ATP10A

ATPase phospholipid transporting 10A (putative), the group of ATPase phospholipid transporting|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:25677273-25865184

Previous symbols: [ "ATP10C" ]

Links

ENSG00000206190 ∙ NCBI:57194 ∙ OMIM:605855 ∙ HGNC:13542 ∙ Uniprot:O60312 ∙ 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 ATP10A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP10A 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				18	13	31
missense			124	21	10	155
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				5		5
non coding				1	3	4
Total	0	0	125	40	26

Variants in ATP10A

This is a list of pathogenic ClinVar variants found in the ATP10A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-25679349-A-C		not specified	Uncertain significance (Apr 30, 2025)
15-25679366-C-T		not specified	Uncertain significance (Oct 05, 2023)
15-25679388-G-T		not specified	Likely benign (May 07, 2025)
15-25679403-A-G		not specified	Likely benign (Feb 19, 2025)
15-25679418-G-T		ATP10A-related disorder	Uncertain significance (Jun 12, 2024)
15-25679435-C-G			Likely benign (Dec 31, 2019)
15-25679435-C-T			Likely benign (May 21, 2018)
15-25679436-G-C		not specified	Uncertain significance (May 09, 2024)
15-25679465-G-A		not specified	Uncertain significance (Feb 12, 2025)
15-25679511-A-G		not specified	Uncertain significance (Mar 25, 2025)
15-25679558-G-A		not specified	Uncertain significance (Dec 05, 2022)
15-25679566-G-C			Likely benign (Dec 31, 2019)
15-25679570-G-T		not specified	Uncertain significance (Jun 10, 2025)
15-25679589-C-A		not specified	Uncertain significance (Apr 25, 2025)
15-25679591-G-A			Uncertain significance (Oct 11, 2019)
15-25679615-C-T		not specified	Uncertain significance (Dec 26, 2024)
15-25679621-C-A		not specified	Uncertain significance (Jul 12, 2022)
15-25679625-G-T		not specified	Uncertain significance (Dec 22, 2023)
15-25679637-C-G		not specified	Uncertain significance (Jul 27, 2022)
15-25679650-C-T		ATP10A-related disorder	Likely benign (Feb 04, 2020)
15-25679669-G-A		not specified	Uncertain significance (May 17, 2025)
15-25679673-C-A		not specified	Likely benign (Apr 13, 2022)
15-25679718-T-C		not specified	Uncertain significance (Nov 09, 2024)
15-25679738-C-T		not specified	Uncertain significance (Sep 01, 2021)
15-25679740-G-T		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP10A	protein_coding	protein_coding	ENST00000356865	21	187898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00183	0.998	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	824	888	0.928	0.0000551	9631
Missense in Polyphen		170	227.42	0.74753		2447
Synonymous	0.00321	402	402	1.00	0.0000285	3089
Loss of Function	5.12	17	59.7	0.285	0.00000316	649

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000480	0.000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.000277	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000277	0.000272
South Asian	0.000429	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules (Probable). {ECO:0000305}.
• Pathway: Prader-Willi and Angelman Syndrome;Ion channel transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;Vitamin A (retinol) metabolism;Ion transport by P-type ATPases;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.142
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.86

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.614
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp10a

Gene ontology

• Biological process: regulation of cell shape;ion transmembrane transport;phospholipid translocation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding