ATP2B4
ATPase plasma membrane Ca2+ transporting 4, the group of ATPases Ca2+ transporting|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 1:203626832-203744081
Previous symbols: [ "ATP2B2", "MXRA1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (146 variants)
- not_specified (118 variants)
- ATP2B4-related_disorder (26 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2B4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001684.5. 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 | 35 | 15 | 51 | |||
| missense | 147 | 17 | 173 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 0 | 0 | 150 | 52 | 24 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP2B4 | protein_coding | protein_coding | ENST00000357681 | 20 | 117521 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00151 | 0.998 | 125711 | 0 | 37 | 125748 | 0.000147 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 537 | 705 | 0.762 | 0.0000412 | 7904 |
| Missense in Polyphen | 203 | 330.46 | 0.61429 | 3744 | ||
| Synonymous | 0.0507 | 267 | 268 | 0.996 | 0.0000152 | 2419 |
| Loss of Function | 4.85 | 16 | 54.7 | 0.292 | 0.00000321 | 594 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000206 | 0.000206 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.000185 | 0.000185 |
| European (Non-Finnish) | 0.000141 | 0.000141 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.000230 | 0.000229 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium/calmodulin-regulated and magnesium-dependent enzyme that catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell (PubMed:8530416). By regulating sperm cell calcium homeostasis, may play a role in sperm motility (By similarity). {ECO:0000250|UniProtKB:Q6Q477, ECO:0000269|PubMed:8530416}.;
- 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);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
- 0.179
Intolerance Scores
- loftool
- 0.0312
- rvis_EVS
- -0.83
- rvis_percentile_EVS
- 11.51
Haploinsufficiency Scores
- pHI
- 0.395
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.514
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.922
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp2b4
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; immune system phenotype; muscle phenotype;
Gene ontology
- Biological process
- neural retina development;regulation of transcription by RNA polymerase II;cellular calcium ion homeostasis;spermatogenesis;negative regulation of nitric oxide mediated signal transduction;hippocampus development;flagellated sperm motility;positive regulation of peptidyl-serine phosphorylation;ion transmembrane transport;negative regulation of nitric oxide biosynthetic process;negative regulation of nitric-oxide synthase activity;regulation of cytosolic calcium ion concentration;response to hydrostatic pressure;calcium ion transmembrane transport;negative regulation of calcineurin-NFAT signaling cascade;cellular response to epinephrine stimulus;calcium ion transmembrane import into cytosol;calcium ion import across plasma membrane;negative regulation of the force of heart contraction;ATP hydrolysis coupled cation transmembrane transport;negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process;negative regulation of arginine catabolic process;calcium ion export;negative regulation of peptidyl-cysteine S-nitrosylation;regulation of sodium ion transmembrane transport;regulation of cell cycle G1/S phase transition;negative regulation of cardiac muscle hypertrophy in response to stress;negative regulation of citrulline biosynthetic process;regulation of cardiac conduction;positive regulation of cAMP-dependent protein kinase activity
- Cellular component
- plasma membrane;integral component of plasma membrane;caveola;membrane;basolateral plasma membrane;Z disc;T-tubule;protein-containing complex;sperm flagellum;neuron projection;sperm principal piece;glutamatergic synapse;integral component of presynaptic active zone membrane
- Molecular function
- calcium-transporting ATPase activity;protein binding;calmodulin binding;ATP binding;sodium channel regulator activity;protein kinase binding;PDZ domain binding;protein phosphatase 2B binding;nitric-oxide synthase inhibitor activity;metal ion binding;nitric-oxide synthase binding;scaffold protein binding