ATP12A

ATPase H+/K+ transporting non-gastric alpha2 subunit, the group of ATPase H+/K+ transporting

Basic information

Region (hg38): 13:24680408-24712472

Previous symbols: [ "ATP1AL1" ]

Links

ENSG00000075673 ∙ NCBI:479 ∙ OMIM:182360 ∙ HGNC:13816 ∙ Uniprot:P54707 ∙ 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 ATP12A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP12A 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		1
missense			55			55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding					1	1
Total	0	0	55	1	1

Variants in ATP12A

This is a list of pathogenic ClinVar variants found in the ATP12A region.

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

Position	Type	Phenotype	Significance	ClinVar
13-24680753-G-A			Uncertain significance (-)
13-24681644-A-G		not specified	Uncertain significance (Feb 27, 2024)
13-24685326-C-T		not specified	Uncertain significance (Jan 23, 2024)
13-24688319-G-T		not specified	Uncertain significance (Jan 19, 2024)
13-24688329-G-A		not specified	Uncertain significance (Aug 30, 2021)
13-24688392-C-T		not specified	Uncertain significance (Nov 15, 2021)
13-24688522-C-T			Likely benign (Nov 01, 2022)
13-24690404-A-G		not specified	Uncertain significance (Mar 29, 2022)
13-24690404-A-T		not specified	Uncertain significance (Dec 06, 2022)
13-24690412-G-C		not specified	Uncertain significance (Jul 19, 2023)
13-24690456-C-A		not specified	Uncertain significance (Feb 21, 2024)
13-24690605-T-C		not specified	Uncertain significance (Mar 31, 2023)
13-24690655-G-A		not specified	Uncertain significance (Mar 20, 2023)
13-24690710-C-T		not specified	Uncertain significance (Jul 26, 2021)
13-24690963-G-A			Benign (Dec 31, 2019)
13-24691011-G-A		not specified	Uncertain significance (Apr 18, 2023)
13-24691016-C-G		not specified	Uncertain significance (Dec 13, 2022)
13-24691018-G-A		not specified	Uncertain significance (Jan 03, 2024)
13-24691042-C-T		not specified	Uncertain significance (May 02, 2024)
13-24691056-G-A		not specified	Uncertain significance (Mar 14, 2023)
13-24691065-G-A		not specified	Uncertain significance (May 11, 2022)
13-24691131-A-G		not specified	Uncertain significance (Apr 27, 2022)
13-24691155-G-A		not specified	Uncertain significance (Apr 04, 2024)
13-24692460-C-T		not specified	Uncertain significance (Feb 28, 2023)
13-24692507-G-A		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP12A	protein_coding	protein_coding	ENST00000218548	23	31373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.13e-14	0.989	125260	3	485	125748	0.00194

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.834	547	605	0.905	0.0000337	6856
Missense in Polyphen		229	248.64	0.92103		2894
Synonymous	0.352	235	242	0.971	0.0000149	2052
Loss of Function	2.60	29	48.5	0.598	0.00000229	588

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0182	0.0181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000981	0.000870
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000619	0.000589
Middle Eastern	0.000981	0.000870
South Asian	0.00292	0.00285
Other	0.000654	0.000652

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 potassium absorption in various tissues.
• Pathway: Oxidative phosphorylation - Homo sapiens (human);Ion channel transport;Purine metabolism;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.235

Intolerance Scores

• loftool: 0.0580
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.78

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.469
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.746

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp12a
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: cellular sodium ion homeostasis;regulation of pH;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: plasma membrane;potassium:proton exchanging ATPase complex;basolateral plasma membrane
• Molecular function: sodium:potassium-exchanging ATPase activity;ATP binding;potassium:proton exchanging ATPase activity;metal ion binding