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ATP2B3 ATPase plasma membrane Ca2+ transporting 3 [ Homo sapiens (human) ]

Gene ID: 492, updated on 3-Nov-2024

Summary

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Official Symbol
ATP2B3provided by HGNC
Official Full Name
ATPase plasma membrane Ca2+ transporting 3provided by HGNC
Primary source
HGNC:HGNC:816
See related
Ensembl:ENSG00000067842 MIM:300014; AllianceGenome:HGNC:816
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLA2; OPCA; PMCA3; SCAX1; CFAP39; PMCA3a
Summary
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]
Expression
Biased expression in brain (RPKM 3.7) and adrenal (RPKM 2.1) See more
Orthologs
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Genomic context

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See ATP2B3 in Genome Data Viewer
Location:
Xq28
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153517642..153582929)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (151791198..151856492)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (152783100..152848387)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene HAUS augmin like complex subunit 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152753877-152754691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152756808-152757380 Neighboring gene extracellular matrix protein X-linked, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30036 Neighboring gene biglycan Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152809330-152810182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152825847-152826631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152831014-152831626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21065 Neighboring gene uncharacterized LOC105373383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21066 Neighboring gene cyclin Q

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The ataxia-linked E1081Q mutation affects the sub-plasma membrane Ca(2+)-microdomains by tuning PMCA3 activity.
    Title: The ataxia-linked E1081Q mutation affects the sub-plasma membrane Ca(2+)-microdomains by tuning PMCA3 activity.
  2. Authors report a novel PMCA3 mutation (G733R substitution) in the catalytic P-domain of the pump in a patient affected by non-progressive ataxia, muscular hypotonia, dysmetria and nystagmus.
    Title: A novel PMCA3 mutation in an ataxic patient with hypomorphic phosphomannomutase 2 (PMM2) heterozygote mutations: Biochemical characterization of the pump defect.
  3. The ataxia related G1107D mutation of the PMCA 3 impairs its calcium pumping function. The mutation affects the interplay of calmodulin with its binding domain on the pump, decreasing its stimulation.
    Title: The ataxia related G1107D mutation of the plasma membrane Ca(2+) ATPase isoform 3 affects its interplay with calmodulin and the autoinhibition process.
  4. In summary, the APA-associated ATP2B3(Leu425_Val426del) mutant promotes aldosterone production by at least 2 different mechanisms: 1) a reduced Ca(2+) export due to the loss of the physiological pump function; and 2) an increased Ca(2+) influx due to opening of depolarization-activated Ca(2+) channels as well as a possible Ca(2+) leak through the mutated pump.
    Title: Cellular Pathophysiology of an Adrenal Adenoma-Associated Mutant of the Plasma Membrane Ca(2+)-ATPase ATP2B3.
  5. Mutations in ATP2B3 gene is associated with aldosterone-producing adenomas.
    Title: Novel somatic mutations and distinct molecular signature in aldosterone-producing adenomas.
  6. Different mutations (KCNJ5, ATP1A1, ATP2B3, and CACNA1D) are found in different aldosterone-producing nodules from the same adrenal, suggesting that somatic mutations are independent events triggered by mechanisms that remain to be identified.
    Title: Different Somatic Mutations in Multinodular Adrenals With Aldosterone-Producing Adenoma.
  7. Novel PMCA3 missense mutation co-occurring with a heterozygous mutation in LAMA1 impaired cellular Ca2+ homeostasis in patients with Cerebellar Ataxia.
    Title: A Novel Mutation in Isoform 3 of the Plasma Membrane Ca2+ Pump Impairs Cellular Ca2+ Homeostasis in a Patient with Cerebellar Ataxia and Laminin Subunit 1α Mutations.
  8. Somatic mutations found in KCNJ5, ATP1A1, and ATP2B3 appear to be the driving forces for a higher aldosterone production and proliferations of glomerulosa cells.
    Title: Complementary somatic mutations of KCNJ5, ATP1A1, and ATP2B3 in sporadic aldosterone producing adrenal adenomas.
  9. ATP2B3 mutations are present in aldosterone-producineg adenomas that result in an increase in CYP11B2 gene expression and may account for the dysregulated aldosterone production in a subset of patients with sporadic primary aldosteronism.
    Title: Somatic ATP1A1, ATP2B3, and KCNJ5 mutations in aldosterone-producing adenomas.
  10. Somatic mutations in ATP2B3 gene leads to aldosterone-producing adenomas and secondary hypertension.
    Title: Somatic mutations in ATP1A1 and ATP2B3 lead to aldosterone-producing adenomas and secondary hypertension.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
X-linked progressive cerebellar ataxia
MedGen: C0796205 OMIM: 302500 GeneReviews: Not available
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Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables P-type calcium transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables P-type calcium transporter activity TAS
Traceable Author Statement
more info
  
enables P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration IDA
Inferred from Direct Assay
more info
 PubMed 
enables P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration NAS
Non-traceable Author Statement
more info
 PubMed 
enables calcium ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables calmodulin binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in calcium ion export across plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in monoatomic ion transmembrane transport TAS
Traceable Author Statement
more info
  
involved_in regulation of cardiac conduction TAS
Traceable Author Statement
more info
  
involved_in regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cytosolic calcium ion concentration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of presynaptic cytosolic calcium ion concentration IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in GABA-ergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in GABA-ergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in GABA-ergic synapse NAS
Non-traceable Author Statement
more info
 PubMed 
located_in extracellular vesicle HDA PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in glutamatergic synapse NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in parallel fiber ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in parallel fiber to Purkinje cell synapse ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in presynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
plasma membrane calcium-transporting ATPase 3
Names
ATPase, Ca++ transporting, plasma membrane 3
cilia and flagella associated protein 39
plasma membrane calcium ATPase
plasma membrane calcium pump
NP_001001344.1
NP_001375289.1
NP_001375290.1
NP_001375291.1
NP_001397637.1
NP_068768.2
XP_005274746.1
XP_005274748.1
XP_011529479.1
XP_016885042.1
XP_024308154.1
XP_047298097.1
XP_047298098.1
XP_054183106.1
XP_054183107.1
XP_054183108.1
XP_054183109.1
XP_054183110.1
XP_054183111.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_015896.2 RefSeqGene

    Range
    5002..70289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001001344.3 → NP_001001344.1  plasma membrane calcium-transporting ATPase 3 isoform 3b

    See identical proteins and their annotated locations for NP_001001344.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (3b) contains a longer and distinct C-terminus compared to isoform 3a. Variants 2 and 4 encode the same isoform.
    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS35440.1
    UniProtKB/Swiss-Prot
    B7WNR8, B7WNY5, Q12995, Q16720, Q16858
    Related
    ENSP00000263519.4, ENST00000263519.5
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1146
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  2. NM_001388360.1 → NP_001375289.1  plasma membrane calcium-transporting ATPase 3 isoform 3a

    Status: REVIEWED

    Description
    Transcript Variant: Variants 1 and 3 encode the same isoform (3a).
    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS14722.1
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1145
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  3. NM_001388361.1 → NP_001375290.1  plasma membrane calcium-transporting ATPase 3 isoform 3b

    Status: REVIEWED

    Description
    Transcript Variant: Variants 2 and 4 encode the same isoform (3b).
    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS35440.1
    UniProtKB/Swiss-Prot
    B7WNR8, B7WNY5, Q12995, Q16720, Q16858
    Related
    ENSP00000343886.2, ENST00000349466.6
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1146
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  4. NM_001388362.1 → NP_001375291.1  plasma membrane calcium-transporting ATPase 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AF274858, U82695
    Related
    ENST00000684004.1
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1114
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  5. NM_001410708.1 → NP_001397637.1  plasma membrane calcium-transporting ATPase 3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS94697.1

  6. NM_021949.4 → NP_068768.2  plasma membrane calcium-transporting ATPase 3 isoform 3a

    See identical proteins and their annotated locations for NP_068768.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, but encodes the shortest isoform (3a). Variants 1 and 3 encode the same isoform.
    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS14722.1
    UniProtKB/Swiss-Prot
    Q16720
    Related
    ENSP00000352062.3, ENST00000359149.9
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1145
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    153517642..153582929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005274689.4 → XP_005274746.1  plasma membrane calcium-transporting ATPase 3 isoform X2

    UniProtKB/TrEMBL
    A0A994J5M1
    Related
    ENSP00000516173.1, ENST00000496610.2
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1175
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  2. XM_024452386.2 → XP_024308154.1  plasma membrane calcium-transporting ATPase 3 isoform X6

    Related
    ENSP00000359205.1, ENST00000370186.5
    Conserved Domains (2) summary
    pfam12424
    Location:1086 → 1131
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    cl27747
    Location:27 → 1047
    E1-E2_ATPase; E1-E2 ATPase

  3. XM_005274691.4 → XP_005274748.1  plasma membrane calcium-transporting ATPase 3 isoform X4

    See identical proteins and their annotated locations for XP_005274748.1

    UniProtKB/Swiss-Prot
    Q16720
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1047
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1086 → 1132
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  4. XM_047442141.1 → XP_047298097.1  plasma membrane calcium-transporting ATPase 3 isoform X5

    Related
    ENSP00000516174.1, ENST00000705862.1
    Conserved Domains (2) summary
    TIGR01517
    Location:27 → 1061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam12424
    Location:1100 → 1140
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

  5. XM_011531177.3 → XP_011529479.1  plasma membrane calcium-transporting ATPase 3 isoform X3

    Conserved Domains (7) summary
    TIGR01517
    Location:27 → 1047
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam00122
    Location:164 → 448
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:863 → 1041
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:51 → 121
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam12424
    Location:1086 → 1100
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    pfam12710
    Location:670 → 789
    HAD; haloacid dehalogenase-like hydrolase
    pfam13246
    Location:509 → 598
    Cation_ATPase; Cation transport ATPase (P-type)

  6. XM_047442142.1 → XP_047298098.1  plasma membrane calcium-transporting ATPase 3 isoform X7

    Related
    ENSP00000377425.1, ENST00000393842.5

  7. XM_017029553.2 → XP_016885042.1  plasma membrane calcium-transporting ATPase 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    151791198..151856492
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327132.1 → XP_054183107.1  plasma membrane calcium-transporting ATPase 3 isoform X2

    UniProtKB/TrEMBL
    A0A994J5M1

  2. XM_054327135.1 → XP_054183110.1  plasma membrane calcium-transporting ATPase 3 isoform X6

  3. XM_054327134.1 → XP_054183109.1  plasma membrane calcium-transporting ATPase 3 isoform X4

  4. XM_054327133.1 → XP_054183108.1  plasma membrane calcium-transporting ATPase 3 isoform X3

  5. XM_054327136.1 → XP_054183111.1  plasma membrane calcium-transporting ATPase 3 isoform X7

  6. XM_054327131.1 → XP_054183106.1  plasma membrane calcium-transporting ATPase 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16720.3 GenPept UniProtKB/Swiss-Prot:Q16720

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