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.

not_specified (120 variants)
not_provided (96 variants)

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. These statistics are base on transcript: NM_000000704.3. 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				20 clinvar	19 clinvar	39
missense			135 clinvar	5 clinvar	1 clinvar	141
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	135	25	20

Loading clinvar variants...

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