ATP2B4

ATPase plasma membrane Ca2+ transporting 4, the group of ATPases Ca2+ transporting|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:203626831-203744081

Previous symbols: [ "ATP2B2", "MXRA1" ]

Links

ENSG00000058668 ∙ NCBI:493 ∙ OMIM:108732 ∙ HGNC:817 ∙ Uniprot:P23634 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not provided (103 variants)
• Inborn genetic diseases (38 variants)
• ATP2B4-related condition (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.

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	21	14	36
missense			62	6	9	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			3	3	2	8
non coding				8	2	10
Total	0	0	64	35	25

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)
1-203683266-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 (Jan 18, 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)
1-203698183-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)
1-203698331-G-A			Uncertain significance (Dec 31, 2023)
1-203699483-C-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

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: 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

	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