ATP2B1
ATPase plasma membrane Ca2+ transporting 1, the group of ATPases Ca2+ transporting
Basic information
Region (hg38): 12:89588049-89709366
Links
Transcripts
Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 61.
| Transcript ID | Protein ID | Coding exons | MANE Select | MANE Plus Clinical |
|---|---|---|---|---|
ENST00000359142.8 | ENSP00000352054.3 | 21 | - | - |
ENST00000428670.8 | ENSP00000392043.3 | 20 | yes | - |
ENST00000550716.1 | ENSP00000447096.1 | 3 | - | - |
ENST00000551310.2 | ENSP00000447041.2 | 21 | - | - |
Phenotypes
GenCC
Source:
- intellectual developmental disorder, autosomal dominant 66 (Moderate), mode of inheritance: AD
- intellectual developmental disorder, autosomal dominant 66 (Limited), mode of inheritance: AR
- intellectual developmental disorder, autosomal dominant 66 (Strong), mode of inheritance: AD
- intellectual developmental disorder, autosomal dominant 66 (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder, autosomal dominant 66 | AD | General | Among other findings, the condition can involve congenital heart anomalies, and awareness may allow prompt diagnosis and management | Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic | 35358416 |
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ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (99 variants)
- Inborn_genetic_diseases (78 variants)
- Intellectual_developmental_disorder,_autosomal_dominant_66 (43 variants)
- Neurodevelopmental_disorder (14 variants)
- not_specified (14 variants)
- ATP2B1-related_disorder (5 variants)
- Isolated_Pierre-Robin_syndrome (2 variants)
- Neurodevelopmental_delay (2 variants)
- Clubfoot (2 variants)
- Periventricular_nodular_heterotopia (2 variants)
- Hypocalcemia (2 variants)
- Intellectual_disability,_autosomal_dominant_30 (1 variants)
- Autism (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2B1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001366521.1. 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 | 2 | 4 | 4 | 10 | ||
| missense | 1 | 9 | 179 | 4 | 1 | 194 |
| nonsense | 7 | 6 | 13 | |||
| start loss | 1 | 1 | ||||
| frameshift | 7 | 6 | 13 | |||
| splice donor/acceptor (+/-2bp) | 1 | 6 | 5 | 12 | ||
| Total | 16 | 27 | 187 | 8 | 5 |
Highest pathogenic variant AF is 0.0000030987344
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GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP2B1 | protein_coding | protein_coding | ENST00000428670 | 20 | 121250 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125731 | 0 | 6 | 125737 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 5.29 | 271 | 651 | 0.416 | 0.0000332 | 7990 |
| Missense in Polyphen | 86 | 309.61 | 0.27777 | 3785 | ||
| Synonymous | 1.05 | 202 | 222 | 0.910 | 0.0000114 | 2366 |
| Loss of Function | 6.83 | 1 | 56.3 | 0.0178 | 0.00000305 | 719 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000365 | 0.0000352 |
| Middle Eastern | 0.0000544 | 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);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Mineral absorption - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Vitamin D Receptor Pathway;Splicing factor NOVA regulated synaptic proteins;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;C-MYB transcription factor network;Reduction of cytosolic Ca++ levels;Platelet calcium homeostasis;Platelet homeostasis
(Consensus)
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- loftool
- 0.00551
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 7.94
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Zebrafish Information Network
- Gene name
- atp2b1a
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- has fewer parts of type
Gene ontology
- Biological process
- neural retina development;cellular calcium ion homeostasis;brain development;aging;response to cold;ion transmembrane transport;regulation of cytosolic calcium ion concentration;calcium ion transmembrane transport;cellular response to vitamin D;cellular response to corticosterone stimulus;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
- nucleus;plasma membrane;integral component of plasma membrane;cytoplasmic side of plasma membrane;membrane;basolateral plasma membrane;apical plasma membrane;dendritic spine membrane;neuronal cell body membrane;membrane raft;extracellular exosome;glutamatergic synapse;GABA-ergic synapse;integral component of presynaptic active zone membrane
- 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