ATP2A3

ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3, the group of ATPases Ca2+ transporting

Basic information

Region (hg38): 17:3923868-3964464

Links

ENSG00000074370

∙ NCBI:489 ∙ OMIM:601929 ∙ HGNC:813 ∙ Uniprot:Q93084 ∙ 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 ATP2A3 gene.

not_specified (121 variants)
ATP2A3-related_disorder (40 variants)
not_provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2A3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005173.4. 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				22 clinvar	10 clinvar	32
missense			116 clinvar	8 clinvar	3 clinvar	127
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	116	30	13

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP2A3	protein_coding	protein_coding	ENST00000359983	23	40568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-9	1.00	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	537	671	0.801	0.0000498	6711
Missense in Polyphen		230	351.92	0.65356		3550
Synonymous	-2.53	352	297	1.19	0.0000244	2219
Loss of Function	3.51	23	49.7	0.463	0.00000279	518

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000191	0.000185
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000330	0.0000327
Other	0.000498	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium. Transports calcium ions from the cytosol into the sarcoplasmic/endoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction. {ECO:0000269|PubMed:11956212, ECO:0000269|PubMed:15028735}.;
Pathway: Alzheimer,s disease - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Alzheimers Disease;Myometrial Relaxation and Contraction Pathways;Calcium Regulation in the Cardiac Cell;nfat and hypertrophy of the heart ;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: 0.198

Intolerance Scores

loftool: 0.00675
rvis_EVS: -1.47
rvis_percentile_EVS: 3.74

Haploinsufficiency Scores

pHI: 0.129
hipred: Y
hipred_score: 0.744
ghis: 0.570

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.615

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Atp2a3
Phenotype: muscle phenotype; 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);

Gene ontology

Biological process: calcium ion transport;cellular calcium ion homeostasis;ion transmembrane transport;calcium ion transmembrane transport;ATP hydrolysis coupled cation transmembrane transport;proton transmembrane transport;regulation of cardiac conduction
Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;sarcoplasmic reticulum;platelet dense tubular network membrane;nuclear membrane;sarcoplasmic reticulum membrane
Molecular function: calcium-transporting ATPase activity;ATP binding;proton-exporting ATPase activity, phosphorylative mechanism;metal ion binding