ATP4A

ATPase H+/K+ transporting subunit alpha, the group of ATPase H+/K+ transporting

Basic information

Region (hg38): 19:35550031-35563658

Links

ENSG00000105675 ∙ NCBI:495 ∙ OMIM:137216 ∙ HGNC:819 ∙ Uniprot:P20648 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial gastric type 1 neuroendocrine tumor (Supportive), mode of inheritance: AR
• gastric neuroendocrine neoplasm (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP4A 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	11	18	30
missense			80	5	2	87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding			1	7	6	14
Total	0	0	82	23	26

Variants in ATP4A

This is a list of pathogenic ClinVar variants found in the ATP4A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35550660-G-A			Likely benign (Oct 04, 2023)
19-35550848-C-T			Uncertain significance (Sep 05, 2022)
19-35550851-A-G			Uncertain significance (Nov 19, 2023)
19-35550895-G-A			Likely benign (Nov 16, 2022)
19-35551014-T-C		not specified	Uncertain significance (Mar 20, 2023)
19-35551055-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-35551057-C-T			Benign (Nov 27, 2023)
19-35551068-C-G		not specified	Uncertain significance (Jan 17, 2024)
19-35551086-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-35551431-G-A			Benign (Mar 02, 2023)
19-35551481-G-A		not specified	Uncertain significance (Apr 11, 2023)
19-35551496-G-C		not specified	Uncertain significance (Sep 01, 2021)
19-35551500-A-T		not specified	Uncertain significance (Nov 17, 2022)
19-35551568-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-35553022-C-T			Likely benign (Jan 25, 2024)
19-35553075-G-T			Likely benign (Jan 13, 2024)
19-35553105-C-T		not specified	Uncertain significance (Dec 28, 2023)
19-35553147-A-G		not specified	Uncertain significance (Nov 30, 2022)
19-35553695-C-T			Likely benign (Sep 07, 2022)
19-35553715-A-G		not specified	Uncertain significance (Sep 17, 2021)
19-35553756-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-35553783-A-G		not specified	Uncertain significance (May 23, 2024)
19-35553841-T-C			Benign (Nov 16, 2023)
19-35554973-G-A			Benign (Dec 13, 2023)
19-35554984-C-T		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP4A	protein_coding	protein_coding	ENST00000262623	22	13616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.44e-12	0.999	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.87	455	663	0.686	0.0000420	6709
Missense in Polyphen		187	303.71	0.61572		3087
Synonymous	-0.798	306	289	1.06	0.0000205	2101
Loss of Function	2.98	26	48.3	0.538	0.00000224	534

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000388	0.000388
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000163	0.000163
South Asian	0.000202	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
• Pathway: Gastric acid secretion - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Collecting duct acid secretion - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;Omeprazole Metabolism Pathway;Esomeprazole Metabolism Pathway;Pantoprazole Metabolism Pathway;Lansoprazole Metabolism Pathway;Rabeprazole Metabolism Pathway;Pantoprazole Action Pathway;Rabeprazole Action Pathway;Esomeprazole Action Pathway;Omeprazole Action Pathway;Lansoprazole Action Pathway;Gastric Acid Production;Nizatidine Action Pathway;Cimetidine Action Pathway;Famotidine Action Pathway;Ranitidine Action Pathway;Betazole Action Pathway;Roxatidine acetate Action Pathway;Metiamide Action Pathway;Pirenzepine Action Pathway;Secretion of Hydrochloric Acid in Parietal Cells;Ion channel transport;Purine metabolism;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.123
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.99

Haploinsufficiency Scores

• pHI: 0.0783
• hipred: Y
• hipred_score: 0.671
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp4a
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cellular sodium ion homeostasis;establishment or maintenance of transmembrane electrochemical gradient;ATP hydrolysis coupled proton transport;cellular potassium ion homeostasis;sodium ion export across plasma membrane;potassium ion import across plasma membrane
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane
• Molecular function: magnesium ion binding;sodium:potassium-exchanging ATPase activity;ATP binding;potassium:proton exchanging ATPase activity