ATP10A

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. This gene is maternally expressed. It maps within the most common interval of deletion responsible for Angelman syndrome, also known as 'happy puppet syndrome'. [provided by RefSeq, Jul 2008]

Previous symbols:

ATP10C

MANE transcript

NM_024490.4

Inheritance

—

ClinVar variants

U:259B:81

Top phenotype

ATP10A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr15:25,677,273-25,865,184

External References & Databases

Ensembl (ENSG00000206190)

Transcript & Mutation Effects

hg38 • Region Span ~187.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP10A variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 252

not providedTotal: 65

ATP10A-related disorderTotal: 36

Autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024490.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	31 clinvar	12 clinvar	47
missense			253 clinvar	28 clinvar	10 clinvar	291
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	259	59	22	340

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024490.4	RefSeq	NP_077816.1	21	MANE Select
ENST00000555815.7	Ensembl	ENSP00000450480.2	21	MANE Select
ENST00000356865.11	Ensembl	ENSP00000349325.6	21	Standard
ENST00000389967.9	Ensembl	ENSP00000374617.4	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prader-Willi and Angelman Syndrome
Ion channel transport
Transport of small molecules
Phosphatidylinositol phosphate metabolism
Glycerophospholipid metabolism

Biological Process

regulation of cell shape
ion transmembrane transport
phospholipid translocation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
protein binding
ATP binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356865
Coding exons: 21
Length: 187898
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125748
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.760	824	888	0.928	0.0000551	9631
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00043	0.00042	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.158

Intolerance Scores

LoFtool: 0.142
RVIS EVS: 1.29
RVIS percentile EVS: 93.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.266

Gene Damage Prediction

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