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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
  • EC 4 58
  • 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 3.6.3 58
  • 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 Calcium signaling pathway and Response to elevated platelet cytosolic Ca2+. 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

Regulatory Elements for ATP2B3 Gene

Enhancers for ATP2B3 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
GH0XH153900 1.6 FANTOM5 Ensembl ENCODE 10.2 +384.8 384840 4.2 HDGF GLI4 TCF12 ZNF766 GLIS2 GATA2 ZNF143 FOS REST ZNF658 SNORA70 HCFC1 EMD DKC1 TMEM187 SNORA56 LOC105373383 SLC10A3 PLXNA3 PLXNB3
GH0XH153621 1.5 FANTOM5 ENCODE dbSUPER 1.7 +107.7 107661 7.1 FOXA2 MLX ZFP64 ARID4B DMAP1 YY1 PAF1 SP5 ZHX2 MXD4 DUSP9 ZNF185 ABCD1 PDZD4 ATP2B3 ENSG00000228616
GH0XH153507 1.1 ENCODE dbSUPER 0.4 -10.0 -9968 0.2 RB1 ZSCAN4 ARID4B ZNF2 RAD21 SCRT2 ZNF143 ZNF391 EGR2 SMARCA5 ATP2B3 HAUS7
GH0XH153506 0.8 dbSUPER 0.4 -10.8 -10829 1.4 CTCF TFAP4 RB1 ZSCAN4 ARID4B ZNF2 RAD21 CC2D1A CTBP1 PATZ1 DUSP9 ZNF275 ATP2B3 HAUS7
GH0XH153498 0.7 Ensembl dbSUPER 0.4 -19.0 -18965 0.6 ZNF341 GLIS1 ZIC2 ZFP92 HAUS7 ATP2B3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ATP2B3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ATP2B3 Gene

Genomic Locations for ATP2B3 Gene
65,275 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

Selected DME Specific Peptides for ATP2B3 Gene


Post-translational modifications for ATP2B3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

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

Phenotypes for ATP2B3 Gene

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

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , 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:0006810 transport TAS 8765088
GO:0006811 ion transport IEA --
GO:0006816 calcium ion transport IEA --
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
ATP Nutra Agonist 0
calcium Nutra 0
Magnesium Nutra 0

(2) Additional Compounds for ATP2B3 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
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
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:

Inhibitory RNA Products

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, PaxDb, 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

Primer Products

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 33 34
  • 91.37 (n)
(Bos Taurus)
Mammalia ATP2B3 33 34
  • 90.38 (n)
(Mus musculus)
Mammalia Atp2b3 33 16 34
  • 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 33 34
  • 59.24 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010638 33
  • 63.63 (n)
(Caenorhabditis elegans)
Secernentea mca-3 33 34
  • 60.21 (n)
mca-2 34
  • 59 (a)
R05C11.3 35
  • 58 (a)
mca-1 35 34
  • 54 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PMC1 34 36
  • 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)

Paralogs for ATP2B3 Gene

Paralogs for ATP2B3 Gene

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

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 Sequence Context AA Info Type
rs397514619 Pathogenic, Spinocerebellar ataxia, X-linked 1 (SCAX1) [MIM:302500] 153,565,081(+) CCGGG(A/G)CCTGA nc-transcript-variant, reference, missense
rs724160009 Pathogenic 153,548,788(+) ACTGT(-/GCTGGT)CGTGG nc-transcript-variant, cds-indel
rs724160011 Pathogenic 153,548,789(+) CTGTG(-/CTGGTC)GTGGC nc-transcript-variant, cds-indel
rs724160012 Pathogenic 153,548,793(+) GCTGG(-/TCGTGG)CTGTC nc-transcript-variant, cds-indel
rs368215361 Likely pathogenic 153,565,099(+) TCAGA(C/G/T)GCAGG nc-transcript-variant, reference, missense

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

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

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)

Relevant External Links 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

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

Disorder Aliases PubMed IDs
spinocerebellar ataxia, x-linked 1
  • x-linked progressive cerebellar ataxia
spinocerebellar ataxia, x-linked 5
  • x-linked non progressive cerebellar ataxia
  • microcephalus
alacrima, achalasia, and mental retardation syndrome
  • aamr
intellectual disability
- 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.

Relevant External Links for ATP2B3

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 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 60
  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 60
  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 45 60
  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 60
  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 60

Products for ATP2B3 Gene

Sources for ATP2B3 Gene

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