ATP13A4

ATPase 13A4, the group of ATPase orphan transporters

Basic information

Region (hg38): 3:193398967-193593111

Links

ENSG00000127249 ∙ NCBI:84239 ∙ OMIM:609556 ∙ HGNC:25422 ∙ Uniprot:Q4VNC1 ∙ 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 ATP13A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP13A4 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				10	3	13
missense			71	8	4	83
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1	1	2
Total	0	0	72	19	8

Variants in ATP13A4

This is a list of pathogenic ClinVar variants found in the ATP13A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-193402670-G-A			Benign (Dec 31, 2019)
3-193402704-C-T		not specified	Uncertain significance (Mar 31, 2024)
3-193402711-A-G		not specified	Uncertain significance (May 01, 2024)
3-193402719-A-T		not specified	Uncertain significance (Jan 04, 2022)
3-193402746-G-A		ATP13A4-related disorder	Benign/Likely benign (Feb 23, 2022)
3-193402758-G-A		not specified	Uncertain significance (Jun 11, 2021)
3-193402777-T-C		not specified	Uncertain significance (Dec 19, 2023)
3-193402838-C-T			Benign (Dec 31, 2019)
3-193407315-C-T		not specified	Uncertain significance (Aug 19, 2021)
3-193407324-G-A		not specified	Uncertain significance (Feb 17, 2022)
3-193407331-A-C		not specified	Uncertain significance (Jun 07, 2024)
3-193407365-G-A		not specified	Likely benign (Nov 18, 2023)
3-193410989-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-193410990-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-193411035-C-A		not specified	Uncertain significance (Jan 23, 2023)
3-193411056-C-G		not specified	Uncertain significance (Mar 07, 2024)
3-193412265-C-T		ATP13A4-related disorder • not specified	Likely benign (Jun 12, 2022)
3-193412280-A-G		not specified	Uncertain significance (Nov 30, 2021)
3-193412297-T-C		not specified	Uncertain significance (Nov 12, 2021)
3-193412331-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-193412348-C-T		not specified	Uncertain significance (Jun 04, 2024)
3-193414630-G-A		not specified	Likely benign (Nov 27, 2023)
3-193414642-G-A		not specified	Uncertain significance (Jun 17, 2024)
3-193414646-G-A		ATP13A4-related disorder	Benign (Aug 08, 2019)
3-193414648-C-T		not specified	Uncertain significance (Nov 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP13A4	protein_coding	protein_coding	ENST00000342695	30	191035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.33e-26	0.160	125604	0	144	125748	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0486	636	639	0.995	0.0000334	7841
Missense in Polyphen		211	236.79	0.89108		3042
Synonymous	-0.435	246	237	1.04	0.0000137	2310
Loss of Function	1.90	49	65.6	0.746	0.00000314	793

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00117
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000328	0.000326
Finnish	0.000693	0.000693
European (Non-Finnish)	0.000626	0.000615
Middle Eastern	0.000328	0.000326
South Asian	0.000686	0.000686
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving ATP13A4 is found in 2 patients with specific language impairment (SLI) disorders. Paracentric inversion inv(3)(q25;q29). The inversion produces a disruption of the protein. {ECO:0000269|PubMed:15925480}.
• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• loftool: 0.242
• rvis_EVS: -1.38
• rvis_percentile_EVS: 4.36

Haploinsufficiency Scores

• pHI: 0.0813
• hipred: N
• hipred_score: 0.314
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp13a4

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