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.

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.

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				21	16	37
missense			52	7	5	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	2	5
non coding				1	2	3
Total	0	0	52	29	23

Variants in ATP2A3

This is a list of pathogenic ClinVar variants found in the ATP2A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-3925403-T-C		ATP2A3-related disorder	Benign (Feb 22, 2019)
17-3925408-T-C		ATP2A3-related disorder	Benign (Oct 18, 2019)
17-3925441-T-C		not specified	Uncertain significance (Aug 01, 2024)
17-3927972-G-A		ATP2A3-related disorder	Benign (Jul 31, 2018)
17-3928687-A-G		not specified	Uncertain significance (Nov 28, 2023)
17-3928749-C-T		not specified	Uncertain significance (Sep 11, 2024)
17-3928753-C-T		not specified	Uncertain significance (Nov 14, 2024)
17-3928785-C-T		ATP2A3-related disorder	Benign (Sep 24, 2019)
17-3929420-G-A		not specified	Conflicting classifications of pathogenicity (Mar 25, 2024)
17-3929439-C-T		ATP2A3-related disorder	Benign (Sep 24, 2019)
17-3929440-G-A		not specified	Uncertain significance (Aug 17, 2021)
17-3929442-G-A		ATP2A3-related disorder	Likely benign (Jun 12, 2019)
17-3929444-C-T		not specified	Uncertain significance (Dec 22, 2023)
17-3930308-G-A		not specified	Uncertain significance (Feb 08, 2023)
17-3930325-A-G		not specified	Uncertain significance (May 03, 2023)
17-3930370-T-C		not specified	Uncertain significance (Dec 01, 2022)
17-3930371-C-T		ATP2A3-related disorder	Likely benign (May 10, 2022)
17-3930377-C-T		not specified	Uncertain significance (Dec 01, 2022)
17-3930386-C-T		ATP2A3-related disorder	Benign (Sep 24, 2019)
17-3930403-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-3930413-C-T		not specified	Uncertain significance (Mar 21, 2023)
17-3930414-G-T		ATP2A3-related disorder	Benign (Dec 11, 2017)
17-3935209-T-C		not specified	Likely benign (Jan 10, 2022)
17-3935273-G-A		ATP2A3-related disorder	Likely benign (Apr 25, 2019)
17-3935277-A-C		not specified	Uncertain significance (Mar 07, 2024)

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