ATP1B1

ATPase Na+/K+ transporting subunit beta 1, the group of ATPase Na+/K+ transporting subunits

Basic information

Region (hg38): 1:169105696-169310992

Previous symbols: [ "ATP1B" ]

Links

ENSG00000143153 ∙ NCBI:481 ∙ OMIM:182330 ∙ HGNC:804 ∙ Uniprot:P05026 ∙ 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 ATP1B1 gene.

• Inborn genetic diseases (14 variants)
• not specified (10 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP1B1 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				3	4	7
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			13		1	14
Total	0	0	18	4	5

Variants in ATP1B1

This is a list of pathogenic ClinVar variants found in the ATP1B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-169106829-C-A		not specified	Benign (Jun 15, 2020)
1-169106874-C-T			Likely benign (Jan 11, 2019)
1-169106936-G-C		not specified	Uncertain significance (Jan 13, 2020)
1-169111407-C-T		not specified	Likely benign (Aug 21, 2019)
1-169111489-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-169111494-G-A		not specified	Benign (Nov 02, 2019)
1-169124978-G-A			Benign (Feb 01, 2024)
1-169124994-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-169125039-G-A		not specified	Likely benign (Dec 14, 2021)
1-169127363-G-A		not specified	Benign (Oct 30, 2021)
1-169129990-A-C		not specified	Uncertain significance (Sep 10, 2022)
1-169130013-C-T		Cardiac arrhythmia	Uncertain significance (Aug 18, 2011)
1-169130025-T-A		not specified	Uncertain significance (Nov 30, 2022)
1-169130042-A-C			Benign (Dec 31, 2019)
1-169130053-A-G		not specified	Uncertain significance (Feb 16, 2023)
1-169131424-G-A		not specified	Uncertain significance (Nov 18, 2019)
1-169131433-A-G		not specified	Uncertain significance (Jul 05, 2021)
1-169131451-A-G		not specified	Uncertain significance (Nov 14, 2023)
1-169131454-G-GA		Global developmental delay	Uncertain significance (Jan 01, 2020)
1-169131480-C-T		not specified	Benign/Likely benign (Aug 26, 2023)
1-169132806-G-GAAGT		NME7-related disorder	Likely benign (Aug 30, 2023)
1-169169493-T-C		not specified	Uncertain significance (Apr 04, 2023)
1-169169545-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-169230725-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-169230774-T-C		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP1B1	protein_coding	protein_coding	ENST00000367816	6	27026

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00119	116318	0	1	116319	0.00000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	97	171	0.569	0.00000926	1985
Missense in Polyphen		12	53.156	0.22575		588
Synonymous	-0.00899	64	63.9	1.00	0.00000357	554
Loss of Function	4.10	0	19.5	0.00	0.00000137	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000918	0.00000918
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is the non-catalytic component of the active enzyme, which catalyzes the hydrolysis of ATP coupled with the exchange of Na(+) and K(+) ions across the plasma membrane. The beta subunit regulates, through assembly of alpha/beta heterodimers, the number of sodium pumps transported to the plasma membrane. {ECO:0000269|PubMed:19694409}.
• Pathway: Aldosterone synthesis and secretion - Homo sapiens (human);Cardiac muscle contraction - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Bile secretion - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Proximal tubule bicarbonate reclamation - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Aldosterone-regulated sodium reabsorption - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Mineral absorption - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Levomethadyl Acetate Action Action Pathway;Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Disopyramide Action Pathway;Procainamide (Antiarrhythmic) Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Fosphenytoin (Antiarrhythmic) Action Pathway;Bopindolol Action Pathway;Timolol Action Pathway;Carteolol Action Pathway;Fluoxetine Action Pathway;Citalopram Action Pathway;Escitalopram Action Pathway;Imipramine Action Pathway;Desipramine Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Levallorphan Action Pathway;Dimethylthiambutene Action Pathway;Ethylmorphine Action Pathway;Pentazocine Action Pathway;Naltrexone Action Pathway;Buprenorphine Action Pathway;Alvimopan Action Pathway;Naloxone Action Pathway;Dihydromorphine Action Pathway;Bevantolol Action Pathway;Practolol Action Pathway;Trehalose Degradation;Dobutamine Action Pathway;Isoprenaline Action Pathway;Arbutamine Action Pathway;Amiodarone Action Pathway;Levobunolol Action Pathway;Metipranolol Action Pathway;Mexiletine Action Pathway;Lidocaine (Antiarrhythmic) Action Pathway;Quinidine Action Pathway;Sotalol Action Pathway;Epinephrine Action Pathway;Ethacrynic Acid Action Pathway;Quinethazone Action Pathway;Bendroflumethiazide Action Pathway;Betaxolol Action Pathway;Atenolol Action Pathway;Alprenolol Action Pathway;Acebutolol Action Pathway;Nicotine Action Pathway;Chlorthalidone Action Pathway;Trichlormethiazide Action Pathway;Nalbuphine Action Pathway;Ketobemidone Action Pathway;Iminoglycinuria;Lysinuric Protein Intolerance;Lidocaine (Local Anaesthetic) Action Pathway;Mepivacaine Action Pathway;Chloroprocaine Action Pathway;Cocaine Action Pathway;Dibucaine Action Pathway;Levobupivacaine Action Pathway;Benzocaine Action Pathway;Bupivacaine Action Pathway;Muscle/Heart Contraction;Blue diaper syndrome;Lysinuric protein intolerance (LPI);Diltiazem Action Pathway;Propranolol Action Pathway;Pindolol Action Pathway;Penbutolol Action Pathway;Oxprenolol Action Pathway;Metoprolol Action Pathway;Esmolol Action Pathway;Bisoprolol Action Pathway;Levorphanol Action Pathway;Propoxyphene Action Pathway;Tramadol Action Action Pathway;Bupranolol Action Pathway;Diphenoxylate Action Pathway;Anileridine Action Pathway;Methadone Action Pathway;Oxycodone Action Pathway;Oxybuprocaine Action Pathway;Prilocaine Action Pathway;Procaine Action Pathway;Proparacaine Action Pathway;Ropivacaine Action Pathway;Codeine Action Pathway;Morphine Action Pathway;Heroin Action Pathway;Nebivolol Action Pathway;Cystinuria;Amlodipine Action Pathway;Verapamil Action Pathway;Indapamide Action Pathway;Furosemide Action Pathway;Torsemide Action Pathway;Hartnup Disorder;Glucose Transporter Defect (SGLT2);Nitrendipine Action Pathway;Nisoldipine Action Pathway;Nimodipine Action Pathway;Ibutilide Action Pathway;Tocainide Action Pathway;Flecainide Action Pathway;Kidney Function;Alfentanil Action Pathway;Oxymorphone Action Pathway;Hydrocodone Action Pathway;Hydromorphone Action Pathway;Sufentanil Action Pathway;Remifentanil Action Pathway;Fentanyl Action Pathway;Carfentanil Action Pathway;Isradipine Action Pathway;Nifedipine Action Pathway;Felodipine Action Pathway;Nadolol Action Pathway;Glucose Transporter Defect (SGLT2);Carvedilol Action Pathway;Labetalol Action Pathway;Lactose Degradation;Lactose Intolerance;Metolazone Action Pathway;Hydrochlorothiazide Action Pathway;Cyclothiazide Action Pathway;Hydroflumethiazide Action Pathway;3-Methylthiofentanyl Action Pathway;Methadyl Acetate Action Pathway;Chlorothiazide Action Pathway;Dezocine Action Pathway;Calcium Regulation in the Cardiac Cell;Ion channel transport;Purine metabolism;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions (Consensus)

Recessive Scores

• pRec: 0.248

Intolerance Scores

• loftool: 0.140
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.385
• hipred: Y
• hipred_score: 0.825
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp1b1
• 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; respiratory system phenotype; homeostasis/metabolism phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: atp1b1a
• Affected structure: epidermal cell
• Phenotype tag: abnormal
• Phenotype quality: aggregated

Gene ontology

• Biological process: response to hypoxia;cellular calcium ion homeostasis;cellular sodium ion homeostasis;cell adhesion;establishment or maintenance of transmembrane electrochemical gradient;regulation of gene expression;regulation of cardiac muscle contraction by calcium ion signaling;cellular potassium ion homeostasis;positive regulation of ATPase activity;sodium ion export across plasma membrane;protein transport into plasma membrane raft;ATP metabolic process;protein stabilization;leukocyte migration;relaxation of cardiac muscle;cardiac muscle contraction;protein localization to plasma membrane;membrane repolarization;membrane repolarization during cardiac muscle cell action potential;cell communication by electrical coupling involved in cardiac conduction;positive regulation of potassium ion transmembrane transporter activity;positive regulation of sodium ion export across plasma membrane;positive regulation of calcium:sodium antiporter activity;positive regulation of potassium ion import across plasma membrane;potassium ion import across plasma membrane
• Cellular component: plasma membrane;sodium:potassium-exchanging ATPase complex;caveola;intercalated disc;membrane;basolateral plasma membrane;apical plasma membrane;sarcolemma;myelin sheath;extracellular exosome;extracellular vesicle
• Molecular function: ATPase activator activity;sodium:potassium-exchanging ATPase activity;protein binding;ATP binding;protein C-terminus binding;drug binding;ATPase activity;protein kinase binding;MHC class II protein complex binding;potassium ion binding;sodium ion binding;ATPase binding