ATP4B

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

Basic information

Region (hg38): 13:113648804-113658198

Links

ENSG00000186009 ∙ NCBI:496 ∙ OMIM:137217 ∙ HGNC:820 ∙ Uniprot:P51164 ∙ 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 ATP4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP4B 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						0
missense			19	3		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in ATP4B

This is a list of pathogenic ClinVar variants found in the ATP4B region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113649385-T-A		not specified	Uncertain significance (Sep 26, 2022)
13-113649393-T-C		not specified	Uncertain significance (Oct 06, 2023)
13-113649442-C-T		not specified	Uncertain significance (Mar 16, 2022)
13-113649443-G-T		not specified	Uncertain significance (Mar 05, 2024)
13-113649472-C-T		not specified	Uncertain significance (Nov 30, 2021)
13-113649481-C-T		not specified	Likely benign (May 15, 2023)
13-113650408-G-C		not specified	Uncertain significance (Mar 25, 2024)
13-113650453-C-T		not specified	Uncertain significance (Jun 11, 2024)
13-113650458-G-C		not specified	Uncertain significance (Dec 01, 2022)
13-113650482-G-A		not specified	Uncertain significance (Jan 06, 2023)
13-113650497-C-T		not specified	Uncertain significance (May 31, 2023)
13-113651679-C-T		not specified	Likely benign (Dec 20, 2021)
13-113652931-G-A		not specified	Likely benign (Jan 19, 2024)
13-113652931-G-T		not specified	Uncertain significance (Aug 04, 2023)
13-113652964-G-A		not specified	Uncertain significance (Jan 31, 2023)
13-113653004-A-C		not specified	Uncertain significance (May 05, 2023)
13-113653066-G-A		not specified	Uncertain significance (Apr 15, 2024)
13-113653428-G-T		not specified	Uncertain significance (May 24, 2024)
13-113654823-G-A		not specified	Uncertain significance (Mar 01, 2024)
13-113654835-G-C		not specified	Uncertain significance (Jan 27, 2022)
13-113654876-T-C		not specified	Uncertain significance (Jan 04, 2024)
13-113654877-A-G		not specified	Uncertain significance (Sep 29, 2022)
13-113654916-A-G		not specified	Uncertain significance (Jun 26, 2023)
13-113658068-G-A		not specified	Uncertain significance (Dec 03, 2021)
13-113658095-A-G		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP4B	protein_coding	protein_coding	ENST00000335288	7	9383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000464	0.871	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.166	169	175	0.965	0.0000107	1905
Missense in Polyphen		68	75.37	0.90222		825
Synonymous	-0.0513	79	78.4	1.01	0.00000587	527
Loss of Function	1.42	9	14.9	0.603	6.36e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for stabilization and maturation of the catalytic proton pump alpha subunit and may also involved in cell adhesion and establishing epithelial cell polarity. {ECO:0000269|PubMed:19694409}.
• 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;Ion channel transport;Purine metabolism;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.818
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.197
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp4b
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: cellular sodium ion homeostasis;cell adhesion;response to organonitrogen compound;establishment or maintenance of transmembrane electrochemical gradient;cellular potassium ion homeostasis;response to lipopolysaccharide;positive regulation of ATPase activity;sodium ion export across plasma membrane;proton transmembrane transport;potassium ion import across plasma membrane
• Cellular component: plasma membrane;sodium:potassium-exchanging ATPase complex
• Molecular function: ATPase activator activity;sodium:potassium-exchanging ATPase activity;protein binding;potassium:proton exchanging ATPase activity