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Aliases for ATP13A2 Gene

Aliases for ATP13A2 Gene

  • 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 61
  • EC 61
  • EC 3.6.3.- 4
  • EC 3.6.3 61
  • 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 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 Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Ion channel transport. 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

  • May play a role in intracellular cation homeostasis and the maintenance of neuronal integrity.

Gene Wiki entry 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

Regulatory Elements for ATP13A2 Gene

Enhancers for ATP13A2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G016938 1.1 Ensembl ENCODE dbSUPER 11.3 +72.8 72781 2.2 BCOR SCRT1 CTCF ZNF10 ZMYM3 ZBTB40 ZBTB7A GLIS2 SCRT2 ZBTB33 SDHB LOC105376805 ATP13A2 PADI2 CROCC TRE-TTC3-1 PIR55831 GC01M016886
GH01G016977 1.1 ENCODE dbSUPER 5 +31.8 31845 4.7 PKNOX1 ZSCAN4 SIN3A ZNF48 ZNF121 ZNF143 FOS SMARCA5 CEBPB REST MFAP2 LOC105376805 PADI3 ATP13A2 CROCCP2 ENSG00000226526
GH01G016925 1 ENCODE dbSUPER 4.6 +85.7 85714 2.4 CTCF MXI1 ZIC2 ZKSCAN1 ZNF664 HIC1 ZFHX2 GLIS2 SCRT2 ZNF600 SDHB ESPNP CROCCP2 ATP13A2 GC01M016886 PIR55831
GH01G017188 1.8 FANTOM5 Ensembl ENCODE dbSUPER 1.3 -179.4 -179366 5.2 PKNOX1 FOXA2 ATF1 SIN3A YBX1 YY1 TCF12 GATA2 FOS PPARG LOC400743 NECAP2 PADI3 ATP13A2 ENSG00000282843
GH01G017011 1 ENCODE 0.7 -0.6 -626 2.4 ATF1 CREB3L1 ZFP64 ARID4B SIN3A ETS1 ZNF766 GLIS2 ZNF143 FOS MFAP2 EIF1AXP1 RPL22P3 ATP13A2 SDHB
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ATP13A2 on UCSC Golden Path with GeneCards custom track

Promoters for ATP13A2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000002169 272 1001 ATF1 CREB3L1 ARID4B SIN3A ETS1 GLIS2 ZNF143 FOS KLF7 KLF13

Genomic Location for ATP13A2 Gene

16,985,958 bp from pter
17,011,972 bp from pter
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:
    Probable 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

Selected DME Specific Peptides for ATP13A2 Gene


Post-translational modifications for ATP13A2 Gene

  • Ubiquitination at posLast=6868, posLast=143143, posLast=693693, Lys835, posLast=843843, and Lys859
  • Modification sites at PhosphoSitePlus

Domains & Families for ATP13A2 Gene

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 CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
May play a role in intracellular cation homeostasis and the maintenance of neuronal integrity.

Enzyme Numbers (IUBMB) 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

CRISPR Products

miRNA for ATP13A2 Gene

miRTarBase miRNAs that target ATP13A2

Inhibitory RNA 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.

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 IEA,IDA 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

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
Adenosine triphosphate Approved Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 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:

CRISPR Products

Inhibitory RNA 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, PaxDb, 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

Primer Products

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 35 34
  • 98.95 (n)
(Canis familiaris)
Mammalia ATP13A2 35 34
  • 87.18 (n)
(Bos Taurus)
Mammalia ATP13A2 34 35
  • 86.53 (n)
(Mus musculus)
Mammalia Atp13a2 16 35 34
  • 85.14 (n)
(Rattus norvegicus)
Mammalia Atp13a2 34
  • 84.83 (n)
(Monodelphis domestica)
Mammalia ATP13A2 35
  • 61 (a)
(Ornithorhynchus anatinus)
Mammalia ATP13A2 35
  • 49 (a)
(Gallus gallus)
Aves ATP13A2 35
  • 59 (a)
(Anolis carolinensis)
Reptilia -- 35
  • 36 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2717 34
(Danio rerio)
Actinopterygii atp13a2 34 35
  • 58.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32000 35
  • 29 (a)
(Caenorhabditis elegans)
Secernentea catp-7 35
  • 35 (a)
catp-6 35
  • 34 (a)
catp-5 35
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YPK9 35
  • 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)

Paralogs for ATP13A2 Gene

Paralogs for ATP13A2 Gene

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 Sequence Context AA Info Type
rs121918227 Pathogenic, Kufor-Rakeb syndrome (KRS) [MIM:606693] 16,996,008(-) ACCTG(C/G)GGGGC reference, missense
rs137853967 Kufor-Rakeb syndrome (KRS) [MIM:606693] 16,986,864(-) GTACC(G/T)CATCC reference, missense
rs144701072 Pathogenic, Kufor-Rakeb syndrome (KRS) [MIM:606693] 16,988,455(+) GTCTC(C/T)GCACA reference, missense
rs147277743 Kufor-Rakeb syndrome (KRS) [MIM:606693] 16,991,749(+) GACGG(C/T)GCGGA reference, missense
rs151117874 Kufor-Rakeb syndrome (KRS) [MIM:606693] 17,005,754(+) TGGGC(A/G)TGCTG reference, missense

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)

Relevant External Links 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: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
kufor-rakeb syndrome
  • ceroid lipofuscinosis, neuronal, 12
spastic paraplegia 78, autosomal recessive
  • spg78
cln12 disease
  • atp13a2-related neuronal ceroid-lipofuscinosis
neuronal ceroid-lipofuscinoses
  • neuronal ceroid-lipofuscinosis, infantile
juvenile-onset parkinson disease
- elite association - COSMIC cancer census association via MalaCards


  • 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:22388936}. 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}.

Relevant External Links for ATP13A2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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) Vilarino-Guell C. … Farrer M.J. (Hum. Mutat. 2009) 3 4 46 64
  2. Novel ATP13A2 variant associated with Parkinson disease in Taiwan and Singapore. (PMID: 19015489) Lin C.H. … Wu R.M. (Neurology 2008) 3 4 46 64
  3. ATP13A2 missense mutations in juvenile parkinsonism and young onset Parkinson disease. (PMID: 17485642) Di Fonzo A. … Bonifati V. (Neurology 2007) 3 4 46 64
  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. (Nat. Genet. 2006) 2 3 4 64
  5. PARK9-associated ATP13A2 localizes to intracellular acidic vesicles and regulates cation homeostasis and neuronal integrity. (PMID: 22186024) Ramonet D. … Moore D.J. (Hum. Mol. Genet. 2012) 3 4 64

Products for ATP13A2 Gene

Sources for ATP13A2 Gene

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