ATP13A3

ATPase 13A3, the group of ATPase orphan transporters

Basic information

Region (hg38): 3:194402672-194498364

Links

ENSG00000133657 ∙ NCBI:79572 ∙ OMIM:610232 ∙ HGNC:24113 ∙ Uniprot:Q9H7F0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pulmonary arterial hypertension (Definitive), mode of inheritance: Semidominant

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pulmonary hypertension, primary, 5	AR	Cardiovascular	Individuals with Pulmonary hypertension, primary, may manifest at variable ages, and awareness may allow surveillance, diagnosis of sequelae, and prompt management (including medical and/or surgical management) of disease	Cardiovascular	34493544

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP13A3 gene.

• Pulmonary arterial hypertension (2 variants)
• Pulmonary hypertension, primary, autosomal recessive (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP13A3 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				28	5	33
missense		2	59	2	6	69
nonsense						0
start loss						0
frameshift	3					3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			3	2	3	8
non coding				13	35	48
Total	3	2	60	43	46

Variants in ATP13A3

This is a list of pathogenic ClinVar variants found in the ATP13A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-194405931-G-A			Likely benign (Jun 19, 2023)
3-194405946-T-C		ATP13A3-related disorder	Likely benign (Jan 27, 2023)
3-194406005-C-A		Pulmonary arterial hypertension • Pulmonary hypertension, primary, autosomal recessive	Conflicting classifications of pathogenicity (Jun 15, 2022)
3-194406038-T-C		not specified	Uncertain significance (Nov 27, 2023)
3-194406052-G-C			Uncertain significance (Dec 30, 2023)
3-194406056-T-G			Uncertain significance (Jan 13, 2024)
3-194406058-T-C		ATP13A3-related disorder	Uncertain significance (May 26, 2023)
3-194406082-G-C		not specified	Uncertain significance (Oct 13, 2023)
3-194406093-T-C			Likely benign (Mar 19, 2022)
3-194406104-G-A		not specified	Uncertain significance (Jun 03, 2024)
3-194406320-C-T			Benign (May 10, 2021)
3-194413757-A-G			Uncertain significance (Dec 25, 2021)
3-194413770-T-C		not specified	Uncertain significance (Jan 10, 2023)
3-194413806-T-C			Uncertain significance (Feb 01, 2022)
3-194413815-G-A		not specified	Uncertain significance (May 16, 2022)
3-194413821-G-C			Uncertain significance (Jan 13, 2023)
3-194413825-T-G			Likely benign (Apr 10, 2023)
3-194413986-C-G			Benign (May 11, 2021)
3-194419866-G-A			Likely benign (Apr 09, 2021)
3-194419935-T-A			Uncertain significance (Jul 26, 2021)
3-194419952-G-GA			Pathogenic (Jun 29, 2022)
3-194425487-G-A			Likely benign (Jan 15, 2024)
3-194425507-C-A			Uncertain significance (Feb 27, 2022)
3-194425519-T-C		ATP13A3-related disorder	Benign (Jan 03, 2024)
3-194427078-G-A		ATP13A3-related disorder	Benign (Jan 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP13A3	protein_coding	protein_coding	ENST00000439040	31	95693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000218	124805	0	16	124821	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.01	444	662	0.670	0.0000339	8070
Missense in Polyphen		66	191.34	0.34494		2298
Synonymous	-0.136	230	227	1.01	0.0000124	2312
Loss of Function	6.59	8	65.5	0.122	0.00000305	843

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000278
Ashkenazi Jewish	0.000304	0.000298
East Asian	0.00	0.00
Finnish	0.0000928	0.0000927
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0969

Intolerance Scores

• loftool: 0.124
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.95

Haploinsufficiency Scores

• pHI: 0.776
• hipred: Y
• hipred_score: 0.672
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.403

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp13a3

Gene ontology

• Biological process: cation transport;cellular calcium ion homeostasis
• Cellular component: cell;membrane;integral component of membrane
• Molecular function: ATP binding;ATPase activity;metal ion binding