ATP13A1

ATPase 13A1, the group of ATPase orphan transporters

Basic information

Region (hg38): 19:19645198-19663676

Previous symbols: [ "ATP13A" ]

Links

ENSG00000105726 ∙ NCBI:57130 ∙ OMIM:619118 ∙ HGNC:24215 ∙ Uniprot:Q9HD20 ∙ 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 ATP13A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP13A1 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				7	6	13
missense			78	4	2	84
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	78	11	8

Variants in ATP13A1

This is a list of pathogenic ClinVar variants found in the ATP13A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19645461-C-T			Benign (Dec 31, 2019)
19-19645469-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-19645472-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-19645486-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-19645656-G-C		not specified	Uncertain significance (Jan 26, 2023)
19-19645706-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-19645714-A-G		not specified	Uncertain significance (Sep 27, 2021)
19-19645786-G-A		not specified	Uncertain significance (May 26, 2024)
19-19645972-C-T		not specified	Uncertain significance (Sep 20, 2023)
19-19645978-G-C			Likely benign (Mar 01, 2023)
19-19646209-C-T		not specified	Uncertain significance (Jan 18, 2023)
19-19646210-G-A			Likely benign (Sep 17, 2018)
19-19646232-C-T		not specified	Uncertain significance (Jul 07, 2022)
19-19646255-G-T		not specified	Uncertain significance (Jul 12, 2022)
19-19646264-A-C			Benign (Dec 31, 2019)
19-19646290-T-C		not specified	Likely benign (Jul 13, 2021)
19-19646295-T-C		not specified	Uncertain significance (Feb 17, 2023)
19-19647137-G-A		not specified	Uncertain significance (Jul 12, 2023)
19-19647180-G-C			Likely benign (Feb 01, 2023)
19-19647283-G-A		not specified	Uncertain significance (Jan 11, 2023)
19-19647286-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-19647485-G-C		not specified	Uncertain significance (May 23, 2024)
19-19647489-T-G		not specified	Uncertain significance (May 15, 2023)
19-19647506-C-T		not specified	Uncertain significance (Jan 25, 2023)
19-19647660-G-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP13A1	protein_coding	protein_coding	ENST00000357324	26	18496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0106	125586	0	21	125607	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	526	728	0.722	0.0000470	7631
Missense in Polyphen		145	303.07	0.47843		3205
Synonymous	-0.197	337	332	1.01	0.0000233	2505
Loss of Function	5.82	10	57.8	0.173	0.00000309	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000209
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000982	0.0000969
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates manganese transport into the endoplasmic reticulum. The ATPase activity is required for cellular manganese homeostasis. {ECO:0000269|PubMed:24392018}.
• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Intolerance Scores

• loftool: 0.129
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.34

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.563
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.618

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp13a1

Gene ontology

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