ATP2B2

gene
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Also known as PMCA2

Summary

ATP2B2 (ATPase plasma membrane Ca2+ transporting 2, HGNC:815) is a protein-coding gene on chromosome 3p25.3, encoding Plasma membrane calcium-transporting ATPase 2 (Q01814). ATP-driven Ca(2+) ion pump involved in the maintenance of basal intracellular Ca(2+) levels in specialized cells of cerebellar circuit and vestibular and cochlear systems.

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 2. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 491 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autosomal dominant nonsyndromic hearing loss (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 8
  • Clinical variants (ClinVar): 632 total — 30 pathogenic, 21 likely-pathogenic
  • Phenotypes (HPO): 7
  • MANE Select transcript: NM_001001331

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:815
Approved symbolATP2B2
NameATPase plasma membrane Ca2+ transporting 2
Location3p25.3
Locus typegene with protein product
StatusApproved
AliasesPMCA2
Ensembl geneENSG00000157087
Ensembl biotypeprotein_coding
OMIM108733
Entrez491

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000352432, ENST00000360273, ENST00000397077, ENST00000452124, ENST00000460129, ENST00000467702, ENST00000468426, ENST00000480680, ENST00000638646, ENST00000643662, ENST00000644553, ENST00000644807, ENST00000645850, ENST00000646379

RefSeq mRNA: 5 — MANE Select: NM_001001331 NM_001001331, NM_001330611, NM_001353564, NM_001363862, NM_001683

CCDS: CCDS2601, CCDS33701, CCDS82733, CCDS87040

Canonical transcript exons

ENST00000360273 — 23 exons

ExonStartEnd
ENSE000035016571044934510449862
ENSE000035565101032402310329125
ENSE000035581621040209110402348
ENSE000036020921041061810410815
ENSE000036696761040095310401078
ENSE000038508471050546510505586
ENSE000038891081034603110346137
ENSE000038891711037180910372051
ENSE000038898071035988210360123
ENSE000038901511034538410345575
ENSE000038905961037924310379284
ENSE000038918901037543010375644
ENSE000038925271034275210342965
ENSE000038926881038648010386512
ENSE000038941751034049310340704
ENSE000038944751035869110358925
ENSE000038944881035011210350199
ENSE000038946691033817610338358
ENSE000038951071034024210340349
ENSE000038957161038827710388402
ENSE000038957261035039810350577
ENSE000038957711038526810385327
ENSE000038958571037825210378410

Expression profiles

Bgee: expression breadth ubiquitous, 203 present calls, max score 99.53.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.8314 / max 174.6930, expressed in 150 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
410544.3105154
410670.9944110
410650.781199
410550.7341115
410570.196389
410660.079644
410520.02619
410560.01989

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lateral nuclear group of thalamusUBERON:000273699.53gold quality
endothelial cellCL:000011598.91gold quality
Brodmann (1909) area 46UBERON:000648398.86gold quality
ponsUBERON:000098898.79gold quality
middle temporal gyrusUBERON:000277198.75gold quality
lateral globus pallidusUBERON:000247698.70gold quality
Brodmann (1909) area 23UBERON:001355498.45gold quality
parietal lobeUBERON:000187298.41gold quality
occipital lobeUBERON:000202198.41gold quality
postcentral gyrusUBERON:000258198.27gold quality
superior frontal gyrusUBERON:000266198.26gold quality
primary visual cortexUBERON:000243698.24gold quality
orbitofrontal cortexUBERON:000416797.67gold quality
right hemisphere of cerebellumUBERON:001489097.58gold quality
cerebellar cortexUBERON:000212997.55gold quality
cerebellar hemisphereUBERON:000224597.55gold quality
cerebellumUBERON:000203797.14gold quality
entorhinal cortexUBERON:000272896.65gold quality
parotid glandUBERON:000183196.58gold quality
substantia nigra pars compactaUBERON:000196596.41gold quality
superior vestibular nucleusUBERON:000722796.06gold quality
prefrontal cortexUBERON:000045195.99gold quality
frontal cortexUBERON:000187095.93gold quality
substantia nigra pars reticulataUBERON:000196695.78gold quality
right frontal lobeUBERON:000281095.76gold quality
dorsolateral prefrontal cortexUBERON:000983495.43gold quality
Brodmann (1909) area 9UBERON:001354095.35gold quality
neocortexUBERON:000195094.80gold quality
ventral tegmental areaUBERON:000269194.41gold quality
cerebellar vermisUBERON:000472094.37gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.37

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

299 targeting ATP2B2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4262100.0073.263931
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-3646100.0073.565283
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3163100.0077.238605
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-574-5P100.0066.01989
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-4481100.0066.421669
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-10401-5P99.9965.79948
HSA-MIR-607799.9968.042299
HSA-MIR-4789-3P99.9970.752484

Literature-anchored findings (GeneRIF, showing 28)

  • Alternative splicing of the first intracellular loop of PMCA2 alters its membrane targeting (PMID:12624087)
  • role in the intracellular Ca(2+) extrusion of syncytiotrophoblast-like structure originating from the differentiation of cultured trophoblast cells isolated from human term placenta (PMID:12784250)
  • Decrease in PMCA2 transcript and protein levels and correlation between expression and disease course in two different allergic encephalomyelitis models further highlight the importance of this calcium pump in neuronal dysfunction during inflammation. (PMID:15926914)
  • We conclude that PMCA2 mRNA can be highly overexpressed in some breast cancer cells. (PMID:16216224)
  • plasma-membrane calcium-pump isoform 2 mutants have roles in causing digenic deafness (PMID:17234811)
  • Our results indicate that a loss of PMCA such as occurs in aging brain likely leads to subtle disruptions in normal Ca(2+) signaling and enhanced susceptibility to stresses that can alter the regulation of Ca(2+) homeostasis. (PMID:17488275)
  • The deaf-waddler isoform of PMCA2, operating at 30% efficacy, showed a significantly decreased ability to rescue the Ca(2+) loading of cells expressing TRPML3(A419P). (PMID:19299509)
  • These data indicate that alternative splicing differentially affects the lipid interactions of PMCA2w/b and PMCA2z/b and that the apical localization of PMCA2w/b is lipid raft-dependent and sensitive to cholesterol depletion. (PMID:19379709)
  • Report a novel interaction between endogenous plasma membrane calcium ATPase (PMCA) and eNOS in endothelial cells. PMCA may negatively modulate eNOS activity, and NO-dependent signal transduction pathways. (PMID:20211863)
  • Apical scaffolding protein NHERF2 modulates the localization of alternatively spliced plasma membrane Ca2+ pump 2B variants in polarized epithelial cells. (PMID:20663896)
  • It appears that Ca extrusion via the sarcolemmal Ca ATPase occurs only at the t-tubules, and is not regulated by basal PKA activity. (PMID:20971118)
  • these data suggest that full polarization is a prerequisite for proper positioning of the PMCA2w variants in the apical membrane domain of polarized cells. (PMID:21672522)
  • These results provide converging evidence for an association between ATP2B2 gene variants and autism in male subjects (PMID:21757185)
  • The human mutant of PMCA2 exacerbated the deafness produced by a cadherin 23 mutation. The human mutant failed to impair the Ca(2+) ejection by the pump. (PMID:22047666)
  • G293S and V586M mutations in the PMCA2 Calcium Transporting ATPase of the stereocilia are associated with deafness. (Review) (PMID:22349217)
  • ATP2B2 might play a role in the etiology of autism in Chinese Han population. (PMID:23620727)
  • SERCA and PMCA pump activities are strongly affected by the localization of F508del-CFTR protein. (PMID:25661196)
  • PMCA2b resulted in rapid and highly PMCA abundance-sensitive clearance of store-operated Ca2+ entry-mediated Ca2+ transients. (PMID:25690014)
  • PMCA2 interacts with HER2 in specific actin-rich membrane domains. (PMID:26729871)
  • PMCA2 regulates breast cancer cell proliferation and sensitivity to doxorubicin in basal cell carcinoma. (PMID:27148852)
  • Data show that ATPase, calcium transporting, plasma membrane 2 protein (PMCA2) silencing augmented B-cell leukemia 2 family proteins (Bcl-2) inhibitor ABT-263-mediated MDA-MB-231 breast cancer cell death. (PMID:27613092)
  • NHERF1 acts with PMCA2 to regulate HER2 signaling and membrane retention in breast cancers (PMID:28235801)
  • Cytoskeleton dynamics regulates plasma membrane PMCA2 activity. (PMID:28527708)
  • critical role played by the PMCA2w/a pump in the control of hair cell function and survival, and provide mechanistic insight into the etiology of deafness and vestibular disorders. (PMID:29452611)
  • PMCA2 loss plays a role in the ataxic phenotype, but can paradoxically also minimise calcium rises in cerebellar Purkinje neurons, thereby ensuring their resilience and survival. (PMID:29452612)
  • A V1143F substitution in PMAC2 alters the binding of caslmodulin to the calmodulin-binding domain leading to impaired calcium signaling. (PMID:29655659)
  • Loss-of-function variants of ATP2B2 are associated with rapidly progressive hearing impairment. (PMID:30535804)
  • ATP2B2 de novo variants as a cause of variable neurodevelopmental disorders that feature dystonia, ataxia, intellectual disability, behavioral symptoms, and seizures. (PMID:37675773)

Cross-species orthologs

17 orthologs

OrganismSymbolGene ID
danio_reriosi:dkey-28b4.8ENSDARG00000002840
danio_rerioatp1a3aENSDARG00000018259
danio_rerioatp2b2ENSDARG00000063433
danio_rerioatp1a3bENSDARG00000104139
mus_musculusAtp2b2ENSMUSG00000030302
rattus_norvegicusAtp2b2ENSRNOG00000030269
drosophila_melanogasteranneFBGN0052000
drosophila_melanogasterSPoCkFBGN0052451
drosophila_melanogasterCG45062FBGN0266432
drosophila_melanogasterCG45063FBGN0266433
caenorhabditis_elegansWBGENE00000834
caenorhabditis_elegansWBGENE00003153
caenorhabditis_eleganspmr-1WBGENE00004063
caenorhabditis_elegansWBGENE00012341
caenorhabditis_elegansWBGENE00015338
caenorhabditis_elegansWBGENE00015660
caenorhabditis_elegansWBGENE00019875

Paralogs (21): ATP2C1 (ENSG00000017260), ATP1A2 (ENSG00000018625), ATP2B4 (ENSG00000058668), ATP2C2 (ENSG00000064270), ATP2B3 (ENSG00000067842), ATP2B1 (ENSG00000070961), ATP2A3 (ENSG00000074370), ATP12A (ENSG00000075673), ATP1A3 (ENSG00000105409), ATP4A (ENSG00000105675), ATP13A1 (ENSG00000105726), ATP7B (ENSG00000123191), ATP13A4 (ENSG00000127249), ATP1A4 (ENSG00000132681), ATP13A3 (ENSG00000133657), ATP13A2 (ENSG00000159363), ATP1A1 (ENSG00000163399), ATP7A (ENSG00000165240), ATP2A2 (ENSG00000174437), ATP13A5 (ENSG00000187527), ATP2A1 (ENSG00000196296)

Protein

Protein identifiers

Plasma membrane calcium-transporting ATPase 2Q01814 (reviewed: Q01814)

Alternative names: Plasma membrane calcium ATPase isoform 2, Plasma membrane calcium pump isoform 2

All UniProt accessions (5): Q01814, A0A2R8Y4R4, A0A2R8Y535, A0A2U3TZI3, A0A2U3U055

UniProt curated annotations — full annotation on UniProt →

Function. ATP-driven Ca(2+) ion pump involved in the maintenance of basal intracellular Ca(2+) levels in specialized cells of cerebellar circuit and vestibular and cochlear systems. Uses ATP as an energy source to transport cytosolic Ca(2+) ions across the plasma membrane to the extracellular compartment. Has fast activation and Ca(2+) clearance rate suited to control fast neuronal Ca(2+) dynamics. At parallel fiber to Purkinje neuron synapse, mediates presynaptic Ca(2+) efflux in response to climbing fiber-induced Ca(2+) rise. Provides for fast return of Ca(2+) concentrations back to their resting levels, ultimately contributing to long-term depression induction and motor learning. Plays an essential role in hearing and balance. In cochlear hair cells, shuttles Ca(2+) ions from stereocilia to the endolymph and dissipates Ca(2+) transients generated by the opening of the mechanoelectrical transduction channels. Regulates Ca(2+) levels in the vestibular system, where it contributes to the formation of otoconia. In non-excitable cells, regulates Ca(2+) signaling through spatial control of Ca(2+) ions extrusion and dissipation of Ca(2+) transients generated by store-operated channels. In lactating mammary gland, allows for the high content of Ca(2+) ions in the milk.

Subunit / interactions. Interacts with PDZD11.

Subcellular location. Cell membrane. Synapse Apical cell membrane. Basolateral cell membrane Apical cell membrane. Basolateral cell membrane Basolateral cell membrane Basolateral cell membrane Basolateral cell membrane.

Tissue specificity. Mainly expressed in brain cortex. Found in low levels in skeletal muscle, heart muscle, stomach, liver, kidney and lung. Isoforms containing segment B are found in brain cortex and at low levels in other tissues. Isoforms containing segments X and W are found at low levels in all tissues. Isoforms containing segment A and segment Z are found at low levels in skeletal muscle and heart muscle.

Disease relevance. May act as a disease modifier. ATP2B2 variants may exacerbate the severity of non-syndromic sensorineural hearing loss in patients carrying causative variants in the CDH23 gene. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. Deafness, autosomal dominant, 82 (DFNA82) [MIM:619804] A form of non-syndromic, sensorineural hearing loss. Sensorineural hearing loss results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DNFA82 is characterized by onset of rapidly progressive bilateral sensorineural hearing loss usually early in the first decade. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Up-regulated by calmodulin which increases the affinity of the pump for Ca(2+) ions.

Similarity. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIB subfamily.

Isoforms (8)

UniProt IDNamesCanonical?
Q01814-1WB, AIIICIyes
Q01814-2WA, AIIICII
Q01814-3YA, AIICII
Q01814-4ZA, AICII
Q01814-5YB, AIICI
Q01814-6ZB, AICI
Q01814-7XA
Q01814-8XB

RefSeq proteins (5): NP_001001331, NP_001317540, NP_001340493, NP_001350791, NP_001674 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001757P_typ_ATPaseFamily
IPR004014ATPase_P-typ_cation-transptr_NDomain
IPR006068ATPase_P-typ_cation-transptr_CDomain
IPR006408P-type_ATPase_IIBFamily
IPR008250ATPase_P-typ_transduc_dom_A_sfHomologous_superfamily
IPR018303ATPase_P-typ_P_sitePTM
IPR022141ATP_Ca_trans_CDomain
IPR023214HAD_sfHomologous_superfamily
IPR023298ATPase_P-typ_TM_dom_sfHomologous_superfamily
IPR023299ATPase_P-typ_cyto_dom_NHomologous_superfamily
IPR036412HAD-like_sfHomologous_superfamily
IPR044492P_typ_ATPase_HD_domDomain
IPR059000ATPase_P-type_domADomain

Pfam: PF00122, PF00689, PF00690, PF08282, PF12424, PF13246

Enzyme classification (BRENDA):

  • EC 7.2.2.10 — P-type Ca2+ transporter (BRENDA: 47 organisms, 90 substrates, 341 inhibitors, 34 Km, 18 kcat entries)

Substrate kinetics (BRENDA)

6 substrates with measured Km, best-characterized 6. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
CA2+11
ATP6
CA2+/CIS0.0007–0.00133
CA2+[SIDE 1]0.0002–0.00032
SR2+0.015–0.0352
UTP1

Catalyzed reactions (Rhea), 1 shown:

  • Ca(2+)(in) + ATP + H2O = Ca(2+)(out) + ADP + phosphate + H(+) (RHEA:18105)

UniProt features (61 total): modified residue 14, topological domain 11, transmembrane region 10, region of interest 5, sequence variant 5, sequence conflict 5, splice variant 4, compositionally biased region 3, binding site 2, chain 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q01814-F173.830.20

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 499 (4-aspartylphosphate intermediate)

Ligand- & substrate-binding residues (2): 820; 824

Post-translational modifications (14): 18, 1139, 1178, 1188, 1201, 1211, 1165, 1177, 1151, 1163, 1120, 1132, 1134, 1146

Function

Pathways and Gene Ontology

Reactome pathways

12 pathways

IDPathway
R-HSA-418359Reduction of cytosolic Ca++ levels
R-HSA-5578775Ion homeostasis
R-HSA-936837Ion transport by P-type ATPases
R-HSA-9662360Sensory processing of sound by inner hair cells of the cochlea
R-HSA-9662361Sensory processing of sound by outer hair cells of the cochlea
R-HSA-109582Hemostasis
R-HSA-382551Transport of small molecules
R-HSA-397014Muscle contraction
R-HSA-418346Platelet homeostasis
R-HSA-418360Platelet calcium homeostasis
R-HSA-5576891Cardiac conduction
R-HSA-983712Ion channel transport

MSigDB gene sets: 308 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_CIRCULATORY_SYSTEM_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, TTCCGTT_MIR191, CMYB_01, AAGCCAT_MIR135A_MIR135B, GOBP_NEUROGENESIS, MORF_RAD51L3, SREBP1_02, GOBP_MONOATOMIC_CATION_TRANSPORT, MODULE_66, CATRRAGC_UNKNOWN, JAZAG_TGFB1_SIGNALING_DN, CATTTCA_MIR203

GO Biological Process (9): calcium ion transport (GO:0006816), sensory perception of sound (GO:0007605), neuron differentiation (GO:0030182), monoatomic ion transmembrane transport (GO:0034220), regulation of cytosolic calcium ion concentration (GO:0051480), regulation of cardiac conduction (GO:1903779), monoatomic ion transport (GO:0006811), calcium ion transmembrane transport (GO:0070588), regulation of postsynaptic cytosolic calcium ion concentration (GO:0099566)

GO Molecular Function (11): P-type calcium transporter activity (GO:0005388), calcium ion binding (GO:0005509), calmodulin binding (GO:0005516), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), PDZ domain binding (GO:0030165), metal ion binding (GO:0046872), P-type calcium transporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration (GO:1905059), nucleotide binding (GO:0000166), transporter activity (GO:0005215), protein binding (GO:0005515)

GO Cellular Component (11): cytoplasm (GO:0005737), plasma membrane (GO:0005886), basolateral plasma membrane (GO:0016323), apical plasma membrane (GO:0016324), dendritic spine membrane (GO:0032591), extracellular exosome (GO:0070062), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), membrane (GO:0016020), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Sensory processing of sound2
Platelet calcium homeostasis1
Cardiac conduction1
Ion channel transport1
Hemostasis1
Platelet homeostasis1
Muscle contraction1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
plasma membrane region2
synapse2
metal ion transport1
sensory perception of mechanical stimulus1
cell differentiation1
generation of neurons1
monoatomic ion transport1
transmembrane transport1
intracellular calcium ion homeostasis1
regulation of heart contraction1
cardiac conduction1
transport1
calcium ion transport1
monoatomic cation transmembrane transport1
regulation of cytosolic calcium ion concentration1
postsynapse1
calcium ion transmembrane transporter activity1
P-type ion transporter activity1
ATPase-coupled monoatomic cation transmembrane transporter activity1
metal ion binding1
protein binding1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
ribonucleoside triphosphate phosphatase activity1
ATP-dependent activity1
protein domain specific binding1
cation binding1
P-type calcium transporter activity1
regulation of postsynaptic cytosolic calcium ion concentration1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
binding1
intracellular anatomical structure1
membrane1
cell periphery1
basal plasma membrane1
apical part of cell1
neuron projection membrane1

Protein interactions and networks

STRING

3524 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ATP2B2CDH23Q9H251897
ATP2B2CALM1P02593895
ATP2B2CALML3P27482892
ATP2B2CALML5Q9NZT1892
ATP2B2CALML6Q8TD86887
ATP2B2CALML4Q96GE6887
ATP2B2PCDH15Q96QU1800
ATP2B2OC90Q02509789
ATP2B2OTOP1Q7RTM1759
ATP2B2NHERF1O14745728
ATP2B2NHERF2Q15599697
ATP2B2MYO7AP78427689
ATP2B2SLC8A1P32418671
ATP2B2ITPR1Q14643670
ATP2B2E9PNW1E9PNW1667

IntAct

113 interactions, top by confidence:

ABTypeScore
RXYLT1FKTNpsi-mi:“MI:0914”(association)0.710
NIPAL1ESYT2psi-mi:“MI:0914”(association)0.640
EIF2B2SLC27A2psi-mi:“MI:0914”(association)0.640
CXCR4TMEM120Bpsi-mi:“MI:0914”(association)0.530
HTR2CKLRG2psi-mi:“MI:0914”(association)0.530
LPAR4POTEFpsi-mi:“MI:0914”(association)0.530
SLC2A5RBFOX3psi-mi:“MI:0914”(association)0.530
VSIG4TCAF2psi-mi:“MI:0914”(association)0.530
PCDHGB1FAM171A2psi-mi:“MI:0914”(association)0.530
EFNB2FAM171A2psi-mi:“MI:0914”(association)0.530
NUFIP1PDE2Apsi-mi:“MI:0914”(association)0.530
SPRING1PLSCR1psi-mi:“MI:0914”(association)0.530
GALNT6NDUFS4psi-mi:“MI:0914”(association)0.530
GPR161USP12psi-mi:“MI:0914”(association)0.530
PTGIRTMEM63Apsi-mi:“MI:0914”(association)0.530
SLC22A16APBA3psi-mi:“MI:0914”(association)0.530
ENTPD7PGK2psi-mi:“MI:0914”(association)0.530
FAM174ABLTP3Bpsi-mi:“MI:0914”(association)0.530
CCR6PODXLpsi-mi:“MI:0914”(association)0.530
NPTNTNPO2psi-mi:“MI:0914”(association)0.530
CALCAATP2B4psi-mi:“MI:0914”(association)0.500
ATP2B2CALCApsi-mi:“MI:0915”(physical association)0.500
SCRIBATP2B2psi-mi:“MI:0407”(direct interaction)0.440
PTPRQNHERF1psi-mi:“MI:0914”(association)0.350
TSPOpsi-mi:“MI:0914”(association)0.350
CD81PVRpsi-mi:“MI:0914”(association)0.350
SSTATP1A2psi-mi:“MI:0914”(association)0.350
ITM2BILVBLpsi-mi:“MI:0914”(association)0.350
ATP2B2ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (295): ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS)

ESM2 similar proteins: A0A143ZZK9, A5IYF2, A6ZQM4, B3LQ11, B9QMJ0, B9WLN5, D3K0R6, G5E829, G5EFR6, J9VQQ3, O13397, O13398, P11505, P11506, P13586, P13587, P20020, P22189, P23220, P23634, P32660, P38929, P39677, P54678, P54679, P58165, Q00804, Q01814, Q01896, Q06698, Q12675, Q12691, Q16720, Q54L53, Q54SW3, Q54TV1, Q54TV2, Q55CP6, Q5A6N1, Q64542

Diamond homologs: A3FIN4, B1AWN4, C7EXK4, D4AA47, G0S196, G2X7W6, O43520, O54827, O60312, O94296, O94823, P11506, P32660, P39524, P54678, P57792, P70704, P98196, P98197, P98198, P98199, P98200, P98204, Q01814, Q09891, Q12675, Q148W0, Q29449, Q5BL50, Q6DFW5, Q6UQ17, Q8K2X1, Q8TF62, Q9GKS6, Q9LI83, Q9LK90, Q9LNQ4, Q9LVK9, Q9N0Z4, Q9NTI2

SIGNOR signaling

2 interactions.

AEffectBMechanism
ATP8B1up-regulatesATP2B2
ATP2B2“down-regulates quantity”calcium(2+)relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 168 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ion transport by P-type ATPases610.9×3e-03
Class A/1 (Rhodopsin-like receptors)106.5×2e-03
G alpha (s) signalling events95.8×3e-03
GPCR ligand binding105.6×3e-03
Signaling by GPCR124.2×3e-03
GPCR downstream signalling114.2×6e-03

GO biological processes:

GO termPartnersFoldFDR
regulation of cytosolic calcium ion concentration512.9×6e-03
adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway68.9×8e-03
positive regulation of cytosolic calcium ion concentration118.7×7e-05
phospholipase C-activating G protein-coupled receptor signaling pathway98.0×6e-04
adenylate cyclase-activating G protein-coupled receptor signaling pathway107.6×3e-04
G protein-coupled receptor signaling pathway184.4×8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

632 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic30
Likely pathogenic21
Uncertain significance290
Likely benign165
Benign98

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1360768NM_001001331.4(ATP2B2):c.3058dup (p.Arg1020fs)Pathogenic
1400721NM_001001331.4(ATP2B2):c.1713C>A (p.Cys571Ter)Pathogenic
148687GRCh38/hg38 3p25.3(chr3:9875909-10572677)x1Pathogenic
148942GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3Pathogenic
1525986NM_001001331.4(ATP2B2):c.955del (p.Ala319fs)Pathogenic
1525987NM_001001331.4(ATP2B2):c.2329C>T (p.Arg777Ter)Pathogenic
1525988NM_001001331.4(ATP2B2):c.1963G>T (p.Glu655Ter)Pathogenic
1525989NM_001001331.4(ATP2B2):c.1998C>A (p.Cys666Ter)Pathogenic
1699521NM_001001331.4(ATP2B2):c.2461G>A (p.Gly821Arg)Pathogenic
1997758NM_001001331.4(ATP2B2):c.532C>T (p.Gln178Ter)Pathogenic
2006763NM_001001331.4(ATP2B2):c.2920G>T (p.Glu974Ter)Pathogenic
2018216NM_001001331.4(ATP2B2):c.2726_2729dup (p.Met910fs)Pathogenic
2080750NM_001001331.4(ATP2B2):c.1924dup (p.Ala642fs)Pathogenic
2424613NC_000003.11:g.(?10094051)(11078652_?)delPathogenic
2816938NM_001001331.4(ATP2B2):c.1989del (p.Met664fs)Pathogenic
2836858NM_001001331.4(ATP2B2):c.1123A>T (p.Lys375Ter)Pathogenic
2844808NM_001001331.4(ATP2B2):c.178del (p.Leu60fs)Pathogenic
2976958NM_001001331.4(ATP2B2):c.896_899del (p.Lys299fs)Pathogenic
3067646NM_001001331.4(ATP2B2):c.2515del (p.Ile839fs)Pathogenic
3336824NM_001001331.4(ATP2B2):c.3259del (p.Ser1087fs)Pathogenic
3366952NM_001001331.4(ATP2B2):c.1043-2A>GPathogenic
3661593NM_001001331.4(ATP2B2):c.2492C>T (p.Ala831Val)Pathogenic
3722000NM_001001331.4(ATP2B2):c.1761dup (p.Arg588fs)Pathogenic
3728302NM_001001331.4(ATP2B2):c.1503del (p.Gly502fs)Pathogenic
4690272NM_001001331.4(ATP2B2):c.358G>A (p.Gly120Arg)Pathogenic
4714251NM_001001331.4(ATP2B2):c.2870del (p.Gly957fs)Pathogenic
4724146NM_001001331.4(ATP2B2):c.2261_2264del (p.Phe754fs)Pathogenic
4730226NM_001001331.4(ATP2B2):c.272del (p.Lys91fs)Pathogenic
4822875NM_001001331.4(ATP2B2):c.2152del (p.Arg718fs)Pathogenic
917514NM_001001331.4(ATP2B2):c.1033C>T (p.Gln345Ter)Pathogenic

SpliceAI

4103 predictions. Top by Δscore:

VariantEffectΔscore
3:10329121:CGGAT:Cacceptor_gain1.0000
3:10329123:GATCT:Gacceptor_loss1.0000
3:10329126:C:CCacceptor_gain1.0000
3:10329127:T:Gacceptor_loss1.0000
3:10336215:T:TAdonor_gain1.0000
3:10338171:TGTAC:Tdonor_loss1.0000
3:10338172:GTAC:Gdonor_loss1.0000
3:10338173:TA:Tdonor_loss1.0000
3:10338175:C:CGdonor_loss1.0000
3:10338357:ACC:Aacceptor_loss1.0000
3:10338359:C:CCacceptor_gain1.0000
3:10338359:C:Tacceptor_loss1.0000
3:10338360:T:Aacceptor_loss1.0000
3:10340346:CTAT:Cacceptor_gain1.0000
3:10340360:C:CTacceptor_gain1.0000
3:10340361:A:Tacceptor_gain1.0000
3:10340368:C:CTacceptor_gain1.0000
3:10340369:A:Tacceptor_gain1.0000
3:10340489:CTA:Cdonor_gain1.0000
3:10340490:TAC:Tdonor_loss1.0000
3:10340492:C:CAdonor_loss1.0000
3:10340700:CTCGC:Cacceptor_gain1.0000
3:10340702:CGC:Cacceptor_gain1.0000
3:10340703:GC:Gacceptor_gain1.0000
3:10340704:CC:Cacceptor_gain1.0000
3:10340705:C:CCacceptor_gain1.0000
3:10340705:CTG:Cacceptor_loss1.0000
3:10340709:C:CTacceptor_gain1.0000
3:10342746:GCTCA:Gdonor_loss1.0000
3:10342747:CTCA:Cdonor_loss1.0000

AlphaMissense

8226 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:10329105:G:CF1147L1.000
3:10329105:G:TF1147L1.000
3:10329107:A:GF1147L1.000
3:10338186:A:TI1137N1.000
3:10338189:C:GR1136P1.000
3:10338208:A:GW1130R1.000
3:10338208:A:TW1130R1.000
3:10340250:A:GW1077R1.000
3:10340250:A:TW1077R1.000
3:10340289:A:GW1064R1.000
3:10340289:A:TW1064R1.000
3:10340311:G:CC1056W1.000
3:10340581:C:GR1014P1.000
3:10340582:G:TR1014S1.000
3:10340625:G:CF999L1.000
3:10340625:G:TF999L1.000
3:10340627:A:GF999L1.000
3:10342832:A:TL946H1.000
3:10342859:C:AR937M1.000
3:10342892:G:TA926D1.000
3:10342895:A:GL925P1.000
3:10342895:A:TL925Q1.000
3:10342901:A:GL923P1.000
3:10342907:G:TA921D1.000
3:10342915:G:CD918E1.000
3:10342915:G:TD918E1.000
3:10342916:T:AD918V1.000
3:10342916:T:CD918G1.000
3:10342916:T:GD918A1.000
3:10342917:C:GD918H1.000

dbSNP variants (sampled 300 via entrez): RS1000003964 (3:10608361 C>A), RS1000007150 (3:10457920 C>G,T), RS1000012612 (3:10385770 C>A), RS1000017550 (3:10656472 C>A,T), RS1000019117 (3:10491412 G>A), RS1000022263 (3:10451165 G>T), RS1000027214 (3:10644926 T>C), RS1000032727 (3:10604934 C>T), RS1000043229 (3:10418104 G>A,C), RS1000046425 (3:10611047 C>T), RS1000053378 (3:10383099 T>C,G), RS1000062082 (3:10374649 G>A), RS1000078556 (3:10610783 C>T), RS1000087894 (3:10336088 G>A), RS1000088384 (3:10460251 C>T)

Disease associations

OMIM: gene MIM:108733 | disease phenotypes: MIM:619804, MIM:218000, MIM:616421, MIM:601386, MIM:124900

GenCC curated gene-disease

DiseaseClassificationInheritance
hearing loss, autosomal dominant 82DefinitiveAutosomal dominant
autosomal dominant nonsyndromic hearing lossDefinitiveAutosomal dominant
neurodevelopmental disorderStrongAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
autosomal dominant nonsyndromic hearing lossDefinitiveAD

Mondo (8): hearing loss disorder (MONDO:0005365), neurodevelopmental disorder (MONDO:0700092), hearing loss, autosomal dominant 82 (MONDO:0030719), agenesis of the corpus callosum with peripheral neuropathy (MONDO:0000902), epilepsy with myoclonic atonic seizures (MONDO:0014633), autosomal recessive nonsyndromic hearing loss 12 (MONDO:0011067), intellectual disability (MONDO:0001071), autosomal dominant nonsyndromic hearing loss (MONDO:0019587)

Orphanet (5): Corpus callosum agenesis-neuronopathy syndrome (Orphanet:1496), Epilepsy with myoclonic-atonic seizures (Orphanet:1942), Rare autosomal recessive non-syndromic sensorineural deafness type DFNB (Orphanet:90636), Rare autosomal dominant non-syndromic sensorineural deafness type DFNA (Orphanet:90635), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

7 total (7 of 7 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000360Tinnitus
HP:0000407Sensorineural hearing impairment
HP:0003577Congenital onset
HP:0003596Middle age onset
HP:0003621Juvenile onset
HP:0011463Childhood onset

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000274_8Metabolite levels1.000000e-07
GCST002337_149Amyotrophic lateral sclerosis (sporadic)7.000000e-06
GCST002932_14Manganese levels7.000000e-06
GCST003075_81Cognitive decline rate in late mild cognitive impairment5.000000e-07
GCST004521_106Autism spectrum disorder or schizophrenia2.000000e-08
GCST008103_75Bipolar disorder9.000000e-07
GCST012490_371Femur bone mineral density x serum urate levels interaction3.000000e-08
GCST90020028_769Hip circumference adjusted for BMI7.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0005001phenylalanine measurement
EFO:0007710cognitive decline measurement
EFO:0004531urate measurement
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (5)

DescriptorNameTree numbers
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886Neurodevelopmental DisordersF03.625
C536446Corpus callosum agenesis neuronopathy (supp.)
C563327Deafness, Autosomal Recessive 12 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — P2B P-type ATPases: Ca2+-ATPases

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation3
Valproic Acidaffects expression, increases methylation2
Aflatoxin B1decreases expression, decreases methylation, increases methylation2
aristolochic acid Iincreases expression1
dicrotophosincreases expression1
methylmercuric chlorideincreases expression1
methyleugenoldecreases expression1
O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphateaffects expression, affects response to substance1
ethyl-p-hydroxybenzoatedecreases expression1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
manganese chloridedecreases expression, increases methylation1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
perfluoro-n-nonanoic aciddecreases expression1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic aciddecreases expression1
theaflavin-3,3’-digallateaffects expression1
Sunitinibdecreases expression1
Leflunomideincreases expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Carbamazepineaffects expression1
Methapyrileneincreases methylation1
Triclosandecreases expression1
Urethanedecreases expression1
Vanadiumincreases expression1
1-Methyl-4-phenylpyridiniumdecreases expression1
Uranium Compoundsincreases expression1
Cadmium Chlorideincreases expression1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E9XZHEK293-ATP2B2-RFPTransformed cell lineFemale

Clinical trials (associated diseases)

501 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph
NCT06340633PHASE2RECRUITINGSPI-1005 in Adults Receiving Cochlear Implant
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT00582946PHASE1COMPLETEDWide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding
NCT00584155PHASE1WITHDRAWNProtection From Cisplatin Ototoxicity by Lactated Ringers
NCT01206829PHASE1UNKNOWNHearing Impairment, Cognitive Therapy and Coping
NCT01256229PHASE1COMPLETEDOutcomes In Children With Developmental Delay And Deafness
NCT01343394PHASE1WITHDRAWNSafety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children
NCT01452607PHASE1COMPLETEDStudy to Evaluate the Safety and Pharmacokinetics of SPI-1005
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC