ATP2B3
ATPase plasma membrane Ca2+ transporting 3, the group of ATPases Ca2+ transporting|Cilia and flagella associated
Basic information
Region (hg38): X:153517642-153582939
Previous symbols: [ "SCAX1", "CLA2" ]
Links
Phenotypes
GenCC
Source:
- X-linked progressive cerebellar ataxia (Moderate), mode of inheritance: Unknown
- X-linked progressive cerebellar ataxia (Moderate), mode of inheritance: XL
- X-linked non progressive cerebellar ataxia (Supportive), mode of inheritance: XL
- X-linked progressive cerebellar ataxia (Strong), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spinocerebellar ataxia, X-linked 1 | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 10797423; 22912398 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (88 variants)
- not_provided (79 variants)
- X-linked_progressive_cerebellar_ataxia (24 variants)
- ATP2B3-related_disorder (19 variants)
- not_specified (12 variants)
- Aldosterone-producing_adrenal_cortex_adenoma (3 variants)
- See_cases (2 variants)
- Neurodevelopmental_disorder (1 variants)
- Carious_teeth (1 variants)
- Oral-pharyngeal_dysphagia (1 variants)
- Global_developmental_delay (1 variants)
- Intellectual_disability (1 variants)
- Microcephaly (1 variants)
- Hypotonia (1 variants)
- Muscular_atrophy (1 variants)
- Fetal_akinesia_deformation_sequence_1 (1 variants)
- Spastic_ataxia (1 variants)
- Neonatal_hypotonia (1 variants)
- Arthrogryposis_multiplex_congenita (1 variants)
- Abnormal_cerebral_cortex_morphology (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2B3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001001344.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 21 | 11 | 33 | |||
| missense | 111 | 30 | 150 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 6 | 114 | 51 | 14 |
Highest pathogenic variant AF is 0.000014952
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP2B3 | protein_coding | protein_coding | ENST00000263519 | 20 | 65264 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000548 | 125737 | 2 | 4 | 125743 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.75 | 405 | 593 | 0.683 | 0.0000555 | 7960 |
| Missense in Polyphen | 137 | 262.81 | 0.52129 | 3357 | ||
| Synonymous | -0.144 | 279 | 276 | 1.01 | 0.0000290 | 2481 |
| Loss of Function | 5.00 | 3 | 34.9 | 0.0861 | 0.00000251 | 568 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000760 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000722 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000496 | 0.0000352 |
| Middle Eastern | 0.0000722 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell.;
- Pathway
- Aldosterone synthesis and secretion - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Calcium Regulation in the Cardiac Cell;Ion channel transport;Purine metabolism;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases;Hemostasis;Reduction of cytosolic Ca++ levels;Platelet calcium homeostasis;Platelet homeostasis
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.000758
- rvis_EVS
- -1.68
- rvis_percentile_EVS
- 2.68
Haploinsufficiency Scores
- pHI
- 0.366
- hipred
- Y
- hipred_score
- 0.752
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp2b3
- Phenotype
Gene ontology
- Biological process
- cellular calcium ion homeostasis;ion transmembrane transport;regulation of cytosolic calcium ion concentration;calcium ion transmembrane transport;ATP hydrolysis coupled cation transmembrane transport;regulation of presynaptic cytosolic calcium ion concentration;regulation of cardiac conduction;calcium ion export across plasma membrane
- Cellular component
- Golgi apparatus;plasma membrane;integral component of plasma membrane;presynapse;glutamatergic synapse;GABA-ergic synapse;extracellular vesicle
- Molecular function
- calcium-transporting ATPase activity;protein binding;calmodulin binding;ATP binding;calcium ion transmembrane transporter activity;PDZ domain binding;metal ion binding;calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration