Aliases for ATP13A1 Gene

Aliases for ATP13A1 Gene

  • ATPase 13A1 2 3 5
  • Manganese-Transporting ATPase 13A1 3 4
  • Cation Transporting ATPase 2 3
  • ATPase Type 13A1 2 3
  • KIAA1825 2 4
  • CGI-152 2 3
  • ATP13A 3 4
  • Probable Cation-Transporting ATPase 13A1 3
  • ATPase Type 13A 2
  • EC 51
  • EC 7.2.2.- 4
  • FLJ31858 2
  • EC 3.6.3 51
  • ATP13A1 5

External Ids for ATP13A1 Gene

Previous HGNC Symbols for ATP13A1 Gene

  • ATP13A

Previous GeneCards Identifiers for ATP13A1 Gene

  • GC19M019620
  • GC19M019758
  • GC19M019318

Summaries for ATP13A1 Gene

GeneCards Summary for ATP13A1 Gene

ATP13A1 (ATPase 13A1) is a Protein Coding gene. Diseases associated with ATP13A1 include Cone-Rod Dystrophy, X-Linked, 1 and Migraine, Familial Hemiplegic, 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 ATP13A3.

UniProtKB/Swiss-Prot Summary for ATP13A1 Gene

  • Mediates manganese transport into the endoplasmic reticulum. The ATPase activity is required for cellular manganese homeostasis.

Additional gene information for ATP13A1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATP13A1 Gene

Genomics for ATP13A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATP13A1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP13A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP13A1

Top Transcription factor binding sites by QIAGEN in the ATP13A1 gene promoter:
  • AhR
  • AML1a
  • Arnt
  • CUTL1
  • HTF
  • Ik-1
  • POU2F1
  • POU2F1a
  • Roaz
  • TGIF

Genomic Locations for ATP13A1 Gene

Genomic Locations for ATP13A1 Gene
18,479 bases
Minus strand
18,497 bases
Minus strand

Genomic View for ATP13A1 Gene

Genes around ATP13A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP13A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP13A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP13A1 Gene

Proteins for ATP13A1 Gene

  • Protein details for ATP13A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Manganese-transporting ATPase 13A1
    Protein Accession:
    Secondary Accessions:
    • B3KPJ2
    • B3KTA7
    • Q6NT90
    • Q6ZMG7
    • Q9H6C6

    Protein attributes for ATP13A1 Gene

    1204 amino acids
    Molecular mass:
    132955 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH69211.1; Type=Frameshift; Evidence={ECO:0000305};
    • Depletion of ATP13A1 with siRNAs leads to induction of the unfolded protein response (UPR) and increased activity of glucosylceramide synthase (GlcCer).

    Alternative splice isoforms for ATP13A1 Gene


neXtProt entry for ATP13A1 Gene

Selected DME Specific Peptides for ATP13A1 Gene


Post-translational modifications for ATP13A1 Gene

  • Glycosylation at Asn287 and Asn420
  • Ubiquitination at Lys143, Lys187, and Lys308
  • Modification sites at PhosphoSitePlus

Other Protein References for ATP13A1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for ATP13A1 Gene

Gene Families for ATP13A1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for ATP13A1 Gene

Suggested Antigen Peptide Sequences for ATP13A1 Gene

GenScript: Design optimal peptide antigens:
  • Probable cation-transporting ATPase 13A1 (AT131_HUMAN)
  • ATP13A1 protein (Q6NT90_HUMAN)
  • cDNA FLJ23939 fis, clone HEP01940, highly similar to Cation-transporting ATPase 2 (EC 3.6.3.-) (Q6ZMG7_HUMAN)

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 ATP13A1: view

Function for ATP13A1 Gene

Molecular function for ATP13A1 Gene

UniProtKB/Swiss-Prot Function:
Mediates manganese transport into the endoplasmic reticulum. The ATPase activity is required for cellular manganese homeostasis.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;.

Enzyme Numbers (IUBMB) for ATP13A1 Gene

Phenotypes From GWAS Catalog for ATP13A1 Gene

Gene Ontology (GO) - Molecular Function for ATP13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003674 molecular_function ND --
GO:0005524 ATP binding IEA --
GO:0015410 manganese-transporting ATPase activity TAS --
GO:0016887 ATPase activity IEA --
genes like me logo Genes that share ontologies with ATP13A1: view
genes like me logo Genes that share phenotypes with ATP13A1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for ATP13A1

CRISPR Products

miRNA for ATP13A1 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP13A1

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATP13A1 Gene

Localization for ATP13A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP13A1 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein.

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 ATP13A1 gene
Compartment Confidence
endoplasmic reticulum 4
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ATP13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ATP13A1: view

Pathways & Interactions for ATP13A1 Gene

genes like me logo Genes that share pathways with ATP13A1: view

Pathways by source for ATP13A1 Gene

Gene Ontology (GO) - Biological Process for ATP13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006812 cation transport IEA --
GO:0006874 cellular calcium ion homeostasis IBA 21873635
GO:0008150 biological_process ND --
GO:0034220 ion transmembrane transport TAS --
GO:0071421 manganese ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with ATP13A1: view

No data available for SIGNOR curated interactions for ATP13A1 Gene

Drugs & Compounds for ATP13A1 Gene

(4) Drugs for ATP13A1 Gene - From: HMDB and Novoseek

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, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

(1) Additional Compounds for ATP13A1 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
genes like me logo Genes that share compounds with ATP13A1: view

Transcripts for ATP13A1 Gene

mRNA/cDNA for ATP13A1 Gene

16 NCBI additional mRNA sequence :
15 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 ATP13A1

Alternative Splicing Database (ASD) splice patterns (SP) for ATP13A1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^
SP1: - - - -
SP2: - -
SP3: -
SP4: -
SP8: - - -
SP13: - - -
SP14: - -

ExUns: 20a · 20b ^ 21a · 21b ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29a · 29b ^ 30a · 30b ^ 31 ^ 32
SP1: - - - -
SP2: - - - -
SP3: - - -
SP4: - - - -
SP5: - - - -
SP6: -
SP7: -
SP12: -
SP16: -

Relevant External Links for ATP13A1 Gene

GeneLoc Exon Structure for

Expression for ATP13A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATP13A1 Gene

Protein differential expression in normal tissues from HIPED for ATP13A1 Gene

This gene is overexpressed in Nasal epithelium (37.8) and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATP13A1 Gene

Protein tissue co-expression partners for ATP13A1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP13A1

SOURCE GeneReport for Unigene cluster for ATP13A1 Gene:


Evidence on tissue expression from TISSUES for ATP13A1 Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Bone marrow(4.2)
  • Kidney(4.2)
  • Stomach(2)
genes like me logo Genes that share expression patterns with ATP13A1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP13A1 Gene

Orthologs for ATP13A1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP13A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ATP13A1 30 31
  • 99.5 (n)
(Canis familiaris)
Mammalia ATP13A1 30 31
  • 90.65 (n)
(Bos Taurus)
Mammalia ATP13A1 30 31
  • 90.46 (n)
(Mus musculus)
Mammalia Atp13a1 30 17 31
  • 88.5 (n)
(Rattus norvegicus)
Mammalia Atp13a1 30
  • 88.11 (n)
(Monodelphis domestica)
Mammalia ATP13A1 31
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia ATP13A1 31
  • 72 (a)
(Gallus gallus)
Aves ATP13A1 30 31
  • 75.37 (n)
(Anolis carolinensis)
Reptilia ATP13A1 31
  • 80 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atp13a1 30
  • 70.23 (n)
Str.4425 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.15056 30
(Danio rerio)
Actinopterygii atp13a 30 31
  • 71.06 (n)
wufi75c10 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008085 30
  • 60.84 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG6230 30 31
  • 58.29 (n)
(Caenorhabditis elegans)
Secernentea CELE_C10C6.6 30
  • 53.53 (n)
catp-8 31
  • 53 (a)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AFR354C 30
  • 50.64 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E22265g 30
  • 48.85 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SPF1 30 31 33
  • 47.33 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons PDR2 30
  • 51.34 (n)
(Hordeum vulgare)
Liliopsida Hv.12085 30
Bread mold
(Neurospora crassa)
Ascomycetes NCU04898 30
  • 55.57 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 54 (a)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cta4 30
  • 46.95 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.15535 30
Species where no ortholog for ATP13A1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • 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 Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ATP13A1 Gene

Gene Tree for ATP13A1 (if available)
Gene Tree for ATP13A1 (if available)
Evolutionary constrained regions (ECRs) for ATP13A1: view image

Paralogs for ATP13A1 Gene

(2) SIMAP similar genes for ATP13A1 Gene using alignment to 4 proteins:

  • AT131_HUMAN
  • H7C3H2_HUMAN
  • Q6NT90_HUMAN
genes like me logo Genes that share paralogs with ATP13A1: view

Variants for ATP13A1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP13A1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
691411 Uncertain Significance: Pyloric stenosis; Esophageal atresia 19,654,566(-) G/A MISSENSE_VARIANT
716503 Benign: not provided 19,647,752(-) C/A SYNONYMOUS_VARIANT
717966 Benign: not provided 19,657,090(-) T/C SYNONYMOUS_VARIANT
719051 Likely Benign: not provided 19,659,606(-) G/C MISSENSE_VARIANT
720936 Benign: not provided 19,645,461(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for ATP13A1 Gene

Structural Variations from Database of Genomic Variants (DGV) for ATP13A1 Gene

Variant ID Type Subtype PubMed ID
esv3643853 CNV gain 21293372
nsv1160593 CNV deletion 26073780
nsv509725 CNV insertion 20534489
nsv952427 CNV deletion 24416366

Variation tolerance for ATP13A1 Gene

Residual Variation Intolerance Score: 1.63% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.90; 48.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP13A1 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 ATP13A1 Gene

Disorders for ATP13A1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ATP13A1 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ATP13A1

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 ATP13A1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATP13A1 Gene

Publications for ATP13A1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  3. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PMID: 16335952) Liu T … Smith RD (Journal of proteome research 2005) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for ATP13A1 Gene

  • Biorbyt antibodies for ATP13A1

Sources for ATP13A1 Gene