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

Summary

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: mouse all
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Genomic context

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

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.
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.
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.
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.
Mutations in ATP2B3 gene is associated with aldosterone-producing adenomas.
Title: Novel somatic mutations and distinct molecular signature in aldosterone-producing adenomas.
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.
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.
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.
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.
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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-15046 (e-PCR)
- UniSTS:14600

DXS7001E (e-PCR)
- UniSTS:3345

A006S03 (e-PCR)
- UniSTS:57488

RH80841 (e-PCR)
- UniSTS:88315

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 more info	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

EC 7.2.2.10

NP_001375289.1

EC 7.2.2.10

NP_001375290.1

EC 7.2.2.10

NP_001375291.1

EC 7.2.2.10

NP_001397637.1

EC 7.2.2.10

NP_068768.2

EC 7.2.2.10

XP_005274746.1

EC 7.2.2.10

XP_005274748.1

EC 7.2.2.10

XP_011529479.1

EC 7.2.2.10

XP_016885042.1

EC 7.2.2.10

XP_024308154.1

EC 7.2.2.10

XP_047298097.1

EC 7.2.2.10

XP_047298098.1

EC 7.2.2.10

XP_054183106.1

EC 7.2.2.10

XP_054183107.1

EC 7.2.2.10

XP_054183108.1

EC 7.2.2.10

XP_054183109.1

EC 7.2.2.10

XP_054183110.1

EC 7.2.2.10

XP_054183111.1

EC 7.2.2.10

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

NG_015896.2 RefSeqGene

Range

5002..70289

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

153517642..153582929

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Related

ENSP00000377425.1, ENST00000393842.5
XM_017029553.2 → XP_016885042.1 plasma membrane calcium-transporting ATPase 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

151791198..151856492

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A994J5M1
XM_054327135.1 → XP_054183110.1 plasma membrane calcium-transporting ATPase 3 isoform X6
XM_054327134.1 → XP_054183109.1 plasma membrane calcium-transporting ATPase 3 isoform X4
XM_054327133.1 → XP_054183108.1 plasma membrane calcium-transporting ATPase 3 isoform X3
XM_054327136.1 → XP_054183111.1 plasma membrane calcium-transporting ATPase 3 isoform X7
XM_054327131.1 → XP_054183106.1 plasma membrane calcium-transporting ATPase 3 isoform X1