ATP13A5

ATPase 13A5, the group of ATPase orphan transporters

Basic information

Region (hg38): 3:193274789-193378820

Links

ENSG00000187527 ∙ NCBI:344905 ∙ OMIM:619119 ∙ HGNC:31789 ∙ Uniprot:Q4VNC0 ∙ 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 ATP13A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP13A5 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				2	1	3
missense			63	2		65
nonsense				1		1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	5	2

Variants in ATP13A5

This is a list of pathogenic ClinVar variants found in the ATP13A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-193275045-CA-C			Benign (Jun 23, 2018)
3-193275056-A-G		not specified	Uncertain significance (Jun 02, 2023)
3-193275070-G-C		not specified	Uncertain significance (Nov 13, 2024)
3-193275109-T-C		not specified	Uncertain significance (Feb 28, 2024)
3-193275141-G-C		not specified	Uncertain significance (Dec 09, 2023)
3-193275158-C-T		not specified	Uncertain significance (Nov 13, 2024)
3-193275178-T-C		not specified	Uncertain significance (Dec 08, 2023)
3-193275247-A-C		not specified	Uncertain significance (Aug 16, 2021)
3-193276755-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-193276770-A-G		not specified	Uncertain significance (Apr 07, 2022)
3-193276811-G-A		not specified	Uncertain significance (Aug 12, 2024)
3-193279410-A-G		not specified	Uncertain significance (May 20, 2024)
3-193279433-A-G		not specified	Uncertain significance (Nov 08, 2021)
3-193284915-G-T		not specified	Uncertain significance (Oct 12, 2024)
3-193289938-A-G			Likely benign (Jan 01, 2023)
3-193289943-T-A		not specified	Uncertain significance (Jul 05, 2024)
3-193289944-C-G		not specified	Uncertain significance (Aug 02, 2023)
3-193289985-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-193289993-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-193289994-G-C		not specified	Uncertain significance (Nov 26, 2024)
3-193290053-G-A		not specified	Uncertain significance (Nov 09, 2023)
3-193301249-C-T		not specified	Uncertain significance (Jan 31, 2022)
3-193301257-G-A		not specified	Uncertain significance (Oct 14, 2023)
3-193301288-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-193301299-C-T		not specified	Uncertain significance (Mar 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP13A5	protein_coding	protein_coding	ENST00000342358	30	104054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.41e-49	1.40e-8	119078	99	6571	125748	0.0269

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.606	601	644	0.933	0.0000325	7935
Missense in Polyphen		201	249.43	0.80583		3234
Synonymous	0.664	227	240	0.945	0.0000126	2313
Loss of Function	-0.445	72	68.0	1.06	0.00000323	842

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0260	0.0254
Ashkenazi Jewish	0.0103	0.0103
East Asian	0.00187	0.00185
Finnish	0.0501	0.0499
European (Non-Finnish)	0.0389	0.0389
Middle Eastern	0.00187	0.00185
South Asian	0.00892	0.00883
Other	0.0268	0.0262

dbNSFP

Source: dbNSFP

• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.0798

Intolerance Scores

• loftool: 0.263
• rvis_EVS: 2.04
• rvis_percentile_EVS: 97.72

Haploinsufficiency Scores

• pHI: 0.0882
• hipred: N
• hipred_score: 0.155
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Atp13a5
• Phenotype: hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: cellular calcium ion homeostasis;ion transmembrane transport;ATP hydrolysis coupled cation transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: ATP binding;cation-transporting ATPase activity;metal ion binding