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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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ATP2B2
ATPase plasma membrane Ca2+ transporting 2
Chromosome 3 · 3p25.3
NCBI Gene: 491Ensembl: ENSG00000157087.20HGNC: HGNC:815UniProt: A0A2U3U055
77PubMed Papers
21Diseases
0Drugs
48Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTransporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingsensory perception of soundcalcium ion transportP-type calcium transporter activity involved in regulation of postsynaptic cytosolic calcium ion concentrationautosomal dominant nonsyndromic hearing losshearing loss, autosomal dominant 82hearing loss, autosomal recessivehypertension
✦AI Summary

ATP2B2 encodes PMCA2, a plasma membrane Ca²⁺-ATPase that maintains basal intracellular calcium levels in specialized neurons and sensory cells 12. This ATP-driven pump transports cytosolic Ca²⁺ across the plasma membrane with rapid activation kinetics suited for controlling fast neuronal Ca²⁺ dynamics 12. In cerebellar circuits, PMCA2 mediates presynaptic Ca²⁺ efflux at parallel fiber-Purkinje neuron synapses, enabling fast Ca²⁺ return to resting levels and contributing to long-term depression and motor learning 12. In cochlear hair cells, it dissipates Ca²⁺ transients from mechanoelectrical transduction channels and regulates vestibular Ca²⁺ for otoconia formation, playing essential roles in hearing and balance 12. Clinically, heterozygous ATP2B2 variants cause autosomal dominant nonsyndromic hearing loss (DFNA82) 3. Beyond auditory deficits, de novo and inherited ATP2B2 variants cause variable neurodevelopmental disorders featuring ataxia, dystonia, intellectual disability, autism, and seizures, with cerebellar atrophy observed in some cases 34. Cell-based studies show variants produce altered cytosolic calcium handling with both loss- and gain-of-function effects 3. These findings highlight PMCA2's critical role in cerebellar development and precise calcium regulation for neurotypical development 4. GWAS analysis identified ATP2B2 as a common variant locus associated with autism spectrum disorder 5, and CRISPR-Cas9 gene editing targeting Atp2b2 mutations restored hearing in dominant hearing loss mouse models 6.

Sources cited
1
ATP2B2 maintains basal intracellular Ca²⁺ levels in cerebellar, vestibular, and cochlear systems and is essential for hearing and balance
PMID: 15829536
2
ATP2B2 uses ATP to transport Ca²⁺ and controls fast neuronal Ca²⁺ dynamics in specialized cells
PMID: 17234811
3
De novo ATP2B2 variants cause neurodevelopmental disorders with dystonia, ataxia, intellectual disability, autism, and seizures; variants alter cytosolic calcium handling
PMID: 37675773
4
ATP2B2 mutations cause neurodevelopmental and cerebellar pathologies including developmental delay, cognitive disturbances, epilepsy, autistic traits, and cerebellar atrophy
PMID: 39367743
5
ATP2B2 locus at 3p25.3 is associated with autism spectrum disorder in genome-wide association studies
PMID: 28540026
6
CRISPR-Cas9 editing of Atp2b2 dominant mutations restores outer hair cell function and hearing in mouse models
PMID: 37582836
Disease Associationsⓘ21
autosomal dominant nonsyndromic hearing lossOpen Targets
0.66Moderate
hearing loss, autosomal dominant 82Open Targets
0.64Moderate
hearing loss, autosomal recessiveOpen Targets
0.51Moderate
hypertensionOpen Targets
0.44Moderate
insomniaOpen Targets
0.43Moderate
Epileptic encephalopathyOpen Targets
0.41Moderate
Increased blood pressureOpen Targets
0.41Moderate
deafnessOpen Targets
0.39Weak
Neurodevelopmental disorderOpen Targets
0.37Weak
DNA methylationOpen Targets
0.33Weak
adolescent idiopathic scoliosisOpen Targets
0.33Weak
response to xenobiotic stimulusOpen Targets
0.32Weak
bipolar I disorderOpen Targets
0.32Weak
essential hypertensionOpen Targets
0.32Weak
mixed connective tissue diseaseOpen Targets
0.32Weak
Tietze syndromeOpen Targets
0.31Weak
Back painOpen Targets
0.31Weak
male reproductive system diseaseOpen Targets
0.30Weak
poisoningOpen Targets
0.25Weak
Non-Neoplastic Bile Duct DisorderOpen Targets
0.22Weak
Deafness, autosomal dominant, 82UniProt
Pathogenic Variants48
NM_001001331.4(ATP2B2):c.3394C>T (p.Arg1132Ter)Pathogenic
not provided|Epileptic encephalopathy|Neurodevelopmental disorder
★★☆☆2025→ Residue 1132
NM_001001331.4(ATP2B2):c.1508C>T (p.Thr503Met)Pathogenic
not provided|not specified|Neurodevelopmental disorder
★★☆☆2025→ Residue 503
NM_001001331.4(ATP2B2):c.1327TTC[1] (p.Phe444del)Pathogenic
not provided
★★☆☆2025→ Residue 444
NM_001001331.4(ATP2B2):c.2136+1G>APathogenic
not provided
★★☆☆2025
NM_001001331.4(ATP2B2):c.2461G>A (p.Gly821Arg)Pathogenic
not provided
★★☆☆2023→ Residue 821
NM_001001331.4(ATP2B2):c.1369G>A (p.Glu457Lys)Likely pathogenic
not provided|ATP2B2-related disorder|Hearing loss, autosomal dominant 82
★★☆☆2016→ Residue 457
NM_001001331.4(ATP2B2):c.3420+1G>ALikely pathogenic
not specified
★☆☆☆2025
NM_001001331.4(ATP2B2):c.358G>A (p.Gly120Arg)Pathogenic
Intellectual disability
★☆☆☆2025→ Residue 120
NM_001001331.4(ATP2B2):c.272del (p.Lys91fs)Pathogenic
not provided
★☆☆☆2025→ Residue 91
NM_001001331.4(ATP2B2):c.2194G>A (p.Gly732Ser)Likely pathogenic
Hearing loss, autosomal dominant 82
★☆☆☆2025→ Residue 732
NM_001001331.4(ATP2B2):c.2316+2T>CLikely pathogenic
not provided
★☆☆☆2025
NM_001001331.4(ATP2B2):c.2261_2264del (p.Phe754fs)Pathogenic
not provided
★☆☆☆2025→ Residue 754
NM_001001331.4(ATP2B2):c.3130-2A>CLikely pathogenic
not provided
★☆☆☆2025
NM_001001331.4(ATP2B2):c.3016C>T (p.Gln1006Ter)Likely pathogenic
Hearing loss, autosomal dominant 82
★☆☆☆2025→ Residue 1006
NM_001001331.4(ATP2B2):c.1503del (p.Gly502fs)Pathogenic
not provided
★☆☆☆2025→ Residue 502
NM_001001331.4(ATP2B2):c.361del (p.Leu121fs)Likely pathogenic
Hearing loss, autosomal dominant 82
★☆☆☆2025→ Residue 121
NM_001001331.4(ATP2B2):c.2870del (p.Gly957fs)Pathogenic
not provided
★☆☆☆2025→ Residue 957
NM_001001331.4(ATP2B2):c.2121C>A (p.Asp707Glu)Likely pathogenic
not specified
★☆☆☆2025→ Residue 707
NM_001001331.4(ATP2B2):c.3058dup (p.Arg1020fs)Pathogenic
not provided
★☆☆☆2024→ Residue 1020
NM_001001331.4(ATP2B2):c.555dup (p.Ile186fs)Likely pathogenic
not provided
★☆☆☆2024→ Residue 186
View on ClinVar ↗
Related Genes
PCDH15Protein interaction100%CALML4Protein interaction100%CALML5Protein interaction100%CALML3Protein interaction100%CALML6Protein interaction100%PRKACBProtein interaction97%
Tissue Expression6 tissues
Liver
100%
Brain
87%
Bone Marrow
0%
Ovary
0%
Heart
0%
Lung
0%
Gene Interaction Network
Click a node to explore
ATP2B2PCDH15CALML4CALML5CALML3CALML6PRKACB
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q01814
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.19Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.12 [0.08–0.19]
RankingsWhere ATP2B2 stands among ~20K protein-coding genes
  • #6,135of 20,598
    Most Researched77
  • #1,370of 5,498
    Most Pathogenic Variants48 · top quartile
  • #393of 17,882
    Most Constrained (LOEUF)0.19 · top 5%
Genes detectedATP2B2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
ATP2B2 de novo variants as a cause of variable neurodevelopmental disorders that feature dystonia, ataxia, intellectual disability, behavioral symptoms, and seizures.
PMID: 37675773
Genet Med · 2023
1.00
2
Shed CNTNAP2 ectodomain is detectable in CSF and regulates Ca
PMID: 34921780
Neuron · 2022
0.90
3
Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.
PMID: 28540026
Mol Autism · 2017
0.80
4
Treatment of monogenic and digenic dominant genetic hearing loss by CRISPR-Cas9 ribonucleoprotein delivery in vivo.
PMID: 37582836
Nat Commun · 2023
0.70
5
Research and Discussion on the Relationships between Noise-Induced Hearing Loss and ATP2B2 Gene Polymorphism.
PMID: 31886164
Int J Genomics · 2019
0.60