ATP2B4
Basic information
Region (hg38): 1:203626832-203744081
Previous symbols: [ "ATP2B2", "MXRA1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 35 | 13 | 49 | |||
missense | 88 | 105 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 3 | 4 | 2 | 9 | ||
non coding | 11 | 13 | ||||
Total | 0 | 0 | 90 | 55 | 23 |
Variants in ATP2B4
This is a list of pathogenic ClinVar variants found in the ATP2B4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-203683210-C-T | ATP2B4-related disorder | Benign (Jul 11, 2022) | ||
1-203683224-C-A | ATP2B4-related disorder | Benign (Nov 27, 2023) | ||
1-203683224-C-T | Likely benign (Feb 24, 2023) | |||
1-203683225-G-A | Uncertain significance (Aug 09, 2022) | |||
1-203683244-G-A | Likely benign (Dec 11, 2023) | |||
1-203683246-T-C | Likely benign (Jan 10, 2024) | |||
1-203683257-C-A | not specified | Uncertain significance (Mar 22, 2022) | ||
1-203683258-G-A | Uncertain significance (Apr 18, 2023) | |||
1-203683258-G-T | not specified | Uncertain significance (Apr 29, 2024) | ||
1-203683266-G-A | not specified | Uncertain significance (Dec 06, 2022) | ||
1-203683267-A-C | ATP2B4-related disorder | Uncertain significance (Dec 09, 2022) | ||
1-203683316-A-G | Benign (Jan 31, 2024) | |||
1-203683341-G-A | Benign/Likely benign (May 01, 2024) | |||
1-203683354-G-C | not specified | Uncertain significance (Jul 06, 2021) | ||
1-203683356-G-A | not specified | Uncertain significance (Jul 21, 2021) | ||
1-203683367-C-T | Likely benign (Aug 16, 2022) | |||
1-203683384-C-T | Uncertain significance (Dec 15, 2022) | |||
1-203683389-C-T | not specified | Uncertain significance (Jun 10, 2024) | ||
1-203698183-G-A | not specified | Uncertain significance (May 01, 2022) | ||
1-203698197-G-C | not specified | Uncertain significance (Dec 03, 2021) | ||
1-203698281-T-C | Benign (Jan 31, 2024) | |||
1-203698286-T-C | not specified | Uncertain significance (Jun 05, 2023) | ||
1-203698294-A-T | not specified | Uncertain significance (Mar 06, 2023) | ||
1-203698305-C-T | Likely benign (Sep 19, 2023) | |||
1-203698330-C-T | not specified | Uncertain significance (Dec 13, 2023) |
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