
    Protein Accession:
    Secondary Accessions:
    • O75700
    • Q5JXY1
    • Q5JXY2
    • Q6S9Z9

    Protein attributes for ATP13A2 Gene

    1180 amino acids
    Molecular mass:
    128794 Da
    Quaternary structure:
    No Data Available
    • Sequence=CAA08912.1; Type=Frameshift; Positions=1054; Evidence={ECO:0000305};

    Alternative splice isoforms for ATP13A2 Gene


neXtProt entry for ATP13A2 Gene

Post-translational modifications for ATP13A2 Gene

  • Autophosphorylated.
  • Ubiquitination at Lys859, Lys843, posLast=835835, Lys693, Lys143, and posLast=6868
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ATP13A2 Gene

Domains & Families for ATP13A2 Gene

Gene Families for ATP13A2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type V subfamily.
  • Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type V subfamily.
genes like me logo Genes that share domains with ATP13A2: view

Function for ATP13A2 Gene

Molecular function for ATP13A2 Gene

UniProtKB/Swiss-Prot Function:
ATPase that plays a role in intracellular cation homeostasis and the maintenance of neuronal integrity (PubMed:22186024). Required for a proper lysosomal and mitochondrial maintenance (PubMed:22296644, PubMed:28137957).
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

Enzyme Numbers (IUBMB) for ATP13A2 Gene

Phenotypes From GWAS Catalog for ATP13A2 Gene

Gene Ontology (GO) - Molecular Function for ATP13A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005388 calcium-transporting ATPase activity IBA --
GO:0005515 protein binding IPI 22645275
GO:0005524 ATP binding IEA --
GO:0008270 zinc ion binding ISS 22361905
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATP13A2: view
genes like me logo Genes that share phenotypes with ATP13A2: view

Human Phenotype Ontology for ATP13A2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ATP13A2 Gene

MGI Knock Outs for ATP13A2:

Animal Model Products

miRNA for ATP13A2 Gene

miRTarBase miRNAs that target ATP13A2

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for ATP13A2 Gene

Localization for ATP13A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP13A2 Gene

Membrane; Multi-pass membrane protein. Lysosome. Lysosome membrane.

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 ATP13A2 gene
Compartment Confidence
plasma membrane 5
lysosome 5
endosome 5
mitochondrion 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for ATP13A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IDA,IEA 16964263
GO:0005765 lysosomal membrane TAS 25548531
GO:0005770 late endosome IDA 25392495
GO:0005771 multivesicular body TAS 25548531
GO:0005776 autophagosome IDA 24603074
genes like me logo Genes that share ontologies with ATP13A2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ATP13A2 Gene

Pathways & Interactions for ATP13A2 Gene

genes like me logo Genes that share pathways with ATP13A2: view

Pathways by source for ATP13A2 Gene

1 Cell Signaling Technology pathway for ATP13A2 Gene

Gene Ontology (GO) - Biological Process for ATP13A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006812 cation transport IEA --
GO:0006874 cellular calcium ion homeostasis IDA 22186024
GO:0006879 cellular iron ion homeostasis IMP 26818499
GO:0006882 cellular zinc ion homeostasis IMP 24603074
GO:0010821 regulation of mitochondrion organization IMP 22198378
genes like me logo Genes that share ontologies with ATP13A2: view

No data available for SIGNOR curated interactions for ATP13A2 Gene

Drugs & Compounds for ATP13A2 Gene

(3) Drugs for ATP13A2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for ATP13A2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with ATP13A2: view

Transcripts for ATP13A2 Gene

Unigene Clusters for ATP13A2 Gene

ATPase type 13A2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATP13A2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d ·
SP1: - - - -
SP2: - - -
SP3: - - - -
SP4: -
SP7: - -
SP8: -
SP9: -

ExUns: 15e ^ 16 ^ 17 ^ 18a · 18b · 18c ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27a · 27b ^ 28 ^ 29a · 29b
SP1: - -
SP2: - -
SP3: - - - -
SP5: - -
SP8: - - -
SP9: -

Relevant External Links for ATP13A2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ATP13A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ATP13A2 Gene

Protein differential expression in normal tissues from HIPED for ATP13A2 Gene

This gene is overexpressed in Breast (54.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATP13A2 Gene

Protein tissue co-expression partners for ATP13A2 Gene

NURSA nuclear receptor signaling pathways regulating expression of ATP13A2 Gene:


SOURCE GeneReport for Unigene cluster for ATP13A2 Gene:


mRNA Expression by UniProt/SwissProt for ATP13A2 Gene:

Tissue specificity: Expressed in brain; protein levels are markedly increased in brain from subjects with Parkinson disease and subjects with dementia with Lewy bodies. Detected in pyramidal neurons located throughout the cingulate cortex (at protein level). In the substantia nigra, it is found in neuromelanin-positive dopaminergic neurons (at protein level).

Evidence on tissue expression from TISSUES for ATP13A2 Gene

  • Nervous system(4.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP13A2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • head
  • neck
  • nose
  • olfactory bulb
  • foot
  • lower limb
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with ATP13A2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ATP13A2 Gene

Orthologs for ATP13A2 Gene

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

Orthologs for ATP13A2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ATP13A2 34 33
  • 98.95 (n)
(Canis familiaris)
Mammalia ATP13A2 34 33
  • 87.18 (n)
(Bos Taurus)
Mammalia ATP13A2 34 33
  • 86.53 (n)
(Mus musculus)
Mammalia Atp13a2 16 34 33
  • 85.14 (n)
(Rattus norvegicus)
Mammalia Atp13a2 33
  • 84.83 (n)
(Monodelphis domestica)
Mammalia ATP13A2 34
  • 61 (a)
(Ornithorhynchus anatinus)
Mammalia ATP13A2 34
  • 49 (a)
(Gallus gallus)
Aves ATP13A2 34
  • 59 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 36 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2717 33
(Danio rerio)
Actinopterygii atp13a2 34 33
  • 58.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32000 34
  • 29 (a)
(Caenorhabditis elegans)
Secernentea catp-7 34
  • 35 (a)
catp-6 34
  • 34 (a)
catp-5 34
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YPK9 34
  • 27 (a)
Species where no ortholog for ATP13A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for ATP13A2 Gene

Gene Tree for ATP13A2 (if available)
Gene Tree for ATP13A2 (if available)
Evolutionary constrained regions (ECRs) for ATP13A2: view image

Paralogs for ATP13A2 Gene

Paralogs for ATP13A2 Gene

(3) SIMAP similar genes for ATP13A2 Gene using alignment to 9 proteins:

  • AT132_HUMAN
  • H0Y8I1_HUMAN
  • H0Y8V5_HUMAN
  • H0Y8Z6_HUMAN
  • H0Y953_HUMAN
  • H0Y9K0_HUMAN
  • H0Y9K4_HUMAN
  • Q8N4D4_HUMAN
genes like me logo Genes that share paralogs with ATP13A2: view

Variants for ATP13A2 Gene

Sequence variations from dbSNP and Humsavar for ATP13A2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1057519289 pathogenic, Spastic paraplegia 78, autosomal recessive 16,986,346(-) G/A coding_sequence_variant, missense_variant, stop_gained
rs1057519290 pathogenic, Spastic paraplegia 78, autosomal recessive 16,986,886(-) AGAAGA/AGA coding_sequence_variant, inframe_deletion
rs1057519291 paraplegia 78, autosomal recessive (SPG78) [MIM:617225], pathogenic, Spastic paraplegia 78, autosomal recessive 16,993,828(-) G/A coding_sequence_variant, intron_variant, missense_variant
rs1057519292 pathogenic, Spastic paraplegia 78, autosomal recessive 17,004,805(-) G/A coding_sequence_variant, stop_gained
rs1057519293 pathogenic, Spastic paraplegia 78, autosomal recessive 16,996,262(-) G/A coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for ATP13A2 Gene

Variant ID Type Subtype PubMed ID
dgv108n100 CNV gain 25217958
dgv120n100 CNV gain 25217958
dgv92n100 CNV gain 25217958
esv2758925 CNV gain+loss 17122850
esv3360661 CNV insertion 20981092
nsv428421 CNV gain+loss 18775914
nsv508947 CNV insertion 20534489
nsv834269 CNV loss 17160897
nsv834280 CNV loss 17160897
nsv954854 CNV deletion 24416366

Variation tolerance for ATP13A2 Gene

Residual Variation Intolerance Score: 14.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP13A2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP13A2 Gene

Disorders for ATP13A2 Gene

MalaCards: The human disease database

(16) MalaCards diseases for ATP13A2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
kufor-rakeb syndrome
  • krs
spastic paraplegia 78, autosomal recessive
  • spg78
juvenile-onset parkinson's disease
  • juvenile-onset parkinson disease
neuronal ceroid lipofuscinosis
  • batten disease
early-onset parkinson's disease
  • early-onset parkinson disease
- elite association - COSMIC cancer census association via MalaCards


  • Spastic paraplegia 78, autosomal recessive (SPG78) [MIM:617225]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269 PubMed:27217339, ECO:0000269 PubMed:28137957}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Kufor-Rakeb syndrome (KRS) [MIM:606693]: A rare form of autosomal recessive juvenile or early-onset, levodopa-responsive parkinsonism. In addition to typical parkinsonian signs, clinical manifestations of Kufor-Rakeb syndrome include behavioral problems, facial tremor, pyramidal tract dysfunction, supranuclear gaze palsy, and dementia. {ECO:0000269 PubMed:16964263, ECO:0000269 PubMed:17485642, ECO:0000269 PubMed:18413573, ECO:0000269 PubMed:20683840, ECO:0000269 PubMed:20853184, ECO:0000269 PubMed:21542062, ECO:0000269 PubMed:22296644, ECO:0000269 PubMed:22388936, ECO:0000269 PubMed:22768177, ECO:0000269 PubMed:28137957}. Note=The disease is caused by mutations affecting the gene represented in this entry. KRS has also been referred to as neuronal ceroid lipofuscinosis 12 (CLN12), due to neuronal and glial lipofuscin deposits detected in the cortex, basal nuclei and cerebellum of some patients. {ECO:0000269 PubMed:22388936}.

Additional Disease Information for ATP13A2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ATP13A2: view

No data available for Genatlas for ATP13A2 Gene

Publications for ATP13A2 Gene

  1. ATP13A2 variability in Parkinson disease. (PMID: 19085912) Vilariño-Güell C … Farrer MJ (Human mutation 2009) 3 4 44 58
  2. Novel ATP13A2 variant associated with Parkinson disease in Taiwan and Singapore. (PMID: 19015489) Lin CH … Wu RM (Neurology 2008) 3 4 44 58
  3. ATP13A2 missense mutations in juvenile parkinsonism and young onset Parkinson disease. (PMID: 17485642) Di Fonzo A … Bonifati V (Neurology 2007) 3 4 44 58
  4. Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase. (PMID: 16964263) Ramirez A … Kubisch C (Nature genetics 2006) 2 3 4 58
  5. Loss-of-function mutations in the ATP13A2/PARK9 gene cause complicated hereditary spastic paraplegia (SPG78). (PMID: 28137957) Estrada-Cuzcano A … Schüle R (Brain : a journal of neurology 2017) 3 4 58

Products for ATP13A2 Gene

Sources for ATP13A2 Gene

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