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

ENSG00000058668NCBI:493OMIM:108732HGNC:817Uniprot:P23634AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP2B4 gene.

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
1
clinvar
35
clinvar
13
clinvar
49
missense
88
clinvar
9
clinvar
8
clinvar
105
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
3
4
2
9
non coding
11
clinvar
2
clinvar
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)1626186
1-203683224-C-A ATP2B4-related disorder Benign (Nov 27, 2023)705092
1-203683224-C-T Likely benign (Feb 24, 2023)703903
1-203683225-G-A Uncertain significance (Aug 09, 2022)1505093
1-203683244-G-A Likely benign (Dec 11, 2023)1643189
1-203683246-T-C Likely benign (Jan 10, 2024)1631913
1-203683257-C-A not specified Uncertain significance (Mar 22, 2022)2279332
1-203683258-G-A Uncertain significance (Apr 18, 2023)2986609
1-203683258-G-T not specified Uncertain significance (Apr 29, 2024)3328918
1-203683266-G-A not specified Uncertain significance (Dec 06, 2022)2333328
1-203683267-A-C ATP2B4-related disorder Uncertain significance (Dec 09, 2022)2629689
1-203683316-A-G Benign (Jan 31, 2024)1598820
1-203683341-G-A Benign/Likely benign (May 01, 2024)1584699
1-203683354-G-C not specified Uncertain significance (Jul 06, 2021)2234771
1-203683356-G-A not specified Uncertain significance (Jul 21, 2021)2239057
1-203683367-C-T Likely benign (Aug 16, 2022)2042901
1-203683384-C-T Uncertain significance (Dec 15, 2022)2009191
1-203683389-C-T not specified Uncertain significance (Jun 10, 2024)3328885
1-203698183-G-A not specified Uncertain significance (May 01, 2022)2396216
1-203698197-G-C not specified Uncertain significance (Dec 03, 2021)2264587
1-203698281-T-C Benign (Jan 31, 2024)1600570
1-203698286-T-C not specified Uncertain significance (Jun 05, 2023)2556781
1-203698294-A-T not specified Uncertain significance (Mar 06, 2023)2494372
1-203698305-C-T Likely benign (Sep 19, 2023)2989802
1-203698330-C-T not specified Uncertain significance (Dec 13, 2023)3131578

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATP2B4protein_codingprotein_codingENST00000357681 20117521
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001510.9981257110371257480.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.255377050.7620.00004127904
Missense in Polyphen203330.460.614293744
Synonymous0.05072672680.9960.00001522419
Loss of Function4.851654.70.2920.00000321594

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002060.000206
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.0001850.000185
European (Non-Finnish)0.0001410.000141
Middle Eastern0.0002180.000217
South Asian0.0002300.000229
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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