Aliases for ATP13A4 Gene

Aliases for ATP13A4 Gene

  • ATPase 13A4 2 3 5
  • Probable Cation-Transporting ATPase 13A4 3 4
  • ATPase Type 13A4 2 3
  • Cation-Transporting P5-ATPase 3
  • P5-ATPase Isoform 4 4
  • DKFZp761I1011 2
  • EC 51
  • EC 3.6.3.n1 51
  • EC 51
  • EC 7.2.2.- 4
  • P5-ATPase 3
  • FLJ37958 2
  • EC 3.6.3 51
  • ATP13A4 5

External Ids for ATP13A4 Gene

Previous GeneCards Identifiers for ATP13A4 Gene

  • GC03M194603
  • GC03M193119
  • GC03M190507

Summaries for ATP13A4 Gene

GeneCards Summary for ATP13A4 Gene

ATP13A4 (ATPase 13A4) is a Protein Coding gene. Diseases associated with ATP13A4 include Specific Language Impairment and Combined Oxidative Phosphorylation Deficiency 23. 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 ATP13A5.

Additional gene information for ATP13A4 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 ATP13A4 Gene

Genomics for ATP13A4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATP13A4 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
GH03J193592 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 612.7 -0.7 -687 3.6 BRCA1 SP1 CREB1 GATAD2A TEAD4 YBX1 PRDM10 ZNF629 TFE3 SIX5 ATP13A4 EEF1A1P23 OPA1 lnc-ATP13A4-5 piR-31922-011 LOC102724877
GH03J193554 Promoter/Enhancer 0.9 EPDnew Ensembl ENCODE 600.3 +38.2 38225 1.4 FOXA1 ATP13A4-AS1 ATP13A4 OPA1 lnc-ATP13A4-5 EEF1A1P23 ATP13A5
GH03J193419 Promoter 0.3 EPDnew 600.1 +174.1 174076 0.1 ATP13A4 ATP13A5-AS1 piR-46847-163 lnc-ATP13A5-2 ATP13A5
GH03J193659 Enhancer 1.1 Ensembl ENCODE 25.1 -68.7 -68711 4 ZNF512 LEF1 IKZF1 JUND DDX20 MTA2 PKNOX1 ZNF24 MTA1 NR2C1 ATP13A4 OPA1-AS1 EEF1A1P23 piR-43106-152 LOC102724808 OPA1 LOC102724877
GH03J193656 Enhancer 1 Ensembl ENCODE 25.3 -64.1 -64087 3.2 KDM1A BRD9 DPF2 TCF12 EP300 SCRT2 MGA MTA3 CTBP1 HES1 ATP13A4 OPA1-AS1 OPA1 piR-43106-152 LOC102724808 LOC102724877
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP13A4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP13A4

Top Transcription factor binding sites by QIAGEN in the ATP13A4 gene promoter:
  • CREB
  • deltaCREB

Genomic Locations for ATP13A4 Gene

Genomic Locations for ATP13A4 Gene
194,148 bases
Minus strand
191,035 bases
Minus strand

Genomic View for ATP13A4 Gene

Genes around ATP13A4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP13A4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP13A4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP13A4 Gene

Proteins for ATP13A4 Gene

  • Protein details for ATP13A4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable cation-transporting ATPase 13A4
    Protein Accession:
    Secondary Accessions:
    • B7WPC7
    • Q6UY23
    • Q8N1Q9
    • Q9H043

    Protein attributes for ATP13A4 Gene

    1196 amino acids
    Molecular mass:
    133987 Da
    Quaternary structure:
    No Data Available
    • Sequence=CAC21667.2; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305};
    • [Isoform 2]: Dubious isoform lacking mature mRNA evidence.

    Alternative splice isoforms for ATP13A4 Gene


neXtProt entry for ATP13A4 Gene

Selected DME Specific Peptides for ATP13A4 Gene


Post-translational modifications for ATP13A4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for ATP13A4 Gene

Gene Families for ATP13A4 Gene

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

Suggested Antigen Peptide Sequences for ATP13A4 Gene

GenScript: Design optimal peptide antigens:
  • P5-ATPase isoform 4 (AT134_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 ATP13A4: view

Function for ATP13A4 Gene

Molecular function for ATP13A4 Gene

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;.
UniProtKB/Swiss-Prot Induction:
Decreased by half in the SLI patient lymphoblasts.

Enzyme Numbers (IUBMB) for ATP13A4 Gene

Phenotypes From GWAS Catalog for ATP13A4 Gene

Gene Ontology (GO) - Molecular Function for ATP13A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0005524 ATP binding IEA --
GO:0016887 ATPase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ATP13A4: view
genes like me logo Genes that share phenotypes with ATP13A4: view

Animal Model Products

  • Taconic Biosciences Mouse Models for ATP13A4

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP13A4

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATP13A4 Gene

Localization for ATP13A4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP13A4 Gene

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 ATP13A4 gene
Compartment Confidence
plasma membrane 5
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ATP13A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ATP13A4: view

Pathways & Interactions for ATP13A4 Gene

genes like me logo Genes that share pathways with ATP13A4: view

Pathways by source for ATP13A4 Gene

Gene Ontology (GO) - Biological Process for ATP13A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006812 cation transport IEA --
GO:0006874 cellular calcium ion homeostasis IBA 21873635
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with ATP13A4: view

No data available for SIGNOR curated interactions for ATP13A4 Gene

Drugs & Compounds for ATP13A4 Gene

(3) Drugs for ATP13A4 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, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

(1) Additional Compounds for ATP13A4 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 ATP13A4: view

Transcripts for ATP13A4 Gene

mRNA/cDNA for ATP13A4 Gene

8 NCBI additional mRNA sequence :
11 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 ATP13A4

Alternative Splicing Database (ASD) splice patterns (SP) for ATP13A4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b ^ 22 ^ 23 ^
SP1: -
SP3: -

ExUns: 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28 ^ 29a · 29b ^ 30 ^ 31 ^ 32 ^ 33a · 33b
SP1: - - -
SP3: - - - -
SP4: -

Relevant External Links for ATP13A4 Gene

GeneLoc Exon Structure for

Expression for ATP13A4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATP13A4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ATP13A4 Gene

This gene is overexpressed in Thyroid (x9.3), Lung (x4.8), and Esophagus - Mucosa (x4.0).

Protein differential expression in normal tissues from HIPED for ATP13A4 Gene

This gene is overexpressed in Spleen (64.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ATP13A4 Gene

Protein tissue co-expression partners for ATP13A4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP13A4

SOURCE GeneReport for Unigene cluster for ATP13A4 Gene:


mRNA Expression by UniProt/SwissProt for ATP13A4 Gene:

Tissue specificity: Expressed in heart, placenta, liver, skeletal muscles, and pancreas. Lower levels of expression are also detected in brain, lung and kidney. Weakly expressed in the adult brain. Expression in fetal brain is higher than in adult brain, with levels similar to several other fetal tissues including spleen and skeletal muscle. In adult brain expressed at low levels in all tissues examined, including the temporal lobe and putamen.

Evidence on tissue expression from TISSUES for ATP13A4 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with ATP13A4: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP13A4 Gene

Orthologs for ATP13A4 Gene

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

Orthologs for ATP13A4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ATP13A4 30 31
  • 99.33 (n)
(Canis familiaris)
Mammalia ATP13A4 30 31
  • 90.87 (n)
(Bos Taurus)
Mammalia ATP13A4 30 31
  • 90.01 (n)
(Mus musculus)
Mammalia Atp13a4 30 17 31
  • 85.71 (n)
(Rattus norvegicus)
Mammalia Atp13a4 30
  • 85.46 (n)
(Monodelphis domestica)
Mammalia ATP13A4 31
  • 79 (a)
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 62 (a)
(Gallus gallus)
Aves ATP13A4 30 31
  • 68.39 (n)
(Anolis carolinensis)
Reptilia ATP13A4 31
  • 39 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atp13a4 30
  • 65.28 (n)
Str.15658 30
(Danio rerio)
Actinopterygii CU694233.1 31
  • 34 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta CG32000 31
  • 30 (a)
(Caenorhabditis elegans)
Secernentea catp-7 31
  • 34 (a)
catp-6 31
  • 32 (a)
catp-5 31
  • 32 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YPK9 31
  • 26 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 39 (a)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3249 30
Species where no ortholog for ATP13A4 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 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 ATP13A4 Gene

Gene Tree for ATP13A4 (if available)
Gene Tree for ATP13A4 (if available)
Evolutionary constrained regions (ECRs) for ATP13A4: view image

Paralogs for ATP13A4 Gene

(3) SIMAP similar genes for ATP13A4 Gene using alignment to 5 proteins:

  • AT134_HUMAN
  • F8W9W3_HUMAN
  • H0Y4Z2_HUMAN
  • H7C1P5_HUMAN
genes like me logo Genes that share paralogs with ATP13A4: view

Variants for ATP13A4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP13A4 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
673600 Likely Benign: not provided 193,592,798(-) A/C
729133 Likely Benign: not provided 193,412,265(-) C/T MISSENSE_VARIANT
729134 Likely Benign: not provided 193,414,733(-) A/G MISSENSE_VARIANT
730890 Likely Benign: not provided 193,457,395(-) C/G MISSENSE_VARIANT
734313 Benign: not provided 193,402,746(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for ATP13A4 Gene

Structural Variations from Database of Genomic Variants (DGV) for ATP13A4 Gene

Variant ID Type Subtype PubMed ID
dgv309n21 CNV loss 19592680
dgv8816n54 CNV loss 21841781
dgv8817n54 CNV loss 21841781
dgv8818n54 CNV loss 21841781
dgv8819n54 CNV loss 21841781
esv2421348 CNV deletion 20811451
esv26041 CNV loss 19812545
esv2662072 CNV deletion 23128226
esv2665959 CNV deletion 23128226
esv2675964 CNV deletion 23128226
esv2726425 CNV deletion 23290073
esv2726426 CNV deletion 23290073
esv2759212 CNV gain 17122850
esv3563120 CNV deletion 23714750
esv3563121 CNV deletion 23714750
esv3569204 CNV loss 25503493
esv3599184 CNV loss 21293372
esv3599185 CNV gain 21293372
esv3599186 CNV loss 21293372
esv3893849 CNV loss 25118596
esv4085 CNV loss 18987735
esv7599 CNV loss 19470904
nsv1003505 CNV gain 25217958
nsv1009030 CNV loss 25217958
nsv1136795 CNV deletion 24896259
nsv1139189 CNV deletion 24896259
nsv249 CNV deletion 15895083
nsv4175 CNV deletion 18451855
nsv435748 CNV deletion 17901297
nsv437908 CNV loss 16468122
nsv499028 CNV loss 21111241
nsv526405 CNV loss 19592680
nsv592942 CNV loss 21841781
nsv956257 CNV deletion 24416366

Variation tolerance for ATP13A4 Gene

Residual Variation Intolerance Score: 18.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.30; 97.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP13A4 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 ATP13A4 Gene

Disorders for ATP13A4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ATP13A4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
specific language impairment
  • language impairment, specific
combined oxidative phosphorylation deficiency 23
  • coxpd23
proprotein convertase 1/3 deficiency
  • obesity and endocrinopathy due to impaired processing of prohormones
benign epilepsy with centrotemporal spikes
  • centrotemporal epilepsy
- elite association - COSMIC cancer census association via MalaCards


  • Note=A chromosomal aberration involving ATP13A4 is found in 2 patients with specific language impairment (SLI) disorders. Paracentric inversion inv(3)(q25;q29). The inversion produces a disruption of the protein. {ECO:0000269 PubMed:15925480}.

Additional Disease Information for ATP13A4

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 ATP13A4: view

No data available for Genatlas for ATP13A4 Gene

Publications for ATP13A4 Gene

  1. Characterization of a novel cation transporter ATPase gene (ATP13A4) interrupted by 3q25-q29 inversion in an individual with language delay. (PMID: 15925480) Kwasnicka-Crawford DA … Scherer SW (Genomics 2005) 3 4 23
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 2 3 4
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  5. The full-ORF clone resource of the German cDNA Consortium. (PMID: 17974005) Bechtel S … Schupp I (BMC genomics 2007) 4

Products for ATP13A4 Gene

Sources for ATP13A4 Gene