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Aliases for ATP2B3 Gene

Aliases for ATP2B3 Gene

  • ATPase Plasma Membrane Ca2+ Transporting 3 2 3 5
  • Plasma Membrane Calcium-Transporting ATPase 3 2 3
  • ATPase, Ca++ Transporting, Plasma Membrane 3 2 3
  • Cilia And Flagella Associated Protein 39 2 3
  • PMCA3 3 4
  • Plasma Membrane Calcium ATPase Isoform 3 4
  • Plasma Membrane Calcium Pump Isoform 3 4
  • Spinocerebellar Ataxia, X-Linked 1 2
  • Plasma Membrane Calcium ATPase 3
  • Cerebellar Ataxia 2 (X-Linked) 2
  • Plasma Membrane Calcium Pump 3
  • EC 4
  • CFAP39 3
  • PMCA3a 3
  • SCAX1 3
  • OPCA 3
  • CLA2 3

External Ids for ATP2B3 Gene

Previous HGNC Symbols for ATP2B3 Gene

  • SCAX1
  • CLA2

Previous GeneCards Identifiers for ATP2B3 Gene

  • GC0XP146939
  • GC0XP149256
  • GC0XP150387
  • GC0XP151269
  • GC0XP152322
  • GC0XP152436
  • GC0XP152783
  • GC0XP141461

Summaries for ATP2B3 Gene

Entrez Gene Summary for ATP2B3 Gene

  • The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 3. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for ATP2B3 Gene

ATP2B3 (ATPase Plasma Membrane Ca2+ Transporting 3) is a Protein Coding gene. Diseases associated with ATP2B3 include Spinocerebellar Ataxia, X-Linked 1 and Spinocerebellar Ataxia, X-Linked 5. 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 calcium-transporting ATPase activity. An important paralog of this gene is ATP2B2.

UniProtKB/Swiss-Prot for ATP2B3 Gene

  • This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell.

Gene Wiki entry for ATP2B3 Gene

Additional gene information for ATP2B3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATP2B3 Gene

Genomics for ATP2B3 Gene

GeneHancer (GH) Regulatory Elements for ATP2B3 Gene

Promoters and enhancers for ATP2B3 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
GH0XJ153900 Enhancer 1.4 FANTOM5 Ensembl ENCODE 10.2 +384.8 384840 4.2 HDGF GLI4 TCF12 ZNF766 GLIS2 GATA2 ZNF143 FOS REST ATF4 AVPR2 HCFC1 SNORA70 DKC1 PLXNA3 TMEM187 SNORA56 EMD ENSG00000260081 SLC10A3
GH0XJ153621 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 1.7 +107.7 107661 7.1 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 YY1 PAF1 RXRA SP5 DUSP9 ZNF185 ABCD1 PDZD4 ATP2B3 LOC105373384
GH0XJ153507 Enhancer 1 ENCODE dbSUPER 0.4 -10.0 -9967 0.2 RB1 ZSCAN4 ARID4B SIN3A KLF14 ZNF2 RAD21 ARID2 SCRT2 ZNF143 ATP2B3 BGN HAUS7
GH0XJ153506 Enhancer 0.8 dbSUPER 0.4 -10.8 -10829 1.4 CTCF TFAP4 RB1 ZSCAN4 ARID4B SIN3A KLF14 ZNF2 RAD21 CC2D1A DUSP9 ZNF275 ATP2B3 HAUS7 BGN
GH0XJ153498 Enhancer 0.6 Ensembl dbSUPER 0.4 -19.0 -18964 0.6 GLIS1 ZNF341 ZIC2 ZFP92 HAUS7 BGN ATP2B3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP2B3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ATP2B3 gene promoter:
  • FAC1
  • MRF-2
  • Meis-1b
  • Meis-1
  • HOXA9B
  • HOXA9
  • RORalpha1
  • E47
  • Tal-1
  • Pax-4a

Genomic Locations for ATP2B3 Gene

Genomic Locations for ATP2B3 Gene
65,275 bases
Plus strand
65,264 bases
Plus strand

Genomic View for ATP2B3 Gene

Genes around ATP2B3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP2B3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP2B3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP2B3 Gene

Proteins for ATP2B3 Gene

  • Protein details for ATP2B3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Plasma membrane calcium-transporting ATPase 3
    Protein Accession:
    Secondary Accessions:
    • B7WNR8
    • B7WNY5
    • Q12995
    • Q16858

    Protein attributes for ATP2B3 Gene

    1220 amino acids
    Molecular mass:
    134197 Da
    Quaternary structure:
    • Interacts with PDZD11.

    Alternative splice isoforms for ATP2B3 Gene

neXtProt entry for ATP2B3 Gene

Post-translational modifications for ATP2B3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ATP2B3 Gene

Domains & Families for ATP2B3 Gene

Gene Families for ATP2B3 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for ATP2B3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIB subfamily.
  • Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIB subfamily.
genes like me logo Genes that share domains with ATP2B3: view

Function for ATP2B3 Gene

Molecular function for ATP2B3 Gene

UniProtKB/Swiss-Prot Function:
This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O + Ca(2+)(Side 1) = ADP + phosphate + Ca(2+)(Side 2).
GENATLAS Biochemistry:
ATPase,Ca++ transporting,B3 plasma membrane,mediating the extrusion of CA2+ from the cell

Enzyme Numbers (IUBMB) for ATP2B3 Gene

Gene Ontology (GO) - Molecular Function for ATP2B3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005388 calcium-transporting ATPase activity TAS,IBA --
GO:0005515 protein binding IPI 18029012
GO:0005516 calmodulin binding IEA --
GO:0005524 ATP binding IEA --
GO:0015085 calcium ion transmembrane transporter activity IDA 18029012
genes like me logo Genes that share ontologies with ATP2B3: view
genes like me logo Genes that share phenotypes with ATP2B3: view

Human Phenotype Ontology for ATP2B3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for ATP2B3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP2B3

Clone Products

No data available for Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for ATP2B3 Gene

Localization for ATP2B3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP2B3 Gene

Cell 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 ATP2B3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
golgi apparatus 5
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATP2B3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ATP2B3: view

Pathways & Interactions for ATP2B3 Gene

genes like me logo Genes that share pathways with ATP2B3: view

Gene Ontology (GO) - Biological Process for ATP2B3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006816 calcium ion transport IEA --
GO:0006874 cellular calcium ion homeostasis IBA --
GO:0034220 ion transmembrane transport TAS --
GO:0051480 regulation of cytosolic calcium ion concentration IDA 18029012
genes like me logo Genes that share ontologies with ATP2B3: view

No data available for SIGNOR curated interactions for ATP2B3 Gene

Drugs & Compounds for ATP2B3 Gene

(4) Drugs for ATP2B3 Gene - From: HMDB

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

(2) Additional Compounds for ATP2B3 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
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
genes like me logo Genes that share compounds with ATP2B3: view

Transcripts for ATP2B3 Gene

Unigene Clusters for ATP2B3 Gene

ATPase, Ca++ transporting, plasma membrane 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP2B3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATP2B3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b · 21c · 21d ^
SP1: - -
SP2: - - - - -
SP5: - -

ExUns: 22

Relevant External Links for ATP2B3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ATP2B3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ATP2B3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ATP2B3 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x6.6), Brain - Cerebellar Hemisphere (x5.8), Brain - Cerebellum (x5.7), Brain - Cortex (x5.6), and Brain - Anterior cingulate cortex (BA24) (x5.0).

Protein differential expression in normal tissues from HIPED for ATP2B3 Gene

This gene is overexpressed in Brain (29.9) and Frontal cortex (27.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ATP2B3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ATP2B3 Gene:


SOURCE GeneReport for Unigene cluster for ATP2B3 Gene:


mRNA Expression by UniProt/SwissProt for ATP2B3 Gene:

Tissue specificity: Highly expressed in the cerebellum, particulary in the presynaptic terminals of parallel fibers-Purkinje neurons. Isoform XE and isoform XB are the most abundant isoforms and are detected at low levels in brain and fetal skeletal muscle. The other isoforms are only found at lower levels and not in fetal tissues.

Evidence on tissue expression from TISSUES for ATP2B3 Gene

  • Nervous system(4.9)
  • Adrenal gland(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP2B3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with ATP2B3: view

No data available for Protein tissue co-expression partners for ATP2B3 Gene

Orthologs for ATP2B3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP2B3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ATP2B3 34
  • 100 (a)
(Canis familiaris)
Mammalia ATP2B3 34 33
  • 91.37 (n)
(Bos Taurus)
Mammalia ATP2B3 34 33
  • 90.38 (n)
(Mus musculus)
Mammalia Atp2b3 16 34 33
  • 89.1 (n)
(Ornithorhynchus anatinus)
Mammalia ATP2B3 34
  • 89 (a)
(Rattus norvegicus)
Mammalia Atp2b3 33
  • 87.47 (n)
(Monodelphis domestica)
Mammalia ATP2B3 34
  • 84 (a)
(Anolis carolinensis)
Reptilia ATP2B3 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia atp2b3 33
  • 75.02 (n)
(Danio rerio)
Actinopterygii atp2b3a 34
  • 79 (a)
atp2b3b 34 33
  • 76.04 (n)
wufk54d07 33
fruit fly
(Drosophila melanogaster)
Insecta BEST:CK01140 35
  • 64 (a)
PMCA 34 33
  • 59.24 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010638 33
  • 63.63 (n)
(Caenorhabditis elegans)
Secernentea mca-3 34 33
  • 60.21 (n)
mca-2 34
  • 59 (a)
R05C11.3 35
  • 58 (a)
mca-1 34 35
  • 51 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PMC1 36 34
  • 35 (a)
(Glycine max)
eudicotyledons Gma.1047 33
(Oryza sativa)
Liliopsida Os03g0616400 33
  • 50.94 (n)
(Triticum aestivum)
Liliopsida Ta.10263 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 65 (a)
Species where no ortholog for ATP2B3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for ATP2B3 Gene

Gene Tree for ATP2B3 (if available)
Gene Tree for ATP2B3 (if available)
Evolutionary constrained regions (ECRs) for ATP2B3: view image

Paralogs for ATP2B3 Gene

Paralogs for ATP2B3 Gene

(6) SIMAP similar genes for ATP2B3 Gene using alignment to 3 proteins:

  • A1L3B5_HUMAN
  • A1X4Q0_HUMAN
genes like me logo Genes that share paralogs with ATP2B3: view

Variants for ATP2B3 Gene

Sequence variations from dbSNP and Humsavar for ATP2B3 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs368215361 likely-pathogenic, Inborn genetic diseases 153,565,099(+) C/G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs397514619 pathogenic, likely-pathogenic, Spinocerebellar ataxia, X-linked 1, not provided, Spinocerebellar ataxia, X-linked 1 (SCAX1) [MIM:302500] 153,565,081(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs724160009 pathogenic, Aldosterone Producing Adrenal Cortex Adenoma 153,548,786(+) GTGCTGGT/GT coding_sequence_variant, inframe_deletion, non_coding_transcript_variant
rs724160011 pathogenic, Aldosterone Producing Adrenal Cortex Adenoma 153,548,789(+) CTGGTC/ coding_sequence_variant, inframe_deletion, non_coding_transcript_variant
rs724160012 pathogenic, Aldosterone Producing Adrenal Cortex Adenoma 153,548,790(+) TGGTCGTGG/TGG coding_sequence_variant, inframe_deletion, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for ATP2B3 Gene

Variant ID Type Subtype PubMed ID
esv2740632 CNV deletion 23290073
esv33199 CNV gain+loss 17666407
esv3559497 CNV deletion 23714750
esv3575024 CNV loss 25503493

Variation tolerance for ATP2B3 Gene

Residual Variation Intolerance Score: 5.47% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.22; 40.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP2B3 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 ATP2B3 Gene

Disorders for ATP2B3 Gene

MalaCards: The human disease database

(13) MalaCards diseases for ATP2B3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Spinocerebellar ataxia, X-linked 1 (SCAX1) [MIM:302500]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAX1 is characterized by hypotonia at birth, delayed motor development, gait ataxia, difficulty standing, dysarthria, and slow eye movements. Brain MRI shows cerebellar ataxia. {ECO:0000269 PubMed:22912398}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ATP2B3

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 ATP2B3: view

No data available for Genatlas for ATP2B3 Gene

Publications for ATP2B3 Gene

  1. Mutation of plasma membrane Ca2+ ATPase isoform 3 in a family with X-linked congenital cerebellar ataxia impairs Ca2+ homeostasis. (PMID: 22912398) Zanni G … Carafoli E (Proceedings of the National Academy of Sciences of the United States of America 2012) 2 3 4 58
  2. Localization of two genes encoding plasma membrane Ca2+ ATPases isoforms 2 (ATP2B2) and 3 (ATP2B3) to human chromosomes 3p26-->p25 and Xq28, respectively. (PMID: 8187550) Wang MG … McBride OW (Cytogenetics and cell genetics 1994) 2 3 4 58
  3. Case-control study of six genes asymmetrically expressed in the two cerebral hemispheres: association of BAIAP2 with attention-deficit/hyperactivity disorder. (PMID: 19733838) Ribasés M … Cormand B (Biological psychiatry 2009) 3 44 58
  4. Comparative genome sequence analysis of the Bpa/Str region in mouse and Man. (PMID: 10854409) Mallon AM … Brown SD (Genome research 2000) 3 4 58
  5. Primary structure of human plasma membrane Ca(2+)-ATPase isoform 3. (PMID: 8765088) Brown BJ … Strehler EE (Biochimica et biophysica acta 1996) 3 4 58

Products for ATP2B3 Gene

Sources for ATP2B3 Gene

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